Starting phenix.real_space_refine
on Tue May 20 02:35:31 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8sx8_40827/05_2025/8sx8_40827_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sx8_40827/05_2025/8sx8_40827.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sx8_40827/05_2025/8sx8_40827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sx8_40827/05_2025/8sx8_40827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sx8_40827/05_2025/8sx8_40827_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sx8_40827/05_2025/8sx8_40827_trim.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    6117      2.51       5
     N    1580      2.21       5
     O    1682      1.98       5
     H    9610      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 19025
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 18997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1175, 18997
          Classifications: {'peptide': 1175}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 1139}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'XPG': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 8.49, per 1000 atoms: 0.45
  Number of scatterers: 19025
  At special positions: 0
  Unit cell: (82.665, 96.86, 145.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     O    1682      8.00
     N    1580      7.00
     C    6117      6.00
     H    9610      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.56
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      72.3% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 26
      No H-bonds generated for 'chain 'A' and resid 24 through 26'
    Processing helix  chain 'A' and resid 27 through 37
    Processing helix  chain 'A' and resid 40 through 44
      removed outlier: 4.036A  pdb=" N   MET A  44 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.689A  pdb=" N   GLU A  58 " --> pdb=" O   GLN A  54 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LEU A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   TYR A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 93
      removed outlier: 6.434A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 122
      removed outlier: 3.530A  pdb=" N   THR A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      removed outlier: 3.513A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 180
      removed outlier: 4.067A  pdb=" N   ARG A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 190 through 201
      removed outlier: 3.766A  pdb=" N   LEU A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 208
      removed outlier: 3.941A  pdb=" N   ASP A 206 " --> pdb=" O   ASN A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 234
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 236 through 289
      removed outlier: 3.950A  pdb=" N   GLY A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      Proline residue:  A 249  - end of helix
      removed outlier: 4.130A  pdb=" N   ALA A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   ARG A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 342
      removed outlier: 3.567A  pdb=" N   PHE A 295 " --> pdb=" O   TRP A 291 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 367
      removed outlier: 3.708A  pdb=" N   ALA A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 391
      removed outlier: 3.553A  pdb=" N   VAL A 381 " --> pdb=" O   SER A 377 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER A 382 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 511
    Processing helix  chain 'A' and resid 513 through 520
    Processing helix  chain 'A' and resid 522 through 525
    Processing helix  chain 'A' and resid 536 through 551
    Processing helix  chain 'A' and resid 561 through 565
      removed outlier: 4.306A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 581 through 585
      removed outlier: 4.436A  pdb=" N   GLU A 584 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 598
      removed outlier: 3.815A  pdb=" N   LEU A 597 " --> pdb=" O   GLN A 593 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS A 598 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 593 through 598'
    Processing helix  chain 'A' and resid 697 through 707
      removed outlier: 3.816A  pdb=" N   TYR A 701 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 745
      removed outlier: 3.660A  pdb=" N   ILE A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 808
      removed outlier: 3.743A  pdb=" N   GLY A 766 " --> pdb=" O   ASN A 762 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 815
      removed outlier: 3.851A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 827
      removed outlier: 3.523A  pdb=" N   ILE A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ARG A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   PHE A 825 " --> pdb=" O   ILE A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 834
    Processing helix  chain 'A' and resid 834 through 861
