Starting phenix.real_space_refine
on Wed Mar 12 09:36:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdg_13337/03_2025/7pdg_13337.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdg_13337/03_2025/7pdg_13337.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pdg_13337/03_2025/7pdg_13337.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdg_13337/03_2025/7pdg_13337.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdg_13337/03_2025/7pdg_13337.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdg_13337/03_2025/7pdg_13337.cif"
  }
  resolution = 4.3
  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=   0.000 sd=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    4936      2.51       5
     N    1269      2.21       5
     O    1381      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7642
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6676
          Classifications: {'peptide': 842}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 20, 'TRANS': 821}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 966
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
  Time building chain proxies: 5.96, per 1000 atoms: 0.78
  Number of scatterers: 7642
  At special positions: 0
  Unit cell: (96.276, 82.038, 148.482, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1381      8.00
     N    1269      7.00
     C    4936      6.00
    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: 1.93
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      63.6% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 97 through 107
      removed outlier: 4.222A  pdb=" N   MET A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 136
      removed outlier: 3.763A  pdb=" N   THR A 112 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 163
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 4.320A  pdb=" N   GLN A 193 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 236
      removed outlier: 3.696A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 260
    Processing helix  chain 'A' and resid 279 through 338
      removed outlier: 3.722A  pdb=" N   THR A 309 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLY A 320 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LYS A 321 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ASP A 322 " --> pdb=" O   MET A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 351 through 358
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 3.531A  pdb=" N   ALA A 408 " --> pdb=" O   LYS A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 433
    Processing helix  chain 'A' and resid 457 through 481
      removed outlier: 3.506A  pdb=" N   CYS A 461 " --> pdb=" O   ASP A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 524
      removed outlier: 4.262A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 782 through 808
      removed outlier: 3.567A  pdb=" N   SER A 786 " --> pdb=" O   SER A 782 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   SER A 787 " --> pdb=" O   ALA A 783 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 788 " --> pdb=" O   THR A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 844
    Processing helix  chain 'A' and resid 849 through 856
      removed outlier: 3.900A  pdb=" N   LYS A 853 " --> pdb=" O   MET A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 885
      Proline residue:  A 876  - end of helix
      removed outlier: 4.479A  pdb=" N   HIS A 883 " --> pdb=" O   ALA A 879 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   VAL A 884 " --> pdb=" O   VAL A 880 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 908
      removed outlier: 4.438A  pdb=" N   THR A 895 " --> pdb=" O   ASN A 891 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   MET A 896 " --> pdb=" O   ILE A 892 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLN A 908 " --> pdb=" O   THR A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 936
      Proline residue:  A 931  - end of helix
    Processing helix  chain 'A' and resid 977 through 1037
      removed outlier: 3.803A  pdb=" N   PHE A 996 " --> pdb=" O   LEU A 992 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER A1004 " --> pdb=" O   GLU A1000 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A1013 " --> pdb=" O   TYR A1009 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLU A1014 " --> pdb=" O   HIS A1010 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLN A1023 " --> pdb=" O   ARG A1019 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   SER A1024 " --> pdb=" O   THR A1020 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   MET A1025 " --> pdb=" O   LYS A1021 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1046
    Processing helix  chain 'A' and resid 1068 through 1072
      removed outlier: 4.078A  pdb=" N   TYR A1072 " --> pdb=" O   SER A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1098
      removed outlier: 4.252A  pdb=" N   TYR A1083 " --> pdb=" O   GLY A1079 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A1097 " --> pdb=" O   PHE A1093 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A1098 " --> pdb=" O   ASP A1094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1157
