Starting phenix.real_space_refine
on Mon Mar 11 02:42:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/03_2024/7pd4_13330.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/03_2024/7pd4_13330.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/03_2024/7pd4_13330.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/03_2024/7pd4_13330.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/03_2024/7pd4_13330.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/03_2024/7pd4_13330.pdb"
  }
  resolution = 4.9
  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      55      5.16       5
     C    4329      2.51       5
     N    1098      2.21       5
     O    1194      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  109": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  114": "NH1" <-> "NH2"
    Residue "A ARG  117": "NH1" <-> "NH2"
    Residue "A PHE  121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  159": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  164": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  170": "NH1" <-> "NH2"
    Residue "A TYR  235": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  256": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  299": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  307": "NH1" <-> "NH2"
    Residue "A ARG  340": "NH1" <-> "NH2"
    Residue "A ASP  351": "OD1" <-> "OD2"
    Residue "A ASP  421": "OD1" <-> "OD2"
    Residue "A ASP  427": "OD1" <-> "OD2"
    Residue "A TYR  446": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  471": "NH1" <-> "NH2"
    Residue "A ARG  504": "NH1" <-> "NH2"
    Residue "A TYR  538": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  540": "OD1" <-> "OD2"
    Residue "A TYR  543": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  831": "OE1" <-> "OE2"
    Residue "A PHE  843": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  912": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  996": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1002": "OE1" <-> "OE2"
    Residue "A ASP 1030": "OD1" <-> "OD2"
    Residue "A TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1115": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 1127": "NH1" <-> "NH2"
    Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 1148": "NH1" <-> "NH2"
    Residue "A PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG 1206": "NH1" <-> "NH2"
    Residue "A TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 6676
  Number of models: 1
  Model: ""
    Number of chains: 1
    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
  Time building chain proxies: 4.11, per 1000 atoms: 0.62
  Number of scatterers: 6676
  At special positions: 0
  Unit cell: (82.62, 78.57, 144.99, 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      55     16.00
     O    1194      8.00
     N    1098      7.00
     C    4329      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  - 3.50
        Amino acid           : False - 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: 3.04
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1578

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      65.4% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 97 through 108
      removed outlier: 3.539A  pdb=" N   MET A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 137
      removed outlier: 4.130A  pdb=" N   THR A 112 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 164
      removed outlier: 4.377A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 169
      removed outlier: 3.891A  pdb=" N   ALA A 169 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 192
    Processing helix  chain 'A' and resid 219 through 237
      removed outlier: 4.399A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 260
    Processing helix  chain 'A' and resid 279 through 336
    Processing helix  chain 'A' and resid 339 through 348
      removed outlier: 3.704A  pdb=" N   LYS A 348 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 359
      removed outlier: 4.297A  pdb=" N   GLU A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 413 through 434
    Processing helix  chain 'A' and resid 457 through 478
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.621A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 540
      removed outlier: 4.207A  pdb=" N   TYR A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ASP A 540 " --> pdb=" O   ALA A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 807
    Processing helix  chain 'A' and resid 817 through 844
      removed outlier: 4.476A  pdb=" N   LEU A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 858
      removed outlier: 4.325A  pdb=" N   LYS A 853 " --> pdb=" O   MET A 849 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TRP A 858 " --> pdb=" O   ARG A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 875
    Processing helix  chain 'A' and resid 875 through 885
      removed outlier: 4.035A  pdb=" N   HIS A 883 " --> pdb=" O   ALA A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 907
    Processing helix  chain 'A' and resid 908 through 911
    Processing helix  chain 'A' and resid 917 through 938
      Proline residue:  A 931  - end of helix
    Processing helix  chain 'A' and resid 978 through 1037
    Processing helix  chain 'A' and resid 1039 through 1048
    Processing helix  chain 'A' and resid 1067 through 1072
      removed outlier: 3.677A  pdb=" N   PHE A1071 " --> pdb=" O   ASN A1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1098
    Processing helix  chain 'A' and resid 1134 through 1157
      removed outlier: 3.512A  pdb=" N   ASN A1155 " --> pdb=" O   ASP A1151 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN A1156 " --> pdb=" O   ASP A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1201
      removed outlier: 3.946A  pdb=" N   ASN A1193 " --> pdb=" O   GLY A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1211 through 1219
    Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 441
      removed outlier: 5.473A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 441
      removed outlier: 5.473A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 8.584A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1107
      removed outlier: 3.763A  pdb=" N   SER A1119 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1107
      removed outlier: 3.763A  pdb=" N   SER A1119 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   HIS A1170 " --> pdb=" O   SER A1210 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)

    488 hydrogen bonds defined for protein.
