Starting phenix.real_space_refine
on Wed Feb 12 09:34:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdg_13337/02_2025/7pdg_13337.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdg_13337/02_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_13337/02_2025/7pdg_13337.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdg_13337/02_2025/7pdg_13337.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdg_13337/02_2025/7pdg_13337.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdg_13337/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.28, per 1000 atoms: 0.69
  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: 2.04
  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: 0.83
  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: 2.38

  Time building geometry restraints manager: 2.37 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:             3.050
  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:         0.080
  Set scattering table:                    0.080
  Process input model:                     21.530
  Find NCS groups from input model:        0.110
  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:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.340
-------------------------------------------------------------------------------
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  : 0.872 
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: 30.3752
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  : 0.951 
-------------------------------------------------------------------------------
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 = 51)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.059774 restraints weight = 42907.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.061391 restraints weight = 25098.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.062439 restraints weight = 17144.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
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  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8885 (m) cc_final: 0.8581 (m)
REVERT: A  229 GLU cc_start: 0.9055 (mp0) cc_final: 0.8564 (mp0)
REVERT: A  465 MET cc_start: 0.8995 (mmm) cc_final: 0.8160 (mmm)
REVERT: A  469 MET cc_start: 0.9291 (mmp) cc_final: 0.9085 (mmp)
REVERT: A  483 MET cc_start: 0.7304 (mmt) cc_final: 0.7071 (mmp)
REVERT: A  545 MET cc_start: 0.7600 (mmp) cc_final: 0.7058 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1682
  time to fit residues: 26.7839
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  : 0.937 
-------------------------------------------------------------------------------
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:    0.8980
   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:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0980
   chunk 23 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 HIS
A1023 GLN
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.089863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.065039 restraints weight = 46789.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.066837 restraints weight = 26042.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.068039 restraints weight = 17241.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.2165

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= 0.175
  Angle     :  0.633  10.789  10563  Z= 0.319
  Chirality :  0.039   0.177   1209
  Planarity :  0.004   0.047   1323
  Dihedral  :  4.551  19.508   1036
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  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: -0.02 (0.27), residues: 954
  helix:  0.92 (0.21), residues: 611
  sheet: -0.48 (0.53), residues: 90
  loop : -2.10 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 995 
 HIS   0.006   0.001   HIS A 530 
 PHE   0.016   0.001   PHE A 232 
 TYR   0.013   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
  120 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  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  465 MET cc_start: 0.9055 (mmm) cc_final: 0.7905 (mmm)
REVERT: A  469 MET cc_start: 0.9255 (mmp) cc_final: 0.8929 (mmt)
REVERT: A  483 MET cc_start: 0.7205 (mmt) cc_final: 0.6979 (mmp)
REVERT: A  486 MET cc_start: 0.8666 (tpp) cc_final: 0.7930 (tpp)
REVERT: A  545 MET cc_start: 0.7634 (mmp) cc_final: 0.7091 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1586
  time to fit residues: 27.7485
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  : 0.914 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 67 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 44 optimal weight:   20.0000
   chunk 7 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    3.5586

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.084277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.059349 restraints weight = 43818.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.060987 restraints weight = 25675.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.062061 restraints weight = 17529.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7806  Z= 0.239
  Angle     :  0.673  11.317  10563  Z= 0.342
  Chirality :  0.041   0.175   1209
  Planarity :  0.004   0.046   1323
  Dihedral  :  4.688  20.058   1036
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  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: -0.19 (0.26), residues: 954
  helix:  0.74 (0.20), residues: 613
  sheet: -0.77 (0.53), residues: 92
  loop : -1.92 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  78 
 HIS   0.007   0.001   HIS A 866 
 PHE   0.019   0.002   PHE A 912 
 TYR   0.021   0.002   TYR A 252 
 ARG   0.005   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
  112 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.7574 (mmm) cc_final: 0.7344 (mmm)
REVERT: A  156 CYS cc_start: 0.8799 (m) cc_final: 0.8579 (m)
REVERT: A  387 MET cc_start: 0.8214 (pmm) cc_final: 0.8014 (pmm)
REVERT: A  465 MET cc_start: 0.9123 (mmm) cc_final: 0.8686 (mmm)
REVERT: A  469 MET cc_start: 0.9311 (mmp) cc_final: 0.9060 (mmp)
REVERT: A  483 MET cc_start: 0.7175 (mmt) cc_final: 0.6915 (mmp)
REVERT: A  545 MET cc_start: 0.7789 (mmp) cc_final: 0.7271 (mmm)
REVERT: A 1083 TYR cc_start: 0.8966 (m-80) cc_final: 0.8514 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1699
  time to fit residues: 27.5176
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  : 1.006 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 76 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0870
   chunk 70 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.8162