      removed outlier: 4.183A  pdb=" N   GLN A1137 " --> pdb=" O   GLN A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1190 through 1201
      removed outlier: 4.031A  pdb=" N   ILE A1194 " --> pdb=" O   ASP A1190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1219
      removed outlier: 4.267A  pdb=" N   LYS A1219 " --> pdb=" O   ARG A1215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 25
      removed outlier: 3.784A  pdb=" N   LYS C  16 " --> pdb=" O   SER C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 49 through 58
    Processing helix  chain 'C' and resid 59 through 68
    Processing helix  chain 'C' and resid 82 through 91
    Processing helix  chain 'C' and resid 92 through 101
    Processing helix  chain 'C' and resid 115 through 123
    Processing helix  chain 'C' and resid 125 through 134
      removed outlier: 4.018A  pdb=" N   ALA C 129 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS C 134 " --> pdb=" O   GLU C 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 441
      removed outlier: 4.765A  pdb=" N   LYS A 437 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   VAL A 448 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A 439 " --> pdb=" O   TYR A 446 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR A 446 " --> pdb=" O   SER A 439 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER A 394 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   GLY A 493 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   SER A 394 " --> pdb=" O   HIS A 491 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   HIS A 491 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LEU A 396 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   GLY A 489 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ALA A 398 " --> pdb=" O   ARG A 487 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG A 487 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 531
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1111
      removed outlier: 5.126A  pdb=" N   LYS A1107 " --> pdb=" O   ALA A1118 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ALA A1118 " --> pdb=" O   LYS A1107 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS A1109 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   MET A1116 " --> pdb=" O   LYS A1109 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A1111 " --> pdb=" O   THR A1114 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER A1057 " --> pdb=" O   GLY A1171 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1111
      removed outlier: 5.126A  pdb=" N   LYS A1107 " --> pdb=" O   ALA A1118 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ALA A1118 " --> pdb=" O   LYS A1107 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS A1109 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   MET A1116 " --> pdb=" O   LYS A1109 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A1111 " --> pdb=" O   THR A1114 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER A1057 " --> pdb=" O   GLY A1171 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   GLN A1208 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL A1166 " --> pdb=" O   GLN A1208 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TYR A1241 " --> pdb=" O   VAL A1209 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLY A1228 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1422 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: 2.72

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2436
        1.34 -     1.46: 1619
        1.46 -     1.58: 3663
        1.58 -     1.70: 0
        1.70 -     1.81: 88
  Bond restraints: 7806
  Sorted by residual:
  bond pdb=" CB  TRP A 130 "
       pdb=" CG  TRP A 130 "
    ideal  model  delta    sigma   weight residual
    1.498  1.431  0.067 3.10e-02 1.04e+03 4.66e+00
  bond pdb=" CG  GLU A 229 "
       pdb=" CD  GLU A 229 "
    ideal  model  delta    sigma   weight residual
    1.516  1.482  0.034 2.50e-02 1.60e+03 1.84e+00
  bond pdb=" CG1 ILE A 228 "
       pdb=" CD1 ILE A 228 "
    ideal  model  delta    sigma   weight residual
    1.513  1.466  0.047 3.90e-02 6.57e+02 1.43e+00
  bond pdb=" CG  LEU A 789 "
       pdb=" CD2 LEU A 789 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.29e+00
  bond pdb=" CG1 ILE A1022 "
       pdb=" CD1 ILE A1022 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.17e+00
  ... (remaining 7801 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 10300
        2.19 -     4.38: 217
        4.38 -     6.57: 33
        6.57 -     8.76: 7
        8.76 -    10.94: 6
  Bond angle restraints: 10563
  Sorted by residual:
  angle pdb=" N   PRO A 339 "
        pdb=" CA  PRO A 339 "
        pdb=" C   PRO A 339 "
      ideal   model   delta    sigma   weight residual
     111.33  116.19   -4.86 1.43e+00 4.89e-01 1.15e+01
  angle pdb=" CA  LEU A 195 "
        pdb=" CB  LEU A 195 "
        pdb=" CG  LEU A 195 "
      ideal   model   delta    sigma   weight residual
     116.30  126.71  -10.41 3.50e+00 8.16e-02 8.85e+00
  angle pdb=" CB  MET A 226 "
        pdb=" CG  MET A 226 "
        pdb=" SD  MET A 226 "
      ideal   model   delta    sigma   weight residual
     112.70  103.79    8.91 3.00e+00 1.11e-01 8.82e+00
  angle pdb=" N   ALA A 860 "
        pdb=" CA  ALA A 860 "