    1443 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: 2.65

  Time building geometry restraints manager: 3.27 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: 2098
        1.34 -     1.46: 1574
        1.46 -     1.58: 3064
        1.58 -     1.69: 0
        1.69 -     1.81: 86
  Bond restraints: 6822
  Sorted by residual:
  bond pdb=" CB  TRP A 862 "
       pdb=" CG  TRP A 862 "
    ideal  model  delta    sigma   weight residual
    1.498  1.566 -0.068 3.10e-02 1.04e+03 4.85e+00
  bond pdb=" C   GLY A1179 "
       pdb=" O   GLY A1179 "
    ideal  model  delta    sigma   weight residual
    1.243  1.227  0.015 9.30e-03 1.16e+04 2.69e+00
  bond pdb=" CA  HIS A 297 "
       pdb=" CB  HIS A 297 "
    ideal  model  delta    sigma   weight residual
    1.528  1.508  0.021 1.56e-02 4.11e+03 1.77e+00
  bond pdb=" CA  TRP A 862 "
       pdb=" CB  TRP A 862 "
    ideal  model  delta    sigma   weight residual
    1.529  1.549 -0.020 1.55e-02 4.16e+03 1.73e+00
  bond pdb=" C   GLY A 861 "
       pdb=" O   GLY A 861 "
    ideal  model  delta    sigma   weight residual
    1.238  1.227  0.012 8.90e-03 1.26e+04 1.68e+00
  ... (remaining 6817 not shown)

  Histogram of bond angle deviations from ideal:
       99.10 -   106.23: 130
      106.23 -   113.36: 3840
      113.36 -   120.49: 2821
      120.49 -   127.61: 2375
      127.61 -   134.74: 60
  Bond angle restraints: 9226
  Sorted by residual:
  angle pdb=" N   GLY A 402 "
        pdb=" CA  GLY A 402 "
        pdb=" C   GLY A 402 "
      ideal   model   delta    sigma   weight residual
     114.90  108.60    6.30 1.54e+00 4.22e-01 1.67e+01
  angle pdb=" C   VAL A 907 "
        pdb=" CA  VAL A 907 "
        pdb=" CB  VAL A 907 "
      ideal   model   delta    sigma   weight residual
     112.05  106.09    5.96 1.46e+00 4.69e-01 1.66e+01
  angle pdb=" CA  GLY A 861 "
        pdb=" C   GLY A 861 "
        pdb=" N   TRP A 862 "
      ideal   model   delta    sigma   weight residual
     115.27  118.28   -3.01 7.60e-01 1.73e+00 1.57e+01
  angle pdb=" N   THR A1181 "
        pdb=" CA  THR A1181 "
        pdb=" C   THR A1181 "
      ideal   model   delta    sigma   weight residual
     113.72  108.45    5.27 1.52e+00 4.33e-01 1.20e+01
  angle pdb=" N   GLY A 222 "
        pdb=" CA  GLY A 222 "
        pdb=" C   GLY A 222 "
      ideal   model   delta    sigma   weight residual
     112.64  108.98    3.66 1.21e+00 6.83e-01 9.14e+00
  ... (remaining 9221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3586
       17.90 -    35.81: 361
       35.81 -    53.71: 60
       53.71 -    71.62: 8
       71.62 -    89.52: 4
  Dihedral angle restraints: 4019
    sinusoidal: 1572
      harmonic: 2447
  Sorted by residual:
  dihedral pdb=" CA  LYS A1080 "
           pdb=" C   LYS A1080 "
           pdb=" N   GLU A1081 "
           pdb=" CA  GLU A1081 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.04   21.96     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  TYR A 538 "
           pdb=" C   TYR A 538 "
           pdb=" N   LEU A 539 "
           pdb=" CA  LEU A 539 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.25   21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  CYS A 447 "
           pdb=" C   CYS A 447 "
           pdb=" N   VAL A 448 "
           pdb=" CA  VAL A 448 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.56   21.44     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 675
