Starting phenix.real_space_refine
on Tue Sep 24 09:27:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdg_13337/09_2024/7pdg_13337.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdg_13337/09_2024/7pdg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdg_13337/09_2024/7pdg_13337.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdg_13337/09_2024/7pdg_13337.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdg_13337/09_2024/7pdg_13337.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdg_13337/09_2024/7pdg_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-5461/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: 6.03, per 1000 atoms: 0.79
  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: 2.20
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.42
  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: 4.38

  Time building geometry restraints manager: 2.54 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:             4.690
  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:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     27.680
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:4.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.470
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.819 
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: 0.1602
  time to fit residues: 28.7561
Evaluate side-chains
  93 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
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 fitting.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8825 (m) cc_final: 0.8481 (m)
REVERT: A  229 GLU cc_start: 0.8918 (mp0) cc_final: 0.8511 (mp0)
REVERT: A  465 MET cc_start: 0.8865 (mmm) cc_final: 0.7952 (mmm)
REVERT: A  469 MET cc_start: 0.9131 (mmp) cc_final: 0.8916 (mmp)
REVERT: A  483 MET cc_start: 0.7294 (mmt) cc_final: 0.7058 (mmp)
REVERT: A  545 MET cc_start: 0.7376 (mmp) cc_final: 0.6844 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1712
  time to fit residues: 27.0354
Evaluate side-chains
  89 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 335 HIS
A 491 HIS
A1023 GLN
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7806  Z= 0.267
  Angle     :  0.699  11.249  10563  Z= 0.360
  Chirality :  0.042   0.188   1209
  Planarity :  0.004   0.046   1323
  Dihedral  :  4.885  21.336   1036
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  5.82 %
    Favored  : 94.06 %
  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: -0.55 (0.26), residues: 954
  helix:  0.42 (0.20), residues: 613
  sheet: -0.73 (0.52), residues: 90
  loop : -2.02 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 995 
 HIS   0.008   0.001   HIS A 297 
 PHE   0.022   0.002   PHE A 232 
 TYR   0.022   0.002   TYR A 252 
 ARG   0.005   0.001   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
  113 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.7742 (mmm) cc_final: 0.7494 (mmm)
REVERT: A  156 CYS cc_start: 0.8732 (m) cc_final: 0.8510 (m)
REVERT: A  229 GLU cc_start: 0.8812 (mp0) cc_final: 0.8522 (mp0)
REVERT: A  465 MET cc_start: 0.9033 (mmm) cc_final: 0.7886 (mmm)
REVERT: A  469 MET cc_start: 0.9149 (mmp) cc_final: 0.8893 (mmp)
REVERT: A  483 MET cc_start: 0.7161 (mmt) cc_final: 0.6899 (mmp)
REVERT: A  545 MET cc_start: 0.7452 (mmp) cc_final: 0.6936 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1618
  time to fit residues: 26.3154
Evaluate side-chains
  88 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:   30.0000
   chunk 65 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 41 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9990
   chunk 87 optimal weight:   20.0000
   chunk 92 optimal weight:   50.0000
   chunk 83 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   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 297 HIS
A 335 HIS
C  85 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7806  Z= 0.244
  Angle     :  0.679  11.028  10563  Z= 0.345
  Chirality :  0.041   0.180   1209
  Planarity :  0.004   0.046   1323
  Dihedral  :  4.810  21.620   1036
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  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: -0.49 (0.26), residues: 954
  helix:  0.53 (0.20), residues: 614
  sheet: -0.92 (0.53), residues: 92
  loop : -2.09 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 174 
 HIS   0.007   0.001   HIS A 866 
 PHE   0.017   0.002   PHE A 912 
 TYR   0.019   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
  107 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.913 
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: 0.7630 (mmm) cc_final: 0.7394 (mmm)
REVERT: A  156 CYS cc_start: 0.8691 (m) cc_final: 0.8365 (m)
REVERT: A  465 MET cc_start: 0.9027 (mmm) cc_final: 0.8426 (mmm)
REVERT: A  469 MET cc_start: 0.9155 (mmp) cc_final: 0.8885 (mmp)
REVERT: A  483 MET cc_start: 0.7118 (mmt) cc_final: 0.6872 (mmp)
REVERT: A  486 MET cc_start: 0.8367 (tpp) cc_final: 0.7604 (tpp)
REVERT: A  545 MET cc_start: 0.7477 (mmp) cc_final: 0.7010 (mmm)
REVERT: A 1083 TYR cc_start: 0.8577 (m-80) cc_final: 0.8333 (m-80)
REVERT: C   85 HIS cc_start: 0.9062 (m90) cc_final: 0.8859 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1823
  time to fit residues: 28.1937
Evaluate side-chains
  88 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 1 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7806  Z= 0.213
  Angle     :  0.673  11.056  10563  Z= 0.341
  Chirality :  0.041   0.177   1209
  Planarity :  0.004   0.046   1323
  Dihedral  :  4.737  20.691   1036
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.06 %
    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: -0.30 (0.26), residues: 954
  helix:  0.68 (0.20), residues: 612
  sheet: -1.03 (0.52), residues: 88
  loop : -1.93 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A 866 
 PHE   0.014   0.002   PHE A 912 
 TYR   0.015   0.002   TYR A 252 
 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
  111 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.9081 (mmm) cc_final: 0.7959 (mmm)
REVERT: A  469 MET cc_start: 0.9168 (mmp) cc_final: 0.8859 (mmp)
REVERT: A  483 MET cc_start: 0.7097 (mmt) cc_final: 0.6862 (mmp)
REVERT: A  486 MET cc_start: 0.8498 (tpp) cc_final: 0.7793 (tpp)
REVERT: A  545 MET cc_start: 0.7499 (mmp) cc_final: 0.7029 (mmm)
REVERT: A 1083 TYR cc_start: 0.8623 (m-80) cc_final: 0.8300 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1637
  time to fit residues: 26.3176
Evaluate side-chains
  88 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 92 optimal weight:   40.0000
   chunk 77 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 89 optimal weight:    7.9990
   overall best weight:    2.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7806  Z= 0.199
  Angle     :  0.655  10.942  10563  Z= 0.327
  Chirality :  0.040   0.175   1209
  Planarity :  0.004   0.045   1323
  Dihedral  :  4.645  20.033   1036
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  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: -0.14 (0.26), residues: 954
  helix:  0.80 (0.20), residues: 612
  sheet: -0.87 (0.54), residues: 86
  loop : -1.89 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  78 
 HIS   0.005   0.001   HIS A 866 
 PHE   0.023   0.001   PHE A 184 
 TYR   0.013   0.001   TYR A 235 
 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
  108 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.9114 (mmm) cc_final: 0.7926 (mmm)
REVERT: A  469 MET cc_start: 0.9173 (mmp) cc_final: 0.8867 (mmp)
REVERT: A  483 MET cc_start: 0.7066 (mmt) cc_final: 0.6848 (mmp)
REVERT: A  486 MET cc_start: 0.8542 (tpp) cc_final: 0.7878 (tpp)
REVERT: A  545 MET cc_start: 0.7510 (mmp) cc_final: 0.7041 (mmm)
REVERT: A 1083 TYR cc_start: 0.8622 (m-80) cc_final: 0.8302 (m-80)
REVERT: A 1116 MET cc_start: 0.8886 (ptt) cc_final: 0.8611 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1639
  time to fit residues: 25.8325
Evaluate side-chains
  87 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.0070
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 92 optimal weight:   40.0000
   chunk 57 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.7404