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.087894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.063191 restraints weight = 40174.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.064925 restraints weight = 23405.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.066069 restraints weight = 15856.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7806  Z= 0.151
  Angle     :  0.649  10.715  10563  Z= 0.316
  Chirality :  0.039   0.170   1209
  Planarity :  0.003   0.045   1323
  Dihedral  :  4.390  18.964   1036
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.82 %
    Favored  : 98.06 %
  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:  0.26 (0.27), residues: 954
  helix:  1.13 (0.21), residues: 613
  sheet: -0.72 (0.54), residues: 86
  loop : -1.81 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 174 
 HIS   0.003   0.001   HIS A 866 
 PHE   0.011   0.001   PHE A 232 
 TYR   0.011   0.001   TYR A1083 
 ARG   0.003   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
  124 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.7653 (mmm) cc_final: 0.7414 (mmm)
REVERT: A  465 MET cc_start: 0.9137 (mmm) cc_final: 0.7779 (mmm)
REVERT: A  469 MET cc_start: 0.9244 (mmp) cc_final: 0.8878 (mmt)
REVERT: A  486 MET cc_start: 0.8382 (tpp) cc_final: 0.7658 (tpp)
REVERT: A  545 MET cc_start: 0.7537 (mmp) cc_final: 0.7079 (mmm)
REVERT: A 1083 TYR cc_start: 0.8953 (m-80) cc_final: 0.8460 (m-80)
REVERT: A 1162 PHE cc_start: 0.7137 (m-10) cc_final: 0.6807 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1601
  time to fit residues: 28.9516
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  : 0.916 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 95 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    2.7584

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.085250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.060116 restraints weight = 43003.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.061723 restraints weight = 25360.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.062816 restraints weight = 17492.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7806  Z= 0.205
  Angle     :  0.659  11.150  10563  Z= 0.327
  Chirality :  0.040   0.171   1209
  Planarity :  0.004   0.043   1323
  Dihedral  :  4.493  18.627   1036
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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:  0.12 (0.27), residues: 954
  helix:  0.98 (0.20), residues: 612
  sheet: -0.69 (0.53), residues: 90
  loop : -1.78 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  78 
 HIS   0.005   0.001   HIS A 866 
 PHE   0.025   0.002   PHE A 184 
 TYR   0.016   0.002   TYR A 252 
 ARG   0.003   0.000   ARG A 920 

*********************** 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
  112 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.7545 (mmm) cc_final: 0.7335 (mmm)
REVERT: A  229 GLU cc_start: 0.8794 (mp0) cc_final: 0.8525 (mp0)
REVERT: A  465 MET cc_start: 0.9145 (mmm) cc_final: 0.8123 (mmm)
REVERT: A  469 MET cc_start: 0.9297 (mmp) cc_final: 0.9008 (mmp)
REVERT: A  486 MET cc_start: 0.8426 (tpp) cc_final: 0.7663 (tpp)
REVERT: A  545 MET cc_start: 0.7604 (mmp) cc_final: 0.7130 (mmm)
REVERT: A 1083 TYR cc_start: 0.8932 (m-80) cc_final: 0.8700 (m-80)
REVERT: A 1162 PHE cc_start: 0.7160 (m-80) cc_final: 0.6727 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1626
  time to fit residues: 26.4828
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  : 0.896 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 78 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 34 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
A 883 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.089938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.065863 restraints weight = 46577.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.067588 restraints weight = 26472.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.068720 restraints weight = 17857.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.3083

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= 0.159
  Angle     :  0.664  10.797  10563  Z= 0.325
  Chirality :  0.040   0.166   1209
  Planarity :  0.003   0.044   1323
  Dihedral  :  4.351  19.468   1036
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  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:  0.33 (0.27), residues: 954
  helix:  1.14 (0.21), residues: 613
  sheet: -0.35 (0.54), residues: 90
  loop : -1.81 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 866 
 PHE   0.012   0.001   PHE A 988 
 TYR   0.011   0.001   TYR A1083 
 ARG   0.002   0.000   ARG A 920 