        pdb=" C   ALA A 860 "
      ideal   model   delta    sigma   weight residual
     108.63  113.37   -4.74 1.60e+00 3.91e-01 8.77e+00
  angle pdb=" CA  GLN A 908 "
        pdb=" CB  GLN A 908 "
        pdb=" CG  GLN A 908 "
      ideal   model   delta    sigma   weight residual
     114.10  119.97   -5.87 2.00e+00 2.50e-01 8.61e+00
  ... (remaining 10558 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 4107
       17.30 -    34.60: 393
       34.60 -    51.90: 76
       51.90 -    69.20: 8
       69.20 -    86.50: 11
  Dihedral angle restraints: 4595
    sinusoidal: 1788
      harmonic: 2807
  Sorted by residual:
  dihedral pdb=" CA  GLN A 191 "
           pdb=" C   GLN A 191 "
           pdb=" N   PHE A 192 "
           pdb=" CA  PHE A 192 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.83  -23.17     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  THR A 236 "
           pdb=" C   THR A 236 "
           pdb=" N   VAL A 237 "
           pdb=" CA  VAL A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.92  -22.08     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  ASN A 485 "
           pdb=" C   ASN A 485 "
           pdb=" N   MET A 486 "
           pdb=" CA  MET A 486 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.93  -21.07     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 4592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 808
       0.040 -    0.079: 299
       0.079 -    0.119: 87
       0.119 -    0.159: 11
       0.159 -    0.198: 4
  Chirality restraints: 1209
  Sorted by residual:
  chirality pdb=" CA  LEU A 875 "
            pdb=" N   LEU A 875 "
            pdb=" C   LEU A 875 "
            pdb=" CB  LEU A 875 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.84e-01
  chirality pdb=" CB  VAL A 884 "
            pdb=" CA  VAL A 884 "
            pdb=" CG1 VAL A 884 "
            pdb=" CG2 VAL A 884 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.22e-01
  chirality pdb=" CA  TRP A 130 "
            pdb=" N   TRP A 130 "
            pdb=" C   TRP A 130 "
            pdb=" CB  TRP A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 1206 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1140 "   -0.013 2.00e-02 2.50e+03   1.36e-02 3.22e+00
        pdb=" CG  PHE A1140 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1140 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1140 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1140 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1140 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1140 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 130 "    0.013 2.00e-02 2.50e+03   1.09e-02 2.98e+00
        pdb=" CG  TRP A 130 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 130 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 130 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 130 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 130 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 130 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 130 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 130 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 130 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 226 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   MET A 226 "    0.029 2.00e-02 2.50e+03
        pdb=" O   MET A 226 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   CYS A 227 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 311
        2.71 -     3.26: 8354
        3.26 -     3.80: 12657
        3.80 -     4.35: 14676
        4.35 -     4.90: 23915
  Nonbonded interactions: 59913
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 219 "
            pdb=" OE2 GLU A 982 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" NH1 ARG A1034 "
            pdb=" O   ILE A1037 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" O   ASP A 351 "
            pdb=" OG  SER A 354 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OG1 THR C  43 "
            pdb=" O   HIS C  48 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   GLU A 280 "
            pdb=" OG  SER A 283 "
     model   vdw
     2.209 3.040
  ... (remaining 59908 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=1.00 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:             3.540
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     24.240
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:3.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
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   0.067   7806  Z= 0.301
  Angle     :  0.819  10.945  10563  Z= 0.430
  Chirality :  0.045   0.198   1209
  Planarity :  0.004   0.037   1323
  Dihedral  : 14.586  86.496   2785
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.49 (0.26), residues: 954
  helix:  0.49 (0.21), residues: 587
  sheet:  0.19 (0.59), residues: 76
  loop : -2.08 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 130 
 HIS   0.008   0.001   HIS A 866 
 PHE   0.031   0.003   PHE A1140 
 TYR   0.017   0.002   TYR A1005 
 ARG   0.007   0.001   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8793 (m) cc_final: 0.8433 (m)
REVERT: A  229 GLU cc_start: 0.9070 (mp0) cc_final: 0.8629 (mp0)
