Command: "C:\Program Files\Schrodinger2023-4\mmshare-v6.4\bin\Windows-x64\..\..\python\scripts\prepwizard_driver.py" proteinprep_5.maegz proteinprep_5-out.maegz -fillsidechains -disulfides -assign_all_residues -rehtreat -max_states 1 -epik_pH 7.4 -epik_pHt 2.0 -antibody_cdr_scheme Kabat -samplewater -propka_pH 7.4 -f S-OPLS -rmsd 0.3 -watdist 5.0
Number of input structures: 1
Preparing structure: Phosphoproteins
Fixing common structure mistakes...
  No mistakes were found
Pre-treating metals...
Done treating metals
Assigning bond orders...
  Using CCD: True
  Processing all residues
  No bond orders were changed
Removing and re-adding hydrogens...
Treating metals...
[running at reduced cpu priority]
Creating di-sulfur bonds...
Annotating antibody regions...
WARNING: Sequence similarity score to best reference sequence below cutoff (325). Light: 199.0; Heavy: 204.0.
Detecting missing residue atoms...
  No missing side chains found
Finding het groups (for Epik)...
Epik was not run, as there are no preparable groups
Idealizing hydrogen temperature factors...
Pre-processing has completed
  will sample waters
  Using PROPKA with pH: 7.4
  RUNNING: "C:\Program Files\Schrodinger2023-4\utilities\protassign.exe" "C:\Users\Abbas Khan\AppData\Local\Schrodinger\tmp\proteinprep_5\proteinprep_5-001\Optimize_H-bond_Assignments.maegz" Optimize_H-bond_Assignments-out.maegz -NOJOBID -propka_pH 7.4
Running PROPKA to get pKas

Clustering hydrogen bond network ...
Found 85 clusters

Cluster 1 (1):
    B:ASN 194
Cluster 2 (1):
    B:ASN 239
Cluster 3 (1):
    B:GLN 240
Cluster 4 (2):
    B:ASN 246
    B:SER 248: HG 
Cluster 5 (1):
    B:ASN 259
Cluster 6 (1):
    C:ASN 194
Cluster 7 (1):
    D:ASN 194
Cluster 8 (1):
    B:LYS 182
Cluster 9 (1):
    B:LYS 224
Cluster 10 (1):
    B:LYS 227
Cluster 11 (1):
    B:LYS 229
Cluster 12 (1):
    B:LYS 243
Cluster 13 (1):
    B:LYS 250
Cluster 14 (1):
    B:LYS 254
Cluster 15 (2):
    B:LYS 256
    B:GLU 253
Cluster 16 (1):
    B:LYS 260
Cluster 17 (1):
    C:LYS 182
Cluster 18 (1):
    C:LYS 224
Cluster 19 (1):
    C:LYS 227
Cluster 20 (1):
    C:LYS 229
Cluster 21 (3):
    D:LYS 182
    D:SER 178: HG 
    C:GLU 180
Cluster 22 (4):
    E:LYS 182
    D:SER 184: HG 
    E:SER 178: HG 
    D:GLU 180
Cluster 23 (1):
    E:LYS 224
Cluster 24 (2):
    B:SER 178: HG 
    E:GLU 180
Cluster 25 (1):
    B:SER 184: HG 
Cluster 26 (1):
    B:THR 192: HG1
Cluster 27 (1):
    B:THR 197: HG1
Cluster 28 (1):
    B:THR 201: HG1
Cluster 29 (1):
    B:THR 242: HG1
Cluster 30 (1):
    B:THR 252: HG1
Cluster 31 (1):
    B:SER 266: HG 
Cluster 32 (1):
    C:SER 171: HG 
Cluster 33 (1):
    C:SER 178: HG 
Cluster 34 (1):
    C:SER 184: HG 
Cluster 35 (1):
    C:THR 192: HG1
Cluster 36 (1):
    C:THR 197: HG1
Cluster 37 (1):
    C:THR 201: HG1
Cluster 38 (1):
    D:THR 192: HG1
Cluster 39 (1):
    D:THR 197: HG1
Cluster 40 (1):
    D:THR 201: HG1
Cluster 41 (1):
    E:SER 184: HG 
Cluster 42 (1):
    E:THR 192: HG1
Cluster 43 (1):
    B:GLU 173
Cluster 44 (1):
    B:GLU 177
Cluster 45 (1):
    B:GLU 180
Cluster 46 (1):
    B:GLU 181
Cluster 47 (1):
    B:ASP 205
Cluster 48 (1):
    B:ASP 209
Cluster 49 (1):
    B:GLU 216
Cluster 50 (1):
    B:GLU 217
Cluster 51 (1):
    B:ASP 221
Cluster 52 (1):
    B:GLU 225
Cluster 53 (1):
    B:GLU 232
Cluster 54 (1):
    B:GLU 235
Cluster 55 (1):
    B:GLU 236
Cluster 56 (1):
    B:GLU 237
Cluster 57 (1):
    B:GLU 257
Cluster 58 (1):
    B:GLU 263
Cluster 59 (1):
    B:ASP 264
Cluster 60 (1):
    B:GLU 265
Cluster 61 (1):
    C:GLU 173
Cluster 62 (1):
    C:GLU 177
Cluster 63 (1):
    C:GLU 181
Cluster 64 (1):
    C:ASP 205
Cluster 65 (1):
    C:ASP 209
Cluster 66 (1):
    C:GLU 216
Cluster 67 (1):
    C:GLU 217
Cluster 68 (1):
    C:ASP 221
Cluster 69 (1):
    C:GLU 225
Cluster 70 (1):
    C:GLU 232
Cluster 71 (1):
    D:GLU 173
Cluster 72 (1):
    D:GLU 177
Cluster 73 (1):
    D:GLU 181
Cluster 74 (1):
    D:ASP 205
Cluster 75 (1):
    D:ASP 209
Cluster 76 (1):
    D:GLU 216
Cluster 77 (1):
    D:GLU 217
Cluster 78 (1):
    E:GLU 173
Cluster 79 (1):
    E:GLU 177
Cluster 80 (1):
    E:GLU 181
Cluster 81 (2):
    E:ASP 205
    E:ASP 209
Cluster 82 (1):
    E:GLU 216
Cluster 83 (1):
    E:GLU 217
Cluster 84 (1):
    E:ASP 221
Cluster 85 (1):
    E:GLU 225