      removed outlier: 4.223A  pdb=" N   LEU A 838 " --> pdb=" O   ASP A 834 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLN A 849 " --> pdb=" O   GLN A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 910
      Proline residue:  A 870  - end of helix
      removed outlier: 4.074A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ASP A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER A 898 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
      Proline residue:  A 899  - end of helix
    Processing helix  chain 'A' and resid 910 through 917
    Processing helix  chain 'A' and resid 919 through 970
      removed outlier: 3.606A  pdb=" N   ARG A 951 " --> pdb=" O   TRP A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 987
    Processing helix  chain 'A' and resid 988 through 1017
      removed outlier: 3.778A  pdb=" N   MET A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLN A 994 " --> pdb=" O   MET A 990 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG A 998 " --> pdb=" O   GLN A 994 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A1002 " --> pdb=" O   ARG A 998 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   TYR A1016 " --> pdb=" O   ARG A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1089
      removed outlier: 3.744A  pdb=" N   ILE A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1108
      No H-bonds generated for 'chain 'A' and resid 1106 through 1108'
    Processing helix  chain 'A' and resid 1109 through 1114
    Processing helix  chain 'A' and resid 1130 through 1136
    Processing helix  chain 'A' and resid 1144 through 1153
    Processing helix  chain 'A' and resid 1155 through 1160
    Processing helix  chain 'A' and resid 1171 through 1175
    Processing helix  chain 'A' and resid 1178 through 1193
    Processing helix  chain 'A' and resid 1210 through 1223
    Processing helix  chain 'A' and resid 1224 through 1226
      No H-bonds generated for 'chain 'A' and resid 1224 through 1226'
    Processing helix  chain 'A' and resid 1234 through 1239
      removed outlier: 3.525A  pdb=" N   ILE A1239 " --> pdb=" O   ASN A1236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1264
    Processing helix  chain 'A' and resid 1267 through 1274
    Processing helix  chain 'A' and resid 1277 through 1297
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435
      removed outlier: 5.733A  pdb=" N   GLN A 429 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ALA A 417 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   PHE A 433 " --> pdb=" O   GLN A 413 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   GLN A 413 " --> pdb=" O   PHE A 433 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   VAL A 435 " --> pdb=" O   ASN A 411 " (cutoff:3.500A)
      removed outlier: 5.579A  pdb=" N   ASN A 411 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   PHE A 415 " --> pdb=" O   GLN A 466 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   GLN A 466 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478
      removed outlier: 6.361A  pdb=" N   ALA A 476 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ASP A 559 " --> pdb=" O   ALA A 476 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   VAL A 478 " --> pdb=" O   ASP A 559 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   LEU A 441 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   LEU A 440 " --> pdb=" O   GLN A 602 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   LEU A 604 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ALA A 442 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LEU A 606 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL A 444 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LYS A 607 " --> pdb=" O   MET A 611 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   MET A 611 " --> pdb=" O   LYS A 607 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488
      removed outlier: 3.787A  pdb=" N   GLY A 487 " --> pdb=" O   ILE A 528 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065
      removed outlier: 6.400A  pdb=" N   LYS A1059 " --> pdb=" O   ASN A1047 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ASN A1047 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   LEU A1061 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   VAL A1046 " --> pdb=" O   GLU A1095 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   GLU A1095 " --> pdb=" O   VAL A1046 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1071 through 1075
      removed outlier: 6.428A  pdb=" N   GLY A1072 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   LEU A1247 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ASP A1248 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   LEU A1252 " --> pdb=" O   ASP A1248 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1118 through 1120
      removed outlier: 6.206A  pdb=" N   SER A1118 " --> pdb=" O   ILE A1199 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU A1198 " --> pdb=" O   LEU A1229 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    615 hydrogen bonds defined for protein.