REVERT: A  465 MET cc_start: 0.8583 (mmt) cc_final: 0.7671 (mmm)
REVERT: A  469 MET cc_start: 0.9164 (mmp) cc_final: 0.8939 (mmp)
REVERT: A  545 MET cc_start: 0.7512 (mmp) cc_final: 0.7039 (mmp)
REVERT: A 1094 ASP cc_start: 0.8153 (m-30) cc_final: 0.7919 (m-30)
REVERT: A 1238 MET cc_start: 0.9269 (ttp) cc_final: 0.8953 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1683
  time to fit residues: 30.3456
Evaluate side-chains
  93 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   chunk 75 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    3.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.084943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.059776 restraints weight = 42907.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.061385 restraints weight = 25103.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.062413 restraints weight = 17151.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7806  Z= 0.249
  Angle     :  0.680  11.085  10563  Z= 0.351
  Chirality :  0.041   0.178   1209
  Planarity :  0.004   0.045   1323
  Dihedral  :  4.906  21.364   1036
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  7.52 %
    Favored  : 92.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.42 (0.26), residues: 954
  helix:  0.55 (0.20), residues: 604
  sheet: -0.42 (0.53), residues: 91
  loop : -2.07 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A 866 
 PHE   0.018   0.002   PHE A1140 
 TYR   0.020   0.002   TYR A 252 
 ARG   0.005   0.000   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8884 (m) cc_final: 0.8580 (m)
REVERT: A  229 GLU cc_start: 0.9054 (mp0) cc_final: 0.8564 (mp0)
REVERT: A  465 MET cc_start: 0.8994 (mmm) cc_final: 0.8156 (mmm)
REVERT: A  469 MET cc_start: 0.9289 (mmp) cc_final: 0.9082 (mmp)
REVERT: A  483 MET cc_start: 0.7303 (mmt) cc_final: 0.7070 (mmp)
REVERT: A  545 MET cc_start: 0.7594 (mmp) cc_final: 0.7053 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1663
  time to fit residues: 26.4759
Evaluate side-chains
  89 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 40 optimal weight:   20.0000
   chunk 18 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0070
   chunk 23 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    2.0004

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 297 HIS
A 491 HIS
A1023 GLN
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.086618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.061583 restraints weight = 42516.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.063325 restraints weight = 24169.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.064458 restraints weight = 16283.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7806  Z= 0.182
  Angle     :  0.638  10.880  10563  Z= 0.322
  Chirality :  0.040   0.178   1209
  Planarity :  0.004   0.047   1323
  Dihedral  :  4.602  19.276   1036
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.11 (0.27), residues: 954
  helix:  0.85 (0.21), residues: 611
  sheet: -0.49 (0.53), residues: 90
  loop : -2.11 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 995 
 HIS   0.008   0.001   HIS A 530 
 PHE   0.014   0.002   PHE A1071 
 TYR   0.015   0.001   TYR A 252 
 ARG   0.003   0.000   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.9099 (mmm) cc_final: 0.7985 (mmm)
REVERT: A  469 MET cc_start: 0.9276 (mmp) cc_final: 0.8974 (mmt)
REVERT: A  483 MET cc_start: 0.7214 (mmt) cc_final: 0.6989 (mmp)
REVERT: A  545 MET cc_start: 0.7598 (mmp) cc_final: 0.7051 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1589
  time to fit residues: 27.0349
Evaluate side-chains
  88 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 46 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
C  85 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.085135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.060159 restraints weight = 42585.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.061817 restraints weight = 24707.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.062916 restraints weight = 16872.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7806  Z= 0.205
  Angle     :  0.641  11.168  10563  Z= 0.324
  Chirality :  0.040   0.171   1209
  Planarity :  0.004   0.045   1323
  Dihedral  :  4.586  19.105   1036
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.05 (0.27), residues: 954
  helix:  0.88 (0.20), residues: 613
  sheet: -0.72 (0.53), residues: 94
  loop : -1.98 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 174 
 HIS   0.006   0.001   HIS A 866 
 PHE   0.014   0.002   PHE A 232 
 TYR   0.018   0.002   TYR A 252 
 ARG   0.004   0.000   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.916 
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: A  145 MET cc_start: 0.7609 (mmm) cc_final: 0.7378 (mmm)
REVERT: A  469 MET cc_start: 0.9312 (mmp) cc_final: 0.9074 (mmp)
REVERT: A  483 MET cc_start: 0.7174 (mmt) cc_final: 0.6945 (mmp)
REVERT: A  486 MET cc_start: 0.8444 (tpp) cc_final: 0.7706 (tpp)
REVERT: A  545 MET cc_start: 0.7788 (mmp) cc_final: 0.7275 (mmm)
REVERT: A 1083 TYR cc_start: 0.8954 (m-80) cc_final: 0.8517 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1542
  time to fit residues: 26.0130
Evaluate side-chains