Optimizing cluster #1 ...
Lowest energy: -0.3379
Assignments:
  B:ASN 194       -> Flip

Optimizing cluster #2 ...
Lowest energy: 0.0000
Assignments:
  B:ASN 239       -> No Flip

Optimizing cluster #3 ...
Lowest energy: -0.4872
Assignments:
  B:GLN 240       -> No Flip

Optimizing cluster #4 ...
Lowest energy: -3.8505
Assignments:
  B:ASN 246       -> Flip
  B:SER 248: HG   -> Default 5/8

Optimizing cluster #5 ...
Lowest energy: -0.6107
Assignments:
  B:ASN 259       -> Flip

Optimizing cluster #6 ...
Lowest energy: -0.2601
Assignments:
  C:ASN 194       -> No Flip

Optimizing cluster #7 ...
Lowest energy: 8.7556
Assignments:
  D:ASN 194       -> No Flip

Optimizing cluster #8 ...
Lowest energy: -0.3820
Assignments:
  B:LYS 182       -> Stagger (pKa = 9.95)

Optimizing cluster #9 ...
Lowest energy: 0.0000
Assignments:
  B:LYS 224       -> Stagger (pKa = 10.61)

Optimizing cluster #10 ...
Lowest energy: -1.0100
Assignments:
  B:LYS 227       -> Stagger (pKa = 10.25)

Optimizing cluster #11 ...
Lowest energy: -0.2770
Assignments:
  B:LYS 229       -> Orientation 1/1 (pKa = 10.30)

Optimizing cluster #12 ...
Lowest energy: 0.0000
Assignments:
  B:LYS 243       -> Stagger (pKa = 10.40)

Optimizing cluster #13 ...
Lowest energy: 0.0000
Assignments:
  B:LYS 250       -> Stagger (pKa = 10.37)

Optimizing cluster #14 ...
Lowest energy: 0.0000
Assignments:
  B:LYS 254       -> Stagger (pKa = 10.45)

Optimizing cluster #15 ...
Lowest energy: -0.6205
Assignments:
  B:LYS 256       -> Orientation 1/1 (pKa = 10.30)
  B:GLU 253       -> Charged (pKa = 4.65)

Optimizing cluster #16 ...
Lowest energy: 0.0000
Assignments:
  B:LYS 260       -> Stagger (pKa = 10.40)

Optimizing cluster #17 ...
Lowest energy: 0.0000
Assignments:
  C:LYS 182       -> Stagger (pKa = 10.28)

Optimizing cluster #18 ...
Lowest energy: 0.0000
Assignments:
  C:LYS 224       -> Stagger (pKa = 10.57)

Optimizing cluster #19 ...
Lowest energy: 0.0000
Assignments:
  C:LYS 227       -> Stagger (pKa = 10.45)

Optimizing cluster #20 ...
Lowest energy: 0.0000
Assignments:
  C:LYS 229       -> Stagger (pKa = 10.62)

Optimizing cluster #21 ...
Lowest energy: -3.3472
Assignments:
  D:LYS 182       -> Stagger (pKa = 10.53)
  D:SER 178: HG   -> Stagger 3 11/11
  C:GLU 180       -> Charged (pKa = 3.34)