    1797 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 8.32

  Time building geometry restraints manager: 6.63 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 9593
        1.03 -     1.23: 24
        1.23 -     1.42: 3988
        1.42 -     1.61: 5562
        1.61 -     1.81: 59
  Bond restraints: 19226
  Sorted by residual:
  bond pdb=" CB  GLU A1202 "
       pdb=" HB2 GLU A1202 "
    ideal  model  delta    sigma   weight residual
    0.970  1.091 -0.121 2.00e-02 2.50e+03 3.66e+01
  bond pdb=" CG  GLU A1202 "
       pdb=" HG3 GLU A1202 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" CG  GLU A1202 "
       pdb=" HG2 GLU A1202 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.57e+01
  bond pdb=" CB  GLU A1202 "
       pdb=" HB3 GLU A1202 "
    ideal  model  delta    sigma   weight residual
    0.970  1.089 -0.119 2.00e-02 2.50e+03 3.57e+01
  bond pdb=" C1  XPG A1401 "
       pdb=" O1A XPG A1401 "
    ideal  model  delta    sigma   weight residual
    1.250  1.217  0.033 2.00e-02 2.50e+03 2.71e+00
  ... (remaining 19221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 31991
        1.36 -     2.73: 2614
        2.73 -     4.09: 165
        4.09 -     5.46: 25
        5.46 -     6.82: 7
  Bond angle restraints: 34802
  Sorted by residual:
  angle pdb=" CA  ARG A 951 "
        pdb=" CB  ARG A 951 "
        pdb=" CG  ARG A 951 "
      ideal   model   delta    sigma   weight residual
     114.10  107.28    6.82 2.00e+00 2.50e-01 1.16e+01
  angle pdb=" C   LEU A 181 "
        pdb=" N   SER A 182 "
        pdb=" CA  SER A 182 "
      ideal   model   delta    sigma   weight residual
     120.71  125.30   -4.59 1.42e+00 4.96e-01 1.04e+01
  angle pdb=" CA  TYR A 985 "
        pdb=" CB  TYR A 985 "
        pdb=" CG  TYR A 985 "
      ideal   model   delta    sigma   weight residual
     113.90  108.18    5.72 1.80e+00 3.09e-01 1.01e+01
  angle pdb=" CA  HIS A 153 "
        pdb=" CB  HIS A 153 "
        pdb=" CG  HIS A 153 "
      ideal   model   delta    sigma   weight residual
     113.80  110.70    3.10 1.00e+00 1.00e+00 9.58e+00
  angle pdb=" CA  PHE A 336 "
        pdb=" CB  PHE A 336 "
        pdb=" CG  PHE A 336 "
      ideal   model   delta    sigma   weight residual
     113.80  110.80    3.00 1.00e+00 1.00e+00 9.00e+00
  ... (remaining 34797 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 8187
       17.03 -    34.05: 457
       34.05 -    51.08: 147
       51.08 -    68.10: 160
       68.10 -    85.13: 20
  Dihedral angle restraints: 8971
    sinusoidal: 4863
      harmonic: 4108
  Sorted by residual:
  dihedral pdb=" CA  PRO A1094 "
           pdb=" C   PRO A1094 "
           pdb=" N   GLU A1095 "
           pdb=" CA  GLU A1095 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.51   27.49     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  GLY A 282 "
           pdb=" C   GLY A 282 "
           pdb=" N   ILE A 283 "
           pdb=" CA  ILE A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.58  -27.42     0      5.00e+00 4.00e-02 3.01e+01
  dihedral pdb=" CA  ARG A1114 "
           pdb=" C   ARG A1114 "
           pdb=" N   LYS A1115 "
           pdb=" CA  LYS A1115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.07   23.93     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 8968 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1013
       0.049 -    0.099: 376
       0.099 -    0.148: 91
       0.148 -    0.197: 19
       0.197 -    0.247: 7
  Chirality restraints: 1506
  Sorted by residual:
  chirality pdb=" CA  HIS A 153 "
            pdb=" N   HIS A 153 "
            pdb=" C   HIS A 153 "
            pdb=" CB  HIS A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C8  XPG A1401 "
            pdb=" C12 XPG A1401 "
            pdb=" C7  XPG A1401 "
            pdb=" C9  XPG A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.78    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  THR A 366 "
            pdb=" N   THR A 366 "
            pdb=" C   THR A 366 "
            pdb=" CB  THR A 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1503 not shown)

  Planarity restraints: 2757
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 216 "    0.035 2.00e-02 2.50e+03   3.43e-02 4.70e+01
        pdb=" CG  TRP A 216 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 216 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 216 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 216 "   -0.096 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 216 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 216 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 216 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 216 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 216 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 216 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 216 "    0.086 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 216 "   -0.005 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 216 "    0.015 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 216 "    0.001 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 216 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 994 "    0.042 2.00e-02 2.50e+03   5.12e-02 3.93e+01