       0.039 -    0.079: 281
       0.079 -    0.118: 83
       0.118 -    0.157: 17
       0.157 -    0.197: 1
  Chirality restraints: 1057
  Sorted by residual:
  chirality pdb=" CB  ILE A 294 "
            pdb=" CA  ILE A 294 "
            pdb=" CG1 ILE A 294 "
            pdb=" CG2 ILE A 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.65e-01
  chirality pdb=" CA  ILE A1187 "
            pdb=" N   ILE A1187 "
            pdb=" C   ILE A1187 "
            pdb=" CB  ILE A1187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.09e-01
  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    2.36    0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 1054 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1037 "    0.037 5.00e-02 4.00e+02   5.70e-02 5.19e+00
        pdb=" N   PRO A1038 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A1038 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1038 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 292 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.95e+00
        pdb=" C   HIS A 292 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   HIS A 292 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 293 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 226 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.80e+00
        pdb=" C   MET A 226 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   MET A 226 "    0.013 2.00e-02 2.50e+03
        pdb=" N   CYS A 227 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 154
        2.61 -     3.18: 7321
        3.18 -     3.75: 12025
        3.75 -     4.33: 15922
        4.33 -     4.90: 23364
  Nonbonded interactions: 58786
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1110 "
            pdb=" O   THR A1114 "
     model   vdw
     2.035 2.440
  nonbonded pdb=" O   GLN A 220 "
            pdb=" OG  SER A 223 "
     model   vdw
     2.100 2.440
  nonbonded pdb=" O   LEU A 792 "
            pdb=" OG1 THR A 795 "
     model   vdw
     2.114 2.440
  nonbonded pdb=" O   ALA A 783 "
            pdb=" OG  SER A 786 "
     model   vdw
     2.120 2.440
  nonbonded pdb=" O   CYS A 108 "
            pdb=" NE2 GLN A 111 "
     model   vdw
     2.124 2.520
  ... (remaining 58781 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.270
  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:          5.690
  Check model and map are aligned:         0.100
  Set scattering table:                    0.080
  Process input model:                     23.860
  Find NCS groups from input model:        0.220
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
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   0.068   6822  Z= 0.330
  Angle     :  0.873  10.004   9226  Z= 0.508
  Chirality :  0.046   0.197   1057
  Planarity :  0.004   0.057   1145
  Dihedral  : 14.588  89.520   2441
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 38.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.71 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  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: -4.80 (0.22), residues: 828
  helix: -2.77 (0.16), residues: 514
  sheet: -3.05 (0.51), residues: 70
  loop : -3.66 (0.31), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1188 
 HIS   0.012   0.002   HIS A 297 
 PHE   0.022   0.002   PHE A 785 
 TYR   0.018   0.002   TYR A 133 