*********************** 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
  121 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8919 (m) cc_final: 0.8617 (m)
REVERT: A  465 MET cc_start: 0.9160 (mmm) cc_final: 0.8143 (mmm)
REVERT: A  469 MET cc_start: 0.9275 (mmp) cc_final: 0.8976 (mmp)
REVERT: A  486 MET cc_start: 0.8581 (tpp) cc_final: 0.7934 (tpp)
REVERT: A  545 MET cc_start: 0.7753 (mmp) cc_final: 0.7249 (mmm)
REVERT: A 1083 TYR cc_start: 0.9020 (m-80) cc_final: 0.8677 (m-80)
REVERT: A 1162 PHE cc_start: 0.7215 (m-80) cc_final: 0.6851 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1645
  time to fit residues: 28.8953
Evaluate side-chains
  95 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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
A1170 HIS
C  85 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.087866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.064979 restraints weight = 49180.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.065693 restraints weight = 33662.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.066459 restraints weight = 20603.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7806  Z= 0.236
  Angle     :  0.716  11.248  10563  Z= 0.358
  Chirality :  0.042   0.175   1209
  Planarity :  0.004   0.043   1323
  Dihedral  :  4.600  19.070   1036
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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:  0.01 (0.27), residues: 954
  helix:  0.86 (0.20), residues: 612
  sheet: -0.28 (0.58), residues: 79
  loop : -1.86 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 130 
 HIS   0.007   0.001   HIS A 866 
 PHE   0.032   0.002   PHE A1140 
 TYR   0.020   0.002   TYR A 252 
 ARG   0.003   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
  107 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 MET cc_start: 0.8225 (pmm) cc_final: 0.7999 (pmm)
REVERT: A  465 MET cc_start: 0.9173 (mmm) cc_final: 0.8201 (mmm)
REVERT: A  469 MET cc_start: 0.9359 (mmp) cc_final: 0.9066 (mmp)
REVERT: A  545 MET cc_start: 0.8105 (mmp) cc_final: 0.7664 (mmm)
REVERT: A 1083 TYR cc_start: 0.9014 (m-80) cc_final: 0.8629 (m-80)
REVERT: A 1116 MET cc_start: 0.9037 (ptt) cc_final: 0.8817 (ptm)
REVERT: A 1162 PHE cc_start: 0.7219 (m-80) cc_final: 0.6880 (m-80)
REVERT: C  130 GLU cc_start: 0.8818 (tp30) cc_final: 0.8205 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1613
  time to fit residues: 24.8557
Evaluate side-chains
  82 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 90 optimal weight:   40.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 998 ASN
A1010 HIS
A1055 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.083756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.059031 restraints weight = 46318.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.060612 restraints weight = 26898.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.061642 restraints weight = 18447.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7806  Z= 0.292
  Angle     :  0.767  11.257  10563  Z= 0.390
  Chirality :  0.043   0.192   1209
  Planarity :  0.004   0.043   1323
  Dihedral  :  4.946  21.591   1036
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  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: -0.40 (0.26), residues: 954
  helix:  0.50 (0.20), residues: 607
  sheet: -0.48 (0.59), residues: 78
  loop : -1.85 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 862 
 HIS   0.006   0.001   HIS A 319 
 PHE   0.046   0.002   PHE A 232 
 TYR   0.021   0.002   TYR A 252 
 ARG   0.005   0.001   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
  105 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 MET cc_start: 0.8212 (pmm) cc_final: 0.8002 (pmm)
REVERT: A  465 MET cc_start: 0.9110 (mmm) cc_final: 0.8123 (mmm)
REVERT: A  469 MET cc_start: 0.9282 (mmp) cc_final: 0.8970 (mmp)
REVERT: A  483 MET cc_start: 0.7149 (mmt) cc_final: 0.6940 (mmp)
REVERT: A  486 MET cc_start: 0.8068 (tpp) cc_final: 0.7206 (tpp)
REVERT: A  545 MET cc_start: 0.7655 (mmp) cc_final: 0.7173 (mmm)
REVERT: A 1083 TYR cc_start: 0.9039 (m-80) cc_final: 0.8659 (m-80)
REVERT: A 1162 PHE cc_start: 0.7279 (m-80) cc_final: 0.6645 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1692
  time to fit residues: 25.6124
Evaluate side-chains
  86 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0060
   chunk 27 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0670
   chunk 60 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.4734

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

Flipped N/Q/H residues before XYZ refinement:
A 914 GLN
A 998 ASN
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.091062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.066194 restraints weight = 44692.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.068010 restraints weight = 25071.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.069150 restraints weight = 16623.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.3530

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= 0.163
  Angle     :  0.694  10.310  10563  Z= 0.336
  Chirality :  0.040   0.168   1209
  Planarity :  0.004   0.046   1323
  Dihedral  :  4.445  21.681   1036
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 (0.27), residues: 954
  helix:  1.18 (0.21), residues: 606
  sheet: -0.09 (0.58), residues: 86
  loop : -1.71 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 174 
 HIS   0.006   0.001   HIS A 292 
 PHE   0.020   0.001   PHE A1140 
 TYR   0.012   0.001   TYR A 172 
 ARG   0.002   0.000   ARG A1206 

********************** 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
  118 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8914 (m) cc_final: 0.8621 (m)
REVERT: A  469 MET cc_start: 0.9269 (mmp) cc_final: 0.9009 (mmp)
REVERT: A  486 MET cc_start: 0.8225 (tpp) cc_final: 0.7445 (tpp)
REVERT: A  545 MET cc_start: 0.7705 (mmp) cc_final: 0.7233 (mmm)
REVERT: A 1083 TYR cc_start: 0.9043 (m-80) cc_final: 0.8648 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1635
  time to fit residues: 28.1839
Evaluate side-chains
  91 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 32 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:   30.0000
   chunk 16 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
A 914 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.088253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.063329 restraints weight = 46139.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.065011 restraints weight = 26217.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.066137 restraints weight = 17643.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7806  Z= 0.205
  Angle     :  0.705  11.128  10563  Z= 0.347
  Chirality :  0.041   0.175   1209
  Planarity :  0.004   0.044   1323
  Dihedral  :  4.523  19.887   1036
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  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:  0.23 (0.27), residues: 954
  helix:  1.03 (0.21), residues: 606
  sheet: -0.09 (0.59), residues: 80
  loop : -1.77 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A 866 
 PHE   0.027   0.002   PHE A 184 
 TYR   0.018   0.002   TYR A 252 
 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: 3104.03 seconds
wall clock time: 56 minutes 16.38 seconds (3376.38 seconds total)