        pdb=" CD  GLN A 994 "   -0.038 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 994 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 994 "   -0.080 2.00e-02 2.50e+03
        pdb="HE21 GLN A 994 "   -0.003 2.00e-02 2.50e+03
        pdb="HE22 GLN A 994 "    0.078 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 362 "   -0.348 9.50e-02 1.11e+02   1.20e-01 3.71e+01
        pdb=" NE  ARG A 362 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 362 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 362 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 362 "    0.064 2.00e-02 2.50e+03
        pdb="HH11 ARG A 362 "    0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG A 362 "    0.021 2.00e-02 2.50e+03
        pdb="HH21 ARG A 362 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 362 "   -0.068 2.00e-02 2.50e+03
  ... (remaining 2754 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.16: 722
        2.16 -     2.77: 36465
        2.77 -     3.38: 54063
        3.38 -     3.99: 66173
        3.99 -     4.60: 106360
  Nonbonded interactions: 263783
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 544 "
            pdb="HH12 ARG A 547 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" HG  SER A1051 "
            pdb=" OD1 ASP A1053 "
     model   vdw
     1.569 2.450
  nonbonded pdb=" HG  SER A1049 "
            pdb=" O   PRO A1055 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" OE1 GLU A1020 "
            pdb=" H   GLU A1020 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" HG1 THR A 269 "
            pdb=" OE2 GLU A 306 "
     model   vdw
     1.602 2.450
  ... (remaining 263778 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.370
  Extract box with map and model:          0.820
  Check model and map are aligned:         0.150
  Set scattering table:                    0.190
  Process input model:                     43.690
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9616  Z= 0.232
  Angle     :  0.839   6.820  13029  Z= 0.507
  Chirality :  0.056   0.247   1506
  Planarity :  0.009   0.136   1621
  Dihedral  : 12.224  85.125   3524
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 0.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.18 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.21), residues: 1167
  helix: -1.46 (0.15), residues: 767
  sheet: -0.48 (0.49), residues: 73
  loop : -0.40 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.006   TRP A 216 
 HIS   0.025   0.004   HIS A 153 
 PHE   0.031   0.004   PHE A 948 
 TYR   0.038   0.006   TYR A 155 
 ARG   0.014   0.003   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19154 (  615)
  hydrogen bonds       : angle       7.94408 ( 1797)
  covalent geometry    : bond        0.00489 ( 9616)
  covalent geometry    : angle       0.83855 (13029)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ILE cc_start: 0.8362 (mm) cc_final: 0.8108 (mt)
REVERT: A  276 MET cc_start: 0.7745 (mmm) cc_final: 0.7464 (mmt)
REVERT: A  768 TYR cc_start: 0.7837 (t80) cc_final: 0.7488 (t80)
REVERT: A  892 LEU cc_start: 0.8513 (tp) cc_final: 0.8278 (tp)
REVERT: A 1007 MET cc_start: 0.8796 (mmm) cc_final: 0.7990 (mmm)
REVERT: A 1083 SER cc_start: 0.8924 (m) cc_final: 0.8719 (p)
REVERT: A 1256 ASP cc_start: 0.8679 (t0) cc_final: 0.8319 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.6383
  time to fit residues: 146.0153
Evaluate side-chains
  115 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 88 optimal weight:    2.9990
   chunk 49 optimal weight:   30.0000
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 47 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:   30.0000
   chunk 68 optimal weight:    0.0470
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.7884

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 741 GLN
A 845 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.174425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.125020 restraints weight = 45580.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.126062 restraints weight = 20139.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.127368 restraints weight = 13341.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9616  Z= 0.189
  Angle     :  0.625   6.299  13029  Z= 0.349
  Chirality :  0.040   0.154   1506
  Planarity :  0.005   0.047   1621
  Dihedral  :  5.318  38.345   1304
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  5.78 %
    Favored  : 93.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.23), residues: 1167
  helix:  0.31 (0.18), residues: 762
  sheet: -1.18 (0.48), residues: 73
  loop :  0.38 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 216 
 HIS   0.008   0.002   HIS A  55 
 PHE   0.023   0.002   PHE A 324 
 TYR   0.015   0.002   TYR A 985 
 ARG   0.007   0.001   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06795 (  615)
  hydrogen bonds       : angle       5.31800 ( 1797)
  covalent geometry    : bond        0.00401 ( 9616)
  covalent geometry    : angle       0.62479 (13029)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 1.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1092 SER cc_start: 0.8709 (m) cc_final: 0.8383 (m)