 ARG   0.003   0.001   ARG A 117 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9472 (t80) cc_final: 0.9234 (t80)
REVERT: A  130 TRP cc_start: 0.8952 (m100) cc_final: 0.8419 (m100)
REVERT: A  145 MET cc_start: 0.9256 (mmt) cc_final: 0.8370 (mpp)
REVERT: A  177 LEU cc_start: 0.9454 (tt) cc_final: 0.9230 (mt)
REVERT: A  227 CYS cc_start: 0.9574 (t) cc_final: 0.9300 (t)
REVERT: A  243 TYR cc_start: 0.8095 (p90) cc_final: 0.7680 (m-80)
REVERT: A  256 PHE cc_start: 0.9098 (t80) cc_final: 0.8814 (t80)
REVERT: A  297 HIS cc_start: 0.9383 (t-90) cc_final: 0.9037 (t-90)
REVERT: A  508 ASP cc_start: 0.9422 (m-30) cc_final: 0.8904 (t70)
REVERT: A  881 TYR cc_start: 0.8979 (m-10) cc_final: 0.8704 (m-10)
REVERT: A  888 PHE cc_start: 0.8968 (p90) cc_final: 0.8686 (p90)
REVERT: A 1145 GLU cc_start: 0.9281 (tt0) cc_final: 0.9044 (tt0)
REVERT: A 1183 LEU cc_start: 0.9224 (tp) cc_final: 0.8956 (tp)
REVERT: A 1187 ILE cc_start: 0.9021 (mm) cc_final: 0.8768 (mm)
REVERT: A 1198 MET cc_start: 0.9259 (mmp) cc_final: 0.8903 (mmm)
REVERT: A 1220 MET cc_start: 0.7106 (mtm) cc_final: 0.6790 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1749
  time to fit residues: 34.8869
Evaluate side-chains
  115 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 63 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 ASN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 HIS
A1154 ASN
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6822  Z= 0.232
  Angle     :  0.740  11.189   9226  Z= 0.375
  Chirality :  0.044   0.152   1057
  Planarity :  0.005   0.055   1145
  Dihedral  :  5.606  22.693    905
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 25.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  7.41 %
    Favored  : 92.46 %
  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: -2.87 (0.25), residues: 828
  helix: -1.14 (0.19), residues: 534
  sheet: -3.00 (0.44), residues: 88
  loop : -2.95 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 995 
 HIS   0.017   0.002   HIS A 292 
 PHE   0.021   0.002   PHE A 897 
 TYR   0.023   0.002   TYR A1083 
 ARG   0.005   0.001   ARG A 542 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9419 (mmt) cc_final: 0.9046 (mpp)
REVERT: A  177 LEU cc_start: 0.9528 (tt) cc_final: 0.9325 (mt)
REVERT: A  227 CYS cc_start: 0.9559 (t) cc_final: 0.9225 (t)
REVERT: A  243 TYR cc_start: 0.8031 (p90) cc_final: 0.7567 (m-80)
REVERT: A  256 PHE cc_start: 0.9162 (t80) cc_final: 0.8945 (t80)
REVERT: A  287 LEU cc_start: 0.9387 (mt) cc_final: 0.9167 (mt)
REVERT: A  297 HIS cc_start: 0.9323 (t-90) cc_final: 0.8924 (t-90)
REVERT: A  508 ASP cc_start: 0.9404 (m-30) cc_final: 0.8921 (t70)
REVERT: A  881 TYR cc_start: 0.9046 (m-10) cc_final: 0.8798 (m-10)
REVERT: A  987 PHE cc_start: 0.9635 (m-10) cc_final: 0.9320 (m-10)
REVERT: A 1001 PHE cc_start: 0.9338 (m-10) cc_final: 0.9061 (m-10)
REVERT: A 1083 TYR cc_start: 0.8661 (m-80) cc_final: 0.8345 (m-80)
REVERT: A 1198 MET cc_start: 0.9175 (mmp) cc_final: 0.8554 (ttm)
REVERT: A 1220 MET cc_start: 0.7376 (mtm) cc_final: 0.6830 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1494
  time to fit residues: 28.3399
Evaluate side-chains
  108 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 63 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
A 292 HIS
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 883 HIS
A1170 HIS
A1237 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6822  Z= 0.184
  Angle     :  0.704   9.802   9226  Z= 0.351