  88 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.091442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.066838 restraints weight = 44001.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.068634 restraints weight = 24464.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.069822 restraints weight = 16083.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7806  Z= 0.149
  Angle     :  0.647  10.725  10563  Z= 0.314
  Chirality :  0.039   0.168   1209
  Planarity :  0.003   0.045   1323
  Dihedral  :  4.321  19.151   1036
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.94 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.38 (0.27), residues: 954
  helix:  1.23 (0.21), residues: 613
  sheet: -0.42 (0.53), residues: 88
  loop : -1.89 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 174 
 HIS   0.004   0.001   HIS C  52 
 PHE   0.010   0.001   PHE A 988 
 TYR   0.012   0.001   TYR A1083 
 ARG   0.002   0.000   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  469 MET cc_start: 0.9264 (mmp) cc_final: 0.9032 (mmp)
REVERT: A  486 MET cc_start: 0.8636 (tpp) cc_final: 0.7985 (tpp)
REVERT: A  545 MET cc_start: 0.7694 (mmp) cc_final: 0.7223 (mmm)
REVERT: A 1083 TYR cc_start: 0.9049 (m-80) cc_final: 0.8519 (m-80)
REVERT: A 1162 PHE cc_start: 0.7198 (m-10) cc_final: 0.6838 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1608
  time to fit residues: 30.6758
Evaluate side-chains
  97 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:   30.0000
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 288 HIS
A 297 HIS
A 883 HIS
A1170 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.089699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.065101 restraints weight = 45031.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.066840 restraints weight = 25051.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.068006 restraints weight = 16622.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7806  Z= 0.166
  Angle     :  0.634  10.962  10563  Z= 0.309
  Chirality :  0.039   0.165   1209
  Planarity :  0.003   0.044   1323
  Dihedral  :  4.281  16.541   1036
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.38 (0.27), residues: 954
  helix:  1.20 (0.21), residues: 613
  sheet: -0.41 (0.54), residues: 90
  loop : -1.84 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  56 
 HIS   0.004   0.001   HIS A 866 
 PHE   0.010   0.001   PHE A 988 
 TYR   0.015   0.001   TYR A 252 
 ARG   0.002   0.000   ARG A 428 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.7911 (mmm) cc_final: 0.7695 (mmm)
REVERT: A  465 MET cc_start: 0.9143 (mmm) cc_final: 0.8069 (mmm)
REVERT: A  469 MET cc_start: 0.9251 (mmp) cc_final: 0.8968 (mmp)
REVERT: A  486 MET cc_start: 0.8587 (tpp) cc_final: 0.7905 (tpp)
REVERT: A  545 MET cc_start: 0.7615 (mmp) cc_final: 0.7126 (mmm)
REVERT: A 1083 TYR cc_start: 0.8983 (m-80) cc_final: 0.8704 (m-80)
REVERT: A 1162 PHE cc_start: 0.7132 (m-80) cc_final: 0.6766 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2131
  time to fit residues: 36.3205
Evaluate side-chains
  94 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0670
   chunk 78 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 34 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.3520

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.090343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.065695 restraints weight = 44857.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.067477 restraints weight = 25097.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.068639 restraints weight = 16666.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7806  Z= 0.160
  Angle     :  0.653  10.918  10563  Z= 0.317
  Chirality :  0.039   0.164   1209
  Planarity :  0.003   0.042   1323
  Dihedral  :  4.237  18.982   1036
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.44 (0.27), residues: 954
  helix:  1.24 (0.21), residues: 614
  sheet: -0.34 (0.55), residues: 90
  loop : -1.81 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 866 
 PHE   0.034   0.001   PHE A 184 
 TYR   0.012   0.001   TYR A1083 
 ARG   0.004   0.000   ARG A1084 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.9171 (mmm) cc_final: 0.8156 (mmm)
REVERT: A  469 MET cc_start: 0.9290 (mmp) cc_final: 0.9005 (mmp)
REVERT: A  545 MET cc_start: 0.7701 (mmp) cc_final: 0.7203 (mmm)
REVERT: A 1083 TYR cc_start: 0.9075 (m-80) cc_final: 0.8632 (m-80)
REVERT: A 1116 MET cc_start: 0.8980 (ptt) cc_final: 0.8767 (ptm)
REVERT: A 1162 PHE cc_start: 0.7080 (m-80) cc_final: 0.6748 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1741
  time to fit residues: 30.6193
Evaluate side-chains
  94 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0980
   chunk 29 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.089946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.064866 restraints weight = 46405.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.066589 restraints weight = 26201.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.067728 restraints weight = 17601.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7806  Z= 0.165
  Angle     :  0.669  10.930  10563  Z= 0.325
  Chirality :  0.039   0.163   1209
  Planarity :  0.003   0.043   1323
  Dihedral  :  4.216  18.096   1036