REVERT: A 1146 LEU cc_start: 0.7829 (mt) cc_final: 0.7622 (mt)
REVERT: A 1256 ASP cc_start: 0.8859 (t0) cc_final: 0.8431 (t70)
  outliers start: 8
  outliers final: 8
  residues processed: 127
  average time/residue: 0.5829
  time to fit residues: 100.3638
Evaluate side-chains
  113 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   72 GLU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1208 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 97 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.178399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.125399 restraints weight = 45860.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.130229 restraints weight = 18594.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.132971 restraints weight = 11499.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9616  Z= 0.130
  Angle     :  0.534   5.428  13029  Z= 0.290
  Chirality :  0.038   0.146   1506
  Planarity :  0.004   0.041   1621
  Dihedral  :  5.003  37.232   1304
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.86 %
    Favored  : 92.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.24), residues: 1167
  helix:  1.05 (0.18), residues: 761
  sheet: -1.45 (0.46), residues: 73
  loop :  0.68 (0.37), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 711 
 HIS   0.006   0.001   HIS A 152 
 PHE   0.022   0.001   PHE A 324 
 TYR   0.010   0.001   TYR A  92 
 ARG   0.007   0.000   ARG A 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05854 (  615)
  hydrogen bonds       : angle       4.80833 ( 1797)
  covalent geometry    : bond        0.00267 ( 9616)
  covalent geometry    : angle       0.53360 (13029)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.7323 (tttp) cc_final: 0.7078 (mmtm)
REVERT: A  276 MET cc_start: 0.7601 (mmm) cc_final: 0.7346 (mmt)
REVERT: A 1256 ASP cc_start: 0.8461 (t0) cc_final: 0.8144 (t70)
  outliers start: 9
  outliers final: 7
  residues processed: 123
  average time/residue: 0.5577
  time to fit residues: 92.3490
Evaluate side-chains
  110 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   72 GLU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1119 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 110 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 52 optimal weight:    0.3980
   chunk 79 optimal weight:    7.9990
   chunk 43 optimal weight:   20.0000
   chunk 83 optimal weight:    2.9990
   chunk 92 optimal weight:   10.0000
   chunk 61 optimal weight:    0.5980
   overall best weight:    2.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 344 ASN
A 999 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.174931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.125994 restraints weight = 45692.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.126751 restraints weight = 20532.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.127491 restraints weight = 14136.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9616  Z= 0.189
  Angle     :  0.550   5.216  13029  Z= 0.303
  Chirality :  0.038   0.141   1506
  Planarity :  0.004   0.045   1621
  Dihedral  :  4.903  36.201   1304
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.93 %
    Favored  : 90.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.24), residues: 1167
  helix:  1.11 (0.18), residues: 753
  sheet: -1.63 (0.48), residues: 74
  loop :  0.63 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 733 
 HIS   0.008   0.001   HIS A 153 
 PHE   0.020   0.002   PHE A 336 
 TYR   0.008   0.001   TYR A 728 
 ARG   0.005   0.000   ARG A 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05692 (  615)
  hydrogen bonds       : angle       4.80113 ( 1797)
  covalent geometry    : bond        0.00425 ( 9616)
  covalent geometry    : angle       0.54962 (13029)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1256 ASP cc_start: 0.8700 (t0) cc_final: 0.8291 (t70)
  outliers start: 13
  outliers final: 12
  residues processed: 115
  average time/residue: 0.5185
  time to fit residues: 82.1080
Evaluate side-chains
  111 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  237 CYS
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain A residue 1208 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 111 optimal weight:    0.0980
   chunk 49 optimal weight:   20.0000
   chunk 84 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0980
   chunk 92 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.178193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.129359 restraints weight = 45875.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.130265 restraints weight = 20164.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.131649 restraints weight = 13126.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9616  Z= 0.123
  Angle     :  0.496   5.907  13029  Z= 0.268
  Chirality :  0.037   0.146   1506
  Planarity :  0.003   0.043   1621
  Dihedral  :  4.714  36.492   1304
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.03 %
    Favored  : 90.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1167
  helix:  1.54 (0.19), residues: 755
  sheet: -1.57 (0.47), residues: 74
  loop :  0.74 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 733 