Optimizing cluster #22 ...
Lowest energy: -4.3931
Assignments:
  E:LYS 182       -> Orientation 1/1 (pKa = 11.12)
  D:SER 184: HG   -> Orientation 1/9
  E:SER 178: HG   -> Orientation 1/8
  D:GLU 180       -> Charged (pKa = 3.38)

Optimizing cluster #23 ...
Lowest energy: 0.0000
Assignments:
  E:LYS 224       -> Stagger (pKa = 10.49)

Optimizing cluster #24 ...
Lowest energy: -2.0544
Assignments:
  B:SER 178: HG   -> Stagger 3 7/7
  E:GLU 180       -> Charged (pKa = 4.88)

Optimizing cluster #25 ...
Lowest energy: -0.3348
Assignments:
  B:SER 184: HG   -> Stagger 3 5/5

Optimizing cluster #26 ...
Lowest energy: -1.4438
Assignments:
  B:THR 192: HG1  -> Stagger 3 5/5

Optimizing cluster #27 ...
Lowest energy: -0.9201
Assignments:
  B:THR 197: HG1  -> Stagger 1 2/4

Optimizing cluster #28 ...
Lowest energy: -2.0518
Assignments:
  B:THR 201: HG1  -> Stagger 2 3/4

Optimizing cluster #29 ...
Lowest energy: -0.2493
Assignments:
  B:THR 242: HG1  -> Stagger 3 4/4

Optimizing cluster #30 ...
Lowest energy: -0.7652
Assignments:
  B:THR 252: HG1  -> Orientation 2/7

Optimizing cluster #31 ...
Lowest energy: -0.8701
Assignments:
  B:SER 266: HG   -> Orientation 1/5

Optimizing cluster #32 ...
Lowest energy: -0.6326
Assignments:
  C:SER 171: HG   -> Stagger 1 3/5 (pKa = 7.71)

Optimizing cluster #33 ...
Lowest energy: -0.2719
Assignments:
  C:SER 178: HG   -> Stagger 1 3/5

Optimizing cluster #34 ...
Lowest energy: -1.8649
Assignments:
  C:SER 184: HG   -> Stagger 3 9/9

Optimizing cluster #35 ...
Lowest energy: -1.0718
Assignments:
  C:THR 192: HG1  -> Orientation 1/5

Optimizing cluster #36 ...
Lowest energy: -1.4446
Assignments:
  C:THR 197: HG1  -> Orientation 1/5

Optimizing cluster #37 ...
Lowest energy: -0.4828
Assignments:
  C:THR 201: HG1  -> Orientation 2/5

Optimizing cluster #38 ...
Lowest energy: -0.2823
Assignments:
  D:THR 192: HG1  -> Orientation 1/4

Optimizing cluster #39 ...
Lowest energy: -0.6788
Assignments:
  D:THR 197: HG1  -> Stagger 2 2/3

Optimizing cluster #40 ...
Lowest energy: -0.9692
Assignments:
  D:THR 201: HG1  -> Orientation 1/4

Optimizing cluster #41 ...
Lowest energy: -1.5426
Assignments:
  E:SER 184: HG   -> Orientation 4/8

Optimizing cluster #42 ...
Lowest energy: -1.1669
Assignments:
  E:THR 192: HG1  -> Orientation 1/6

Optimizing cluster #43 ...
Lowest energy: -0.0842
Assignments:
  B:GLU 173       -> Charged (pKa = 4.37)

Optimizing cluster #44 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 177       -> Charged (pKa = 4.71)

Optimizing cluster #45 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 180       -> Charged (pKa = 4.95)

Optimizing cluster #46 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 181       -> Charged (pKa = 4.98)

Optimizing cluster #47 ...
Lowest energy: 0.0000
Assignments:
  B:ASP 205       -> Charged (pKa = 3.89)

Optimizing cluster #48 ...
Lowest energy: -1.6311
Assignments:
  B:ASP 209       -> Charged (pKa = 4.01)

Optimizing cluster #49 ...
Lowest energy: -1.5474
Assignments:
  B:GLU 216       -> Charged (pKa = 4.04)

Optimizing cluster #50 ...
Lowest energy: -0.7168
Assignments:
  B:GLU 217       -> Charged (pKa = 4.43)

Optimizing cluster #51 ...
Lowest energy: -0.1154
Assignments:
  B:ASP 221       -> Charged (pKa = 3.94)

Optimizing cluster #52 ...
Lowest energy: -1.1142
Assignments:
  B:GLU 225       -> Charged (pKa = 4.38)

Optimizing cluster #53 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 232       -> Charged (pKa = 4.82)

Optimizing cluster #54 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 235       -> Charged (pKa = 4.73)

Optimizing cluster #55 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 236       -> Charged (pKa = 4.84)