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.46 (0.27), residues: 954
  helix:  1.24 (0.21), residues: 613
  sheet: -0.12 (0.58), residues: 79
  loop : -1.79 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 130 
 HIS   0.004   0.001   HIS A 292 
 PHE   0.027   0.001   PHE A1140 
 TYR   0.011   0.001   TYR A 252 
 ARG   0.002   0.000   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.9136 (mmm) cc_final: 0.8068 (mmm)
REVERT: A  469 MET cc_start: 0.9292 (mmp) cc_final: 0.8995 (mmp)
REVERT: A  486 MET cc_start: 0.8210 (tpp) cc_final: 0.7383 (tpp)
REVERT: A  545 MET cc_start: 0.7719 (mmp) cc_final: 0.7209 (mmm)
REVERT: A 1083 TYR cc_start: 0.9074 (m-80) cc_final: 0.8647 (m-80)
REVERT: A 1116 MET cc_start: 0.8940 (ptt) cc_final: 0.8723 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2013
  time to fit residues: 33.1526
Evaluate side-chains
  92 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0970
   chunk 84 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
C  85 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.088775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.065425 restraints weight = 46588.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.066691 restraints weight = 28747.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.067157 restraints weight = 16760.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7806  Z= 0.205
  Angle     :  0.695  11.183  10563  Z= 0.343
  Chirality :  0.041   0.169   1209
  Planarity :  0.004   0.042   1323
  Dihedral  :  4.413  18.270   1036
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.31 (0.27), residues: 954
  helix:  1.11 (0.21), residues: 606
  sheet: -0.09 (0.58), residues: 80
  loop : -1.77 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  78 
 HIS   0.005   0.001   HIS A 866 
 PHE   0.028   0.002   PHE A 232 
 TYR   0.017   0.002   TYR A 252 
 ARG   0.003   0.000   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.836 
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: A  387 MET cc_start: 0.8178 (pmm) cc_final: 0.7957 (pmm)
REVERT: A  469 MET cc_start: 0.9351 (mmp) cc_final: 0.9056 (mmp)
REVERT: A  486 MET cc_start: 0.8353 (tpp) cc_final: 0.7510 (tpp)
REVERT: A  545 MET cc_start: 0.8102 (mmp) cc_final: 0.7626 (mmm)
REVERT: A 1083 TYR cc_start: 0.9015 (m-80) cc_final: 0.8617 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1679
  time to fit residues: 28.0289
Evaluate side-chains
  87 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 79 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   overall best weight:    3.3386

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.085193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.060355 restraints weight = 43712.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.061953 restraints weight = 25483.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.063038 restraints weight = 17372.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7806  Z= 0.238
  Angle     :  0.727  11.133  10563  Z= 0.362
  Chirality :  0.042   0.183   1209
  Planarity :  0.004   0.043   1323
  Dihedral  :  4.614  19.453   1036
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.10 (0.27), residues: 954
  helix:  0.91 (0.20), residues: 606
  sheet: -0.07 (0.60), residues: 78
  loop : -1.78 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  78 
 HIS   0.012   0.001   HIS A 866 
 PHE   0.020   0.002   PHE A1140 
 TYR   0.022   0.002   TYR A 235 
 ARG   0.003   0.000   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.9128 (mmm) cc_final: 0.8122 (mmm)
REVERT: A  469 MET cc_start: 0.9249 (mmp) cc_final: 0.8955 (mmp)
REVERT: A  486 MET cc_start: 0.8242 (tpp) cc_final: 0.7448 (tpp)
REVERT: A  545 MET cc_start: 0.7671 (mmp) cc_final: 0.7192 (mmm)
REVERT: A 1083 TYR cc_start: 0.8997 (m-80) cc_final: 0.8623 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1969
  time to fit residues: 31.0165
Evaluate side-chains
  85 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 92 optimal weight:   30.0000
   chunk 32 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0670
   chunk 57 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 76 optimal weight:   20.0000
   overall best weight:    1.5524

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.089792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.064874 restraints weight = 45520.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.066636 restraints weight = 25287.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.067813 restraints weight = 16800.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7806  Z= 0.172
  Angle     :  0.684  10.727  10563  Z= 0.332
  Chirality :  0.040   0.172   1209
  Planarity :  0.004   0.043   1323
  Dihedral  :  4.363  18.128   1036
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.46 (0.27), residues: 954
  helix:  1.22 (0.21), residues: 606
  sheet:  0.01 (0.60), residues: 80
  loop : -1.71 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 130 
 HIS   0.005   0.001   HIS A 292 
 PHE   0.019   0.001   PHE A1140 
 TYR   0.015   0.001   TYR A 235 
 ARG   0.002   0.000   ARG A 920 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3453.15 seconds
wall clock time: 63 minutes 31.22 seconds (3811.22 seconds total)