 HIS   0.006   0.001   HIS A 152 
 PHE   0.017   0.001   PHE A 336 
 TYR   0.010   0.001   TYR A1016 
 ARG   0.007   0.000   ARG A 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05118 (  615)
  hydrogen bonds       : angle       4.44930 ( 1797)
  covalent geometry    : bond        0.00262 ( 9616)
  covalent geometry    : angle       0.49580 (13029)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 1.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1256 ASP cc_start: 0.8811 (t0) cc_final: 0.8393 (t70)
  outliers start: 12
  outliers final: 9
  residues processed: 117
  average time/residue: 0.5033
  time to fit residues: 82.1352
Evaluate side-chains
  109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue 1047 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 91 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 63 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 93 optimal weight:    0.2980
   chunk 66 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.177657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.129129 restraints weight = 45853.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.129753 restraints weight = 20241.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.131206 restraints weight = 13408.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9616  Z= 0.124
  Angle     :  0.488   4.939  13029  Z= 0.264
  Chirality :  0.037   0.149   1506
  Planarity :  0.003   0.041   1621
  Dihedral  :  4.560  36.585   1304
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.13 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.25), residues: 1167
  helix:  1.67 (0.19), residues: 756
  sheet: -1.54 (0.48), residues: 74
  loop :  0.81 (0.38), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 912 
 HIS   0.005   0.001   HIS A 153 
 PHE   0.016   0.001   PHE A 336 
 TYR   0.008   0.001   TYR A1016 
 ARG   0.002   0.000   ARG A 897 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04891 (  615)
  hydrogen bonds       : angle       4.34117 ( 1797)
  covalent geometry    : bond        0.00265 ( 9616)
  covalent geometry    : angle       0.48822 (13029)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1256 ASP cc_start: 0.8787 (t0) cc_final: 0.8423 (t70)
  outliers start: 9
  outliers final: 9
  residues processed: 112
  average time/residue: 0.5003
  time to fit residues: 78.7932
Evaluate side-chains
  109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0050
   chunk 63 optimal weight:    0.8980
   chunk 97 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0670
   overall best weight:    0.5132

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.179249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.133477 restraints weight = 45576.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.136648 restraints weight = 23119.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.137409 restraints weight = 12931.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9616  Z= 0.105
  Angle     :  0.472   5.847  13029  Z= 0.252
  Chirality :  0.036   0.149   1506
  Planarity :  0.003   0.040   1621
  Dihedral  :  4.455  37.299   1304
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.72 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.25), residues: 1167
  helix:  1.90 (0.19), residues: 756
  sheet: -1.51 (0.48), residues: 74
  loop :  0.83 (0.38), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 912 
 HIS   0.003   0.001   HIS A 152 
 PHE   0.015   0.001   PHE A 336 
 TYR   0.009   0.001   TYR A  92 
 ARG   0.008   0.000   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04610 (  615)
  hydrogen bonds       : angle       4.17037 ( 1797)
  covalent geometry    : bond        0.00215 ( 9616)
  covalent geometry    : angle       0.47210 (13029)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 1.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 116
  average time/residue: 0.5154
  time to fit residues: 83.1558
Evaluate side-chains
  109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.176536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.130422 restraints weight = 45710.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.133819 restraints weight = 23739.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.134491 restraints weight = 12864.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9616  Z= 0.163
  Angle     :  0.502   5.461  13029  Z= 0.274
  Chirality :  0.037   0.141   1506
  Planarity :  0.004   0.041   1621
  Dihedral  :  4.510  39.888   1304
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.91 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.25), residues: 1167
  helix:  1.71 (0.19), residues: 756
  sheet: -1.49 (0.48), residues: 74
  loop :  0.75 (0.37), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 733 
 HIS   0.008   0.001   HIS A 153 
 PHE   0.020   0.002   PHE A 882 
 TYR   0.007   0.001   TYR A 728 
 ARG   0.004   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04828 (  615)
  hydrogen bonds       : angle       4.34082 ( 1797)
  covalent geometry    : bond        0.00368 ( 9616)