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7806  Z= 0.182
  Angle     :  0.662  10.927  10563  Z= 0.328
  Chirality :  0.040   0.171   1209
  Planarity :  0.004   0.045   1323
  Dihedral  :  4.495  19.863   1036
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  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:  0.11 (0.27), residues: 954
  helix:  0.98 (0.21), residues: 614
  sheet: -0.45 (0.54), residues: 90
  loop : -1.93 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A 297 
 PHE   0.011   0.001   PHE A 232 
 TYR   0.012   0.001   TYR A 252 
 ARG   0.003   0.000   ARG A 865 

*********************** 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
  115 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8886 (m) cc_final: 0.8547 (m)
REVERT: A  465 MET cc_start: 0.9127 (mmm) cc_final: 0.7975 (mmm)
REVERT: A  469 MET cc_start: 0.9175 (mmp) cc_final: 0.8860 (mmp)
REVERT: A  486 MET cc_start: 0.8567 (tpp) cc_final: 0.7928 (tpp)
REVERT: A  545 MET cc_start: 0.7510 (mmp) cc_final: 0.7047 (mmm)
REVERT: A 1116 MET cc_start: 0.8868 (ptt) cc_final: 0.8523 (ptm)
REVERT: A 1162 PHE cc_start: 0.6991 (m-80) cc_final: 0.6663 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1601
  time to fit residues: 26.8161
Evaluate side-chains
  87 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0770
   chunk 63 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 88 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   overall best weight:    2.0144

-------------------------------------------------------------------------------
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
A1010 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7806  Z= 0.185
  Angle     :  0.683  10.953  10563  Z= 0.336
  Chirality :  0.040   0.168   1209
  Planarity :  0.004   0.048   1323
  Dihedral  :  4.495  21.770   1036
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  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:  0.14 (0.27), residues: 954
  helix:  0.98 (0.20), residues: 613
  sheet: -0.26 (0.58), residues: 79
  loop : -1.88 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  78 
 HIS   0.004   0.001   HIS A 866 
 PHE   0.031   0.002   PHE A 184 
 TYR   0.015   0.001   TYR A 235 
 ARG   0.003   0.000   ARG A1206 