Optimizing cluster #56 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 237       -> Charged (pKa = 4.63)

Optimizing cluster #57 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 257       -> Charged (pKa = 4.61)

Optimizing cluster #58 ...
Lowest energy: 0.0000
Assignments:
  B:GLU 263       -> Charged (pKa = 4.61)

Optimizing cluster #59 ...
Lowest energy: 0.0000
Assignments:
  B:ASP 264       -> Charged (pKa = 4.05)

Optimizing cluster #60 ...
Lowest energy: -0.0551
Assignments:
  B:GLU 265       -> Charged (pKa = 4.56)

Optimizing cluster #61 ...
Lowest energy: -1.4302
Assignments:
  C:GLU 173       -> Charged (pKa = 3.96)

Optimizing cluster #62 ...
Lowest energy: 0.0000
Assignments:
  C:GLU 177       -> Charged (pKa = 4.87)

Optimizing cluster #63 ...
Lowest energy: 0.0000
Assignments:
  C:GLU 181       -> Charged (pKa = 4.62)

Optimizing cluster #64 ...
Lowest energy: -0.1584
Assignments:
  C:ASP 205       -> Charged (pKa = 3.82)

Optimizing cluster #65 ...
Lowest energy: -0.0667
Assignments:
  C:ASP 209       -> Charged (pKa = 4.21)

Optimizing cluster #66 ...
Lowest energy: 0.0000
Assignments:
  C:GLU 216       -> Charged (pKa = 4.94)

Optimizing cluster #67 ...
Lowest energy: 0.0000
Assignments:
  C:GLU 217       -> Charged (pKa = 4.65)

Optimizing cluster #68 ...
Lowest energy: -2.2434
Assignments:
  C:ASP 221       -> Charged (pKa = 2.92)

Optimizing cluster #69 ...
Lowest energy: -0.1050
Assignments:
  C:GLU 225       -> Charged (pKa = 4.59)

Optimizing cluster #70 ...
Lowest energy: -0.0012
Assignments:
  C:GLU 232       -> Charged (pKa = 4.61)

Optimizing cluster #71 ...
Lowest energy: -0.1645
Assignments:
  D:GLU 173       -> Charged (pKa = 4.47)

Optimizing cluster #72 ...
Lowest energy: -0.0528
Assignments:
  D:GLU 177       -> Charged (pKa = 4.84)

Optimizing cluster #73 ...
Lowest energy: 0.0000
Assignments:
  D:GLU 181       -> Charged (pKa = 4.62)

Optimizing cluster #74 ...
Lowest energy: 8.5505
Assignments:
  D:ASP 205       -> Charged (pKa = 4.33)

Optimizing cluster #75 ...
Lowest energy: -0.1590
Assignments:
  D:ASP 209       -> Charged (pKa = 3.92)

Optimizing cluster #76 ...
Lowest energy: 0.0000
Assignments:
  D:GLU 216       -> Charged (pKa = 4.47)

Optimizing cluster #77 ...
Lowest energy: -0.0475
Assignments:
  D:GLU 217       -> Charged (pKa = 4.61)

Optimizing cluster #78 ...
Lowest energy: 0.0000
Assignments:
  E:GLU 173       -> Charged (pKa = 4.27)

Optimizing cluster #79 ...
Lowest energy: 0.0000
Assignments:
  E:GLU 177       -> Charged (pKa = 4.51)

Optimizing cluster #80 ...
Lowest energy: 0.0000
Assignments:
  E:GLU 181       -> Charged (pKa = 4.71)

Optimizing cluster #81 ...
Lowest energy: -0.5793
Assignments:
  E:ASP 205       -> Charged (pKa = 3.75)
  E:ASP 209       -> Charged (pKa = 4.28)

Optimizing cluster #82 ...
Lowest energy: 0.0000
Assignments:
  E:GLU 216       -> Charged (pKa = 4.65)

Optimizing cluster #83 ...
Lowest energy: 8.6746
Assignments:
  E:GLU 217       -> Neutral 1 (pKa = 5.30)

Optimizing cluster #84 ...
Lowest energy: -0.1393
Assignments:
  E:ASP 221       -> Charged (pKa = 4.21)

Optimizing cluster #85 ...
Lowest energy: 0.0000
Assignments:
  E:GLU 225       -> Charged (pKa = 4.76)


Recalculating pKas to identify changes in protonation penalties...
Running PROPKA to get pKas
No changes in protonation penalties found.