  Chirality :  0.042   0.192   1057
  Planarity :  0.004   0.060   1145
  Dihedral  :  5.089  21.619    905
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.08 %
    Favored  : 94.65 %
  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: -1.41 (0.28), residues: 828
  helix:  0.16 (0.21), residues: 536
  sheet: -2.95 (0.41), residues: 98
  loop : -2.64 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 130 
 HIS   0.009   0.001   HIS A 292 
 PHE   0.042   0.002   PHE A 184 
 TYR   0.018   0.002   TYR A 445 
 ARG   0.004   0.000   ARG A 305 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.9328 (mmt) cc_final: 0.9078 (mpp)
REVERT: A  175 THR cc_start: 0.9161 (m) cc_final: 0.8911 (m)
REVERT: A  177 LEU cc_start: 0.9534 (tt) cc_final: 0.9329 (mt)
REVERT: A  180 THR cc_start: 0.9775 (t) cc_final: 0.9540 (t)
REVERT: A  192 PHE cc_start: 0.6111 (t80) cc_final: 0.5705 (t80)
REVERT: A  220 GLN cc_start: 0.9402 (pm20) cc_final: 0.8935 (pm20)
REVERT: A  243 TYR cc_start: 0.7884 (p90) cc_final: 0.7441 (m-80)
REVERT: A  256 PHE cc_start: 0.9212 (t80) cc_final: 0.8997 (t80)
REVERT: A  297 HIS cc_start: 0.9281 (t-90) cc_final: 0.8953 (t-90)
REVERT: A  298 LEU cc_start: 0.9712 (mm) cc_final: 0.9441 (mm)
REVERT: A  347 MET cc_start: 0.8545 (tmm) cc_final: 0.8126 (mmp)
REVERT: A  423 PHE cc_start: 0.9491 (m-10) cc_final: 0.9281 (m-80)
REVERT: A  508 ASP cc_start: 0.9399 (m-30) cc_final: 0.8913 (t70)
REVERT: A  987 PHE cc_start: 0.9603 (m-10) cc_final: 0.9225 (m-10)
REVERT: A 1016 ASP cc_start: 0.9430 (t0) cc_final: 0.9166 (p0)
REVERT: A 1083 TYR cc_start: 0.8706 (m-80) cc_final: 0.8437 (m-10)
REVERT: A 1198 MET cc_start: 0.9022 (mmp) cc_final: 0.8413 (ttt)
REVERT: A 1220 MET cc_start: 0.7499 (mtm) cc_final: 0.6812 (ptp)
  outliers start: 2
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1606
  time to fit residues: 32.8146
Evaluate side-chains
  114 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 39 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 76 optimal weight:   20.0000
   chunk 81 optimal weight:    0.0570
   chunk 40 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.0902

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6822  Z= 0.198
  Angle     :  0.693   9.437   9226  Z= 0.351
  Chirality :  0.042   0.181   1057
  Planarity :  0.004   0.053   1145
  Dihedral  :  4.952  21.097    905
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  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: -0.98 (0.29), residues: 828
  helix:  0.53 (0.22), residues: 544
  sheet: -2.92 (0.40), residues: 98
  loop : -2.64 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 130 
 HIS   0.005   0.001   HIS A 297 
 PHE   0.037   0.002   PHE A 184 
 TYR   0.015   0.001   TYR A 881 
 ARG   0.011   0.001   ARG A1148 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9465 (t80) cc_final: 0.9245 (t80)
REVERT: A  145 MET cc_start: 0.9369 (mmt) cc_final: 0.9139 (mpp)
REVERT: A  177 LEU cc_start: 0.9558 (tt) cc_final: 0.9339 (mt)
REVERT: A  192 PHE cc_start: 0.6074 (t80) cc_final: 0.5700 (t80)
REVERT: A  243 TYR cc_start: 0.7926 (p90) cc_final: 0.7482 (m-80)
REVERT: A  297 HIS cc_start: 0.9239 (t-90) cc_final: 0.8933 (t-90)
REVERT: A  298 LEU cc_start: 0.9718 (mm) cc_final: 0.9448 (mm)
REVERT: A  423 PHE cc_start: 0.9530 (m-10) cc_final: 0.9263 (m-80)
REVERT: A  508 ASP cc_start: 0.9392 (m-30) cc_final: 0.8959 (t70)