*********************** 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
  109 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.9095 (mmm) cc_final: 0.7912 (mmm)
REVERT: A  469 MET cc_start: 0.9184 (mmp) cc_final: 0.8873 (mmp)
REVERT: A  486 MET cc_start: 0.8599 (tpp) cc_final: 0.7947 (tpp)
REVERT: A  545 MET cc_start: 0.7537 (mmp) cc_final: 0.7066 (mmm)
REVERT: A 1083 TYR cc_start: 0.8701 (m-80) cc_final: 0.8441 (m-80)
REVERT: A 1116 MET cc_start: 0.8881 (ptt) cc_final: 0.8548 (ptm)
REVERT: A 1162 PHE cc_start: 0.6957 (m-80) cc_final: 0.6658 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1545
  time to fit residues: 24.6863
Evaluate side-chains
  86 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 88 optimal weight:   20.0000
   chunk 51 optimal weight:    0.2980
   chunk 37 optimal weight:    0.0970
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 91 optimal weight:    0.0770
   overall best weight:    0.8938

-------------------------------------------------------------------------------
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
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.3488

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= 0.155
  Angle     :  0.671  10.716  10563  Z= 0.323
  Chirality :  0.039   0.161   1209
  Planarity :  0.004   0.047   1323
  Dihedral  :  4.345  18.934   1036
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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:  0.48 (0.27), residues: 954
  helix:  1.26 (0.21), residues: 608
  sheet: -0.02 (0.59), residues: 80
  loop : -1.76 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  56 
 HIS   0.004   0.001   HIS A 288 
 PHE   0.017   0.001   PHE A1140 
 TYR   0.012   0.001   TYR A1083 
 ARG   0.002   0.000   ARG A 284 

*********************** 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
  118 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.7998 (mmm) cc_final: 0.7770 (mmm)
REVERT: A  244 LEU cc_start: 0.9077 (pp) cc_final: 0.8859 (pp)
REVERT: A  465 MET cc_start: 0.9115 (mmm) cc_final: 0.7991 (mmm)
REVERT: A  469 MET cc_start: 0.9164 (mmp) cc_final: 0.8877 (mmp)
REVERT: A  486 MET cc_start: 0.8564 (tpp) cc_final: 0.7938 (tpp)
REVERT: A  545 MET cc_start: 0.7535 (mmp) cc_final: 0.7081 (mmm)
REVERT: A 1083 TYR cc_start: 0.8690 (m-80) cc_final: 0.8437 (m-80)
REVERT: A 1116 MET cc_start: 0.8899 (ptt) cc_final: 0.8568 (ptm)
REVERT: C  130 GLU cc_start: 0.8750 (tp30) cc_final: 0.8307 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1512
  time to fit residues: 26.0689
Evaluate side-chains
  89 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 63 optimal weight:    8.9990
   chunk 95 optimal weight:    7.9990
   chunk 88 optimal weight:   30.0000
   chunk 76 optimal weight:    0.0050
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    4.0002

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7806  Z= 0.274
  Angle     :  0.759  11.391  10563  Z= 0.379
  Chirality :  0.042   0.181   1209
  Planarity :  0.004   0.046   1323
  Dihedral  :  4.733  21.502   1036
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  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: -0.11 (0.26), residues: 954
  helix:  0.73 (0.20), residues: 603
  sheet: -0.41 (0.58), residues: 80
  loop : -1.71 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 130 
 HIS   0.007   0.001   HIS A 866 
 PHE   0.022   0.002   PHE A 184 
 TYR   0.029   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 fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.7856 (mmm) cc_final: 0.7640 (mmm)
REVERT: A  465 MET cc_start: 0.9107 (mmm) cc_final: 0.7978 (mmm)
REVERT: A  469 MET cc_start: 0.9180 (mmp) cc_final: 0.8854 (mmp)
REVERT: A  545 MET cc_start: 0.7452 (mmp) cc_final: 0.6969 (mmm)
REVERT: A 1083 TYR cc_start: 0.8728 (m-80) cc_final: 0.8498 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1596
  time to fit residues: 25.3160
Evaluate side-chains
  83 residues out of total 829 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0040
   chunk 66 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   overall best weight:    3.3398

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.084778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.060098 restraints weight = 45154.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.061706 restraints weight = 26548.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.062765 restraints weight = 18104.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7806  Z= 0.234
  Angle     :  0.728  11.026  10563  Z= 0.360
  Chirality :  0.041   0.175   1209
  Planarity :  0.004   0.047   1323
  Dihedral  :  4.734  21.359   1036
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  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: -0.10 (0.26), residues: 954
  helix:  0.74 (0.20), residues: 607
  sheet: -0.40 (0.59), residues: 78
  loop : -1.73 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 862 
 HIS   0.006   0.001   HIS A 866 
 PHE   0.023   0.002   PHE A1140 
 TYR   0.025   0.002   TYR A 235 
 ARG   0.003   0.000   ARG A 920 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1800.96 seconds
wall clock time: 33 minutes 21.37 seconds (2001.37 seconds total)