Combined total energy: -19.1048
Alternative States for B:ASN 194  Gap  0.13 kcals/mol
    Flip      0.00 kcals/mol
    No Flip   0.13 kcals/mol
Alternative States for B:GLN 240  Gap  0.10 kcals/mol
    No Flip   0.00 kcals/mol
    Flip      0.10 kcals/mol
Alternative States for B:ASN 259  Gap  0.61 kcals/mol
    Flip      0.00 kcals/mol
    No Flip   0.61 kcals/mol
Alternative States for E:GLU 217  Gap  0.69 kcals/mol
    Neutral 1  0.00 kcals/mol
    Charged   0.69 kcals/mol

Final pKas:
  B:LYS 182 : 9.95
  B:LYS 224 : 10.61
  B:LYS 227 : 10.25
  B:LYS 229 : 10.30
  B:LYS 243 : 10.40
  B:LYS 250 : 10.37
  B:LYS 254 : 10.45
  B:LYS 256 : 10.30
  B:LYS 260 : 10.40
  C:LYS 182 : 10.28
  C:LYS 224 : 10.57
  C:LYS 227 : 10.45
  C:LYS 229 : 10.62
  D:LYS 182 : 10.53
  E:LYS 182 : 11.12
  E:LYS 224 : 10.49
  C:SER 171: HG  : 7.71
  B:GLU 173 : 4.37
  B:GLU 177 : 4.71
  B:GLU 180 : 4.95
  B:GLU 181 : 4.98
  B:ASP 205 : 3.89
  B:ASP 209 : 4.01
  B:GLU 216 : 4.04
  B:GLU 217 : 4.43
  B:ASP 221 : 3.94
  B:GLU 225 : 4.38
  B:GLU 232 : 4.82
  B:GLU 235 : 4.73
  B:GLU 236 : 4.84
  B:GLU 237 : 4.63
  B:GLU 253 : 4.65
  B:GLU 257 : 4.61
  B:GLU 263 : 4.61
  B:ASP 264 : 4.05
  B:GLU 265 : 4.56
  C:GLU 173 : 3.96
  C:GLU 177 : 4.87
  C:GLU 180 : 3.34
  C:GLU 181 : 4.62
  C:ASP 205 : 3.82
  C:ASP 209 : 4.21
  C:GLU 216 : 4.94
  C:GLU 217 : 4.65
  C:ASP 221 : 2.92
  C:GLU 225 : 4.59
  C:GLU 232 : 4.61
  D:GLU 173 : 4.47
  D:GLU 177 : 4.84
  D:GLU 180 : 3.38
  D:GLU 181 : 4.62
  D:ASP 205 : 4.33
  D:ASP 209 : 3.92
  D:GLU 216 : 4.47
  D:GLU 217 : 4.61
  E:GLU 173 : 4.27
  E:GLU 177 : 4.51
  E:GLU 180 : 4.88
  E:GLU 181 : 4.71
  E:ASP 205 : 3.75
  E:ASP 209 : 4.28
  E:GLU 216 : 4.65
  E:GLU 217 : 5.30
  E:ASP 221 : 4.21
  E:GLU 225 : 4.76
Structure extracted from file: C:\Users\Abbas Khan\AppData\Local\Schrodinger\tmp\proteinprep_5\proteinprep_5-001\Optimize_H-bond_Assignments.maegz
Output structure will be written to: Optimize_H-bond_Assignments-out.maegz

Complete. Output file: Optimize_H-bond_Assignments-out.maegz
Idealizing hydrogen temperature factors...
Optimize H-bond job completed
Running restrained minimization...
  RMSD: 0.3
  Force field: S-OPLS
  all atoms
[running at reduced cpu priority]
[running at reduced cpu priority]
%IMPACT-I (openwt): Request to open FORMATTED file proteinprep_5_ref0.out on unit   2
 Entering IMPACT execution environment 
 Date: Thursday, January 16 2025, at 11:38:35 Pakistan Standard Time
 Impact version 101132
 mmshare version        64132
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

 Windows Host: LAPTOP-ML27RQMS
 Job Name: proteinprep_5
 JobId:    LAPTOP-ML27RQMS-0-6788a957
 SCHRODINGER  directory: C:\Program Files\Schrodinger2023-4
 IMPACT_EXEC  directory: C:\Program Files\Schrodinger2023-4\impact-v10.1\bin\Windows-x64
 MMSHARE_EXEC directory: C:\Program Files\Schrodinger2023-4\mmshare-v6.4\bin\Windows-x64

 Clock-based global random seed:     1737009515
%IMPACT-I(foldmain): calling S-OPLS atomtyping ...
%IMPACT-I(foldmain): finished parameter assignment
 PARM read from file "paramstd.dat"
 Parameter obtained from atomtyping
      Current coord. are written to file: "proteinprep_5.init_coord.rst"
      Box dimensions not written


 Total number of atoms  =  3957
 
 Neighbor List Cutoff Settings
 ==================================
 Cutoff radius:   10.0000000000000     
 Update frequency: every           10  steps
 Species   1 : Neighbors are calculated on a per residue basis
 Species   1 : Cutoff by inter-atomic distances
 