  covalent geometry    : angle       0.50207 (13029)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1255 TYR cc_start: 0.6640 (t80) cc_final: 0.6372 (t80)
  outliers start: 11
  outliers final: 11
  residues processed: 109
  average time/residue: 0.4696
  time to fit residues: 72.0266
Evaluate side-chains
  108 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1102 LYS
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1197 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.175285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.121406 restraints weight = 47294.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.126126 restraints weight = 19697.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.129014 restraints weight = 12551.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9616  Z= 0.121
  Angle     :  0.481   5.436  13029  Z= 0.259
  Chirality :  0.037   0.145   1506
  Planarity :  0.003   0.041   1621
  Dihedral  :  4.464  40.549   1304
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.11 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.25), residues: 1167
  helix:  1.87 (0.19), residues: 755
  sheet: -1.48 (0.49), residues: 74
  loop :  0.70 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 912 
 HIS   0.005   0.001   HIS A 152 
 PHE   0.019   0.001   PHE A 882 
 TYR   0.007   0.001   TYR A1016 
 ARG   0.007   0.000   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04638 (  615)
  hydrogen bonds       : angle       4.19199 ( 1797)
  covalent geometry    : bond        0.00262 ( 9616)
  covalent geometry    : angle       0.48064 (13029)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1255 TYR cc_start: 0.6884 (t80) cc_final: 0.6664 (t80)
  outliers start: 9
  outliers final: 9
  residues processed: 106
  average time/residue: 0.4830
  time to fit residues: 72.5646
Evaluate side-chains
  107 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1102 LYS
Chi-restraints excluded: chain A residue 1119 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 85 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 38 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0870
   chunk 21 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.8762

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.175094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.126752 restraints weight = 45831.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.127069 restraints weight = 20210.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.128357 restraints weight = 13824.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9616  Z= 0.113
  Angle     :  0.480   7.254  13029  Z= 0.257
  Chirality :  0.036   0.143   1506
  Planarity :  0.003   0.041   1621
  Dihedral  :  4.396  41.117   1304
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.21 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.25), residues: 1167
  helix:  1.95 (0.19), residues: 756
  sheet: -1.29 (0.49), residues: 75
  loop :  0.77 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 912 
 HIS   0.004   0.001   HIS A 152 
 PHE   0.035   0.001   PHE A 948 
 TYR   0.008   0.001   TYR A1016 
 ARG   0.009   0.000   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04489 (  615)
  hydrogen bonds       : angle       4.10634 ( 1797)
  covalent geometry    : bond        0.00241 ( 9616)
  covalent geometry    : angle       0.47953 (13029)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  840 TYR cc_start: 0.8642 (m-80) cc_final: 0.8407 (m-80)
REVERT: A 1270 TYR cc_start: 0.7844 (t80) cc_final: 0.7598 (t80)
  outliers start: 8
  outliers final: 8
  residues processed: 113
  average time/residue: 0.4914
  time to fit residues: 77.7551
Evaluate side-chains
  109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1092 SER
Chi-restraints excluded: chain A residue 1102 LYS
Chi-restraints excluded: chain A residue 1119 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 71 optimal weight:    0.8980
   chunk 108 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.174471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.125896 restraints weight = 46030.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.126002 restraints weight = 20380.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.127835 restraints weight = 14327.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9616  Z= 0.132
  Angle     :  0.483   6.218  13029  Z= 0.261
  Chirality :  0.037   0.144   1506
  Planarity :  0.003   0.041   1621
  Dihedral  :  4.402  42.121   1304
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.21 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.25), residues: 1167
  helix:  1.91 (0.19), residues: 757
  sheet: -1.28 (0.49), residues: 75
  loop :  0.83 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 733 
 HIS   0.005   0.001   HIS A 798 
 PHE   0.028   0.001   PHE A 882 
 TYR   0.007   0.001   TYR A1016 
 ARG   0.008   0.000   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04551 (  615)
  hydrogen bonds       : angle       4.15012 ( 1797)
  covalent geometry    : bond        0.00291 ( 9616)
  covalent geometry    : angle       0.48264 (13029)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5659.79 seconds
wall clock time: 98 minutes 26.17 seconds (5906.17 seconds total)