 Step number:          0         Non-bonded count:   897821
 E-pot        RMS grad     Max grad    
  8.72986E+02  1.06056E+01  2.46716E+02
 Step number:         10         Non-bonded count:   897821
 -4.37519E+02  2.19321E+00  3.86206E+01
 Step number:         20         Non-bonded count:   900845
 -5.79315E+02  1.04194E+00  2.40971E+01
 Step number:         30         Non-bonded count:   902274
 -6.28498E+02  7.18970E-01  1.45529E+01
 Step number:         40         Non-bonded count:   902532
 -6.54332E+02  5.20313E-01  8.20893E+00
 Step number:         50         Non-bonded count:   902872
 -6.69432E+02  4.27262E-01  6.04742E+00
 Step number:         60         Non-bonded count:   903326
 -6.79823E+02  3.82087E-01  7.67703E+00
 Step number:         70         Non-bonded count:   903494
 -6.87641E+02  3.44965E-01  9.62608E+00
 Step number:         80         Non-bonded count:   903395
 -6.95060E+02  3.18926E-01  6.39313E+00
 Step number:         90         Non-bonded count:   902616
 -7.00948E+02  2.81196E-01  4.33263E+00
 Step number:        100         Non-bonded count:   902684
 -7.05544E+02  2.56868E-01  4.35828E+00
 Step number:        100         Non-bonded count:   902684
 -7.05544E+02  2.56868E-01  4.35828E+00
      Current coord. are written to file: "proteinprep_5.min0_coord.rst"
      Box dimensions not written
      Current coordinates are read from file: "proteinprep_5.init_coord.rst"
      Box dimensions not read
          read from "proteinprep_5.init_coord.rst"
  
 Energy and Force Generation Info: 
 --------------------------------- 
 Number of E&F called:     266
 PARM read from file "paramstd.dat"
 Parameter obtained from atomtyping
      Current coordinates are read from file: "proteinprep_5.min0_coord.rst"
      Box dimensions not read
          read from "proteinprep_5.min0_coord.rst"


 Total number of atoms  =  3957
 
 Neighbor List Cutoff Settings
 ==================================
 Cutoff radius:   10.0000000000000     
 Update frequency: every           10  steps
 Species   1 : Neighbors are calculated on a per residue basis
 Species   1 : Cutoff by inter-atomic distances
 
 Step number:          0         Non-bonded count:   902684
 E-pot        RMS grad     Max grad    
  9.22505E+02  5.66543E+00  5.56798E+01
 Step number:         10         Non-bonded count:   902684
  3.18135E+02  2.00512E+00  3.73077E+01
 Step number:         20         Non-bonded count:   902173
  1.38446E+02  1.32479E+00  3.88409E+01
 Step number:         30         Non-bonded count:   901150
  7.69977E+01  7.24804E-01  1.16354E+01
 Step number:         40         Non-bonded count:   902298
  4.98098E+01  5.50843E-01  2.15772E+01
 Step number:         50         Non-bonded count:   902128
  3.85459E+01  3.31351E-01  5.31582E+00
 Step number:         60         Non-bonded count:   902489
  3.22624E+01  2.80961E-01  1.10865E+01
 Step number:         70         Non-bonded count:   901994
  2.81895E+01  2.25339E-01  4.99670E+00
 Step number:         80         Non-bonded count:   902147
  2.51129E+01  2.07817E-01  6.36106E+00
 Step number:         90         Non-bonded count:   902147
  2.24744E+01  1.87161E-01  5.03578E+00
 Step number:        100         Non-bonded count:   901843
  2.07440E+01  1.49449E-01  4.26830E+00
 Step number:        100         Non-bonded count:   901938
  2.07462E+01  1.49450E-01  4.26830E+00
  
 Energy and Force Generation Info: 
 --------------------------------- 
 Number of E&F called:     527


Final Energy Reports:
------------------------------------
 Total Energy of the system......  2.07462E+01 kcal/mol
 Total Potential Energy..........  2.07462E+01 kcal/mol
 Total Kinetic Energy............  0.00000E+00 kcal/mol
 Temperature of the system.......        0.000 K
 Bond Stretch Energy.............  8.27795E+01 kcal/mol
 Angle Bending Energy............  4.43136E+02 kcal/mol
 Torsion Angle Energy............  5.32048E+02 kcal/mol
 Restraining Energy for Torsions.  0.00000E+00 kcal/mol
 1,4 Lennard Jones Energy........  1.23112E+03 kcal/mol
 1,4 Electrostatic Energy........  3.85195E+02 kcal/mol
 Lennard Jones Energy............ -1.69874E+03 kcal/mol
 Electrostatic Energy............ -1.17552E+03 kcal/mol
 H-bond Energy...................  0.00000E+00 kcal/mol
 
 Exiting IMPACT execution environment 
 Date: Thursday, January 16 2025, at 11:38:41 Pakistan Standard Time
nblist:WARNING process_pending_messages: The mmjobbe library is uninitialized
Error: No path for jmonitor fifo
%IMPACT-I (timit): Total CPU time =       6.30 seconds (   0.1 minutes)
Total elapsed time = 6 seconds
Beginning refinement level 0
 ** Completed refinement level 0 and rmsd = 0.10750043029659151
[running at reduced cpu priority]
[running at reduced cpu priority]
%IMPACT-I (openwt): Request to open FORMATTED file proteinprep_5_ref1.out on unit   2
 Entering IMPACT execution environment 
 Date: Thursday, January 16 2025, at 11:38:43 Pakistan Standard Time
 Impact version 101132
 mmshare version        64132
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

 Windows Host: LAPTOP-ML27RQMS
 Job Name: proteinprep_5
 JobId:    LAPTOP-ML27RQMS-0-6788a957
 SCHRODINGER  directory: C:\Program Files\Schrodinger2023-4
 IMPACT_EXEC  directory: C:\Program Files\Schrodinger2023-4\impact-v10.1\bin\Windows-x64
 MMSHARE_EXEC directory: C:\Program Files\Schrodinger2023-4\mmshare-v6.4\bin\Windows-x64

 Clock-based global random seed:     1737009523
%IMPACT-I(foldmain): calling S-OPLS atomtyping ...
%IMPACT-I(foldmain): finished parameter assignment
 PARM read from file "paramstd.dat"
 Parameter obtained from atomtyping


 Total number of atoms  =  3957
 
 Neighbor List Cutoff Settings
 ==================================
 Cutoff radius:   10.0000000000000     
 Update frequency: every           10  steps
 Species   1 : Neighbors are calculated on a per residue basis
 Species   1 : Cutoff by inter-atomic distances
 
 Step number:          0         Non-bonded count:   901938
 E-pot        RMS grad     Max grad    
 -1.99953E+02  8.72840E-01  8.54323E+00
 Step number:         10         Non-bonded count:   901938
 -2.93635E+02  8.49782E-01  1.49728E+01
 Step number:         20         Non-bonded count:   905094
 -3.32216E+02  5.56086E-01  1.02866E+01
 Step number:         30         Non-bonded count:   904598
 -3.49773E+02  4.08239E-01  4.38000E+00
 Step number:         40         Non-bonded count:   904018
 -3.58834E+02  3.28773E-01  5.96572E+00
 Step number:         50         Non-bonded count:   903586
 -3.63810E+02  2.32878E-01  4.84163E+00
 Step number:         60         Non-bonded count:   904412
 -3.66149E+02  1.91448E-01  2.61318E+00
 Step number:         70         Non-bonded count:   904371
 -3.68799E+02  1.46510E-01  2.46350E+00
 Step number:         80         Non-bonded count:   904105
 -3.70056E+02  1.26492E-01  1.88163E+00
 Step number:         90         Non-bonded count:   904105
 -3.70872E+02  1.02569E-01  3.12693E+00
 Step number:        100         Non-bonded count:   904168
 -3.71463E+02  9.14998E-02  2.34336E+00
 Step number:        100         Non-bonded count:   904168
 -3.71463E+02  9.14998E-02  2.34336E+00
  
 Energy and Force Generation Info: 
 --------------------------------- 
 Number of E&F called:     273


Final Energy Reports:
------------------------------------
 Total Energy of the system...... -3.71463E+02 kcal/mol
 Total Potential Energy.......... -3.71463E+02 kcal/mol
 Total Kinetic Energy............  0.00000E+00 kcal/mol
 Temperature of the system.......        0.000 K
 Bond Stretch Energy.............  1.18220E+02 kcal/mol
 Angle Bending Energy............  5.06694E+02 kcal/mol
 Torsion Angle Energy............  4.73454E+02 kcal/mol
 Restraining Energy for Torsions.  0.00000E+00 kcal/mol
 1,4 Lennard Jones Energy........  1.10929E+03 kcal/mol
 1,4 Electrostatic Energy........  3.76607E+02 kcal/mol
 Lennard Jones Energy............ -1.87209E+03 kcal/mol
 Electrostatic Energy............ -1.15389E+03 kcal/mol
 H-bond Energy...................  0.00000E+00 kcal/mol
 
 Exiting IMPACT execution environment 
 Date: Thursday, January 16 2025, at 11:38:48 Pakistan Standard Time
nblist:WARNING process_pending_messages: The mmjobbe library is uninitialized
Error: No path for jmonitor fifo
%IMPACT-I (timit): Total CPU time =       5.00 seconds (   0.1 minutes)
Total elapsed time = 5 seconds
Beginning refinement level 1
 ** Completed refinement level 1 and rmsd = 0.20299220636393905
[running at reduced cpu priority]
[running at reduced cpu priority]
%IMPACT-I (openwt): Request to open FORMATTED file proteinprep_5_ref2.out on unit   2
 Entering IMPACT execution environment 
 Date: Thursday, January 16 2025, at 11:38:50 Pakistan Standard Time
 Impact version 101132
 mmshare version        64132
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

 Windows Host: LAPTOP-ML27RQMS
 Job Name: proteinprep_5
 JobId:    LAPTOP-ML27RQMS-0-6788a957
 SCHRODINGER  directory: C:\Program Files\Schrodinger2023-4
 IMPACT_EXEC  directory: C:\Program Files\Schrodinger2023-4\impact-v10.1\bin\Windows-x64
 MMSHARE_EXEC directory: C:\Program Files\Schrodinger2023-4\mmshare-v6.4\bin\Windows-x64

 Clock-based global random seed:     1737009530
%IMPACT-I(foldmain): calling S-OPLS atomtyping ...
%IMPACT-I(foldmain): finished parameter assignment
 PARM read from file "paramstd.dat"
 Parameter obtained from atomtyping


 Total number of atoms  =  3957
 
 Neighbor List Cutoff Settings
 ==================================
 Cutoff radius:   10.0000000000000     
 Update frequency: every           10  steps
 Species   1 : Neighbors are calculated on a per residue basis
 Species   1 : Cutoff by inter-atomic distances
 
 Step number:          0         Non-bonded count:   904168
 E-pot        RMS grad     Max grad    
 -4.41674E+02  2.81689E-01  2.68779E+00
 Step number:         10         Non-bonded count:   904168
 -4.63027E+02  6.62562E-01  6.39753E+00
 Step number:         20         Non-bonded count:   904365
 -4.83518E+02  5.01354E-01  1.17354E+01
 Step number:         30         Non-bonded count:   904894
 -4.94690E+02  3.95511E-01  8.14872E+00
 Step number:         40         Non-bonded count:   904475
 -5.02931E+02  3.58627E-01  6.87446E+00
 Step number:         50         Non-bonded count:   904989
 -5.09225E+02  2.81678E-01  5.35272E+00
 Step number:         60         Non-bonded count:   905873
 -5.13589E+02  2.44942E-01  5.79347E+00
 Step number:         70         Non-bonded count:   906902
 -5.16417E+02  1.99866E-01  4.13217E+00
 Step number:         80         Non-bonded count:   907264
 -5.18473E+02  1.66828E-01  5.99198E+00
 Step number:         90         Non-bonded count:   907790
 -5.20075E+02  1.51895E-01  3.11432E+00
 Step number:        100         Non-bonded count:   908702
 -5.21280E+02  1.32280E-01  2.91198E+00
 Step number:        100         Non-bonded count:   908724
 -5.21334E+02  1.32284E-01  2.91198E+00
  
 Energy and Force Generation Info: 
 --------------------------------- 
 Number of E&F called:     275


Final Energy Reports:
------------------------------------
 Total Energy of the system...... -5.21334E+02 kcal/mol
 Total Potential Energy.......... -5.21334E+02 kcal/mol
 Total Kinetic Energy............  0.00000E+00 kcal/mol
 Temperature of the system.......        0.000 K
 Bond Stretch Energy.............  1.24526E+02 kcal/mol
 Angle Bending Energy............  5.20099E+02 kcal/mol
 Torsion Angle Energy............  4.28644E+02 kcal/mol
 Restraining Energy for Torsions.  0.00000E+00 kcal/mol
 1,4 Lennard Jones Energy........  1.08770E+03 kcal/mol
 1,4 Electrostatic Energy........  3.75000E+02 kcal/mol
 Lennard Jones Energy............ -1.94089E+03 kcal/mol
 Electrostatic Energy............ -1.16037E+03 kcal/mol
 H-bond Energy...................  0.00000E+00 kcal/mol
 
 Exiting IMPACT execution environment 
 Date: Thursday, January 16 2025, at 11:38:55 Pakistan Standard Time
nblist:WARNING process_pending_messages: The mmjobbe library is uninitialized
Error: No path for jmonitor fifo
%IMPACT-I (timit): Total CPU time =       4.94 seconds (   0.1 minutes)
Total elapsed time = 5 seconds
Beginning refinement level 2
 ** Completed refinement level 2 and rmsd = 0.3186128959209252
Refinement finished. Final level: 2
The refined complex file is Clean_Up-impref-out.maegz
[running at reduced cpu priority]
Deleting waters...
Deleting far waters...
done deleting waters
Number of output structures: 1
Subjob completed successfully: proteinprep_5-001
Number of successful preparations: 1
Number of output structures: 1
DONE. Output file: proteinprep_5-out.maegz