REVERT: A  987 PHE cc_start: 0.9601 (m-10) cc_final: 0.9255 (m-80)
REVERT: A 1016 ASP cc_start: 0.9466 (t0) cc_final: 0.9229 (p0)
REVERT: A 1083 TYR cc_start: 0.8790 (m-80) cc_final: 0.8324 (m-80)
REVERT: A 1115 TYR cc_start: 0.9088 (t80) cc_final: 0.8665 (t80)
REVERT: A 1198 MET cc_start: 0.9067 (mmp) cc_final: 0.8548 (ttm)
REVERT: A 1220 MET cc_start: 0.7522 (mtm) cc_final: 0.6895 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1387
  time to fit residues: 27.8997
Evaluate side-chains
  112 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0670
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.9922

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.4673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6822  Z= 0.171
  Angle     :  0.675   9.383   9226  Z= 0.337
  Chirality :  0.042   0.183   1057
  Planarity :  0.005   0.100   1145
  Dihedral  :  4.791  20.427    905
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  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: -0.60 (0.29), residues: 828
  helix:  0.80 (0.22), residues: 544
  sheet: -2.72 (0.43), residues: 98
  loop : -2.50 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 130 
 HIS   0.004   0.001   HIS A1010 
 PHE   0.047   0.002   PHE A 798 
 TYR   0.024   0.002   TYR A 445 
 ARG   0.012   0.001   ARG A1148 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9443 (t80) cc_final: 0.9189 (t80)
REVERT: A  145 MET cc_start: 0.9372 (mmt) cc_final: 0.9169 (mpp)
REVERT: A  180 THR cc_start: 0.9774 (p) cc_final: 0.9539 (p)
REVERT: A  192 PHE cc_start: 0.6195 (t80) cc_final: 0.5800 (t80)
REVERT: A  243 TYR cc_start: 0.7854 (p90) cc_final: 0.7424 (m-80)
REVERT: A  297 HIS cc_start: 0.9290 (t-90) cc_final: 0.8962 (t-90)
REVERT: A  298 LEU cc_start: 0.9714 (mm) cc_final: 0.9443 (mm)
REVERT: A  508 ASP cc_start: 0.9400 (m-30) cc_final: 0.8954 (t70)
REVERT: A  520 MET cc_start: 0.7327 (ptt) cc_final: 0.6663 (ptt)
REVERT: A  987 PHE cc_start: 0.9599 (m-10) cc_final: 0.9179 (m-80)
REVERT: A  995 TRP cc_start: 0.7999 (t60) cc_final: 0.7779 (t60)
REVERT: A 1001 PHE cc_start: 0.9295 (m-10) cc_final: 0.9067 (m-10)
REVERT: A 1016 ASP cc_start: 0.9489 (t0) cc_final: 0.9243 (p0)
REVERT: A 1083 TYR cc_start: 0.8832 (m-80) cc_final: 0.8628 (m-10)
REVERT: A 1198 MET cc_start: 0.9027 (mmp) cc_final: 0.8501 (ttm)
REVERT: A 1220 MET cc_start: 0.7527 (mtm) cc_final: 0.6933 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1473
  time to fit residues: 30.7913
Evaluate side-chains
  115 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6822  Z= 0.169
  Angle     :  0.684   9.468   9226  Z= 0.340
  Chirality :  0.042   0.177   1057
  Planarity :  0.004   0.047   1145
  Dihedral  :  4.669  20.369    905
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.29), residues: 828
  helix:  0.99 (0.22), residues: 534
  sheet: -2.54 (0.45), residues: 98
  loop : -2.25 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A 335 
 PHE   0.034   0.002   PHE A 184 
 TYR   0.013   0.001   TYR A 538 
 ARG   0.012   0.001   ARG A1148 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9441 (t80) cc_final: 0.9161 (t80)
REVERT: A  180 THR cc_start: 0.9774 (p) cc_final: 0.9538 (p)
REVERT: A  243 TYR cc_start: 0.7862 (p90) cc_final: 0.7427 (m-80)
REVERT: A  297 HIS cc_start: 0.9242 (t-90) cc_final: 0.8957 (t-90)
REVERT: A  505 PHE cc_start: 0.9370 (p90) cc_final: 0.8781 (p90)
REVERT: A  508 ASP cc_start: 0.9414 (m-30) cc_final: 0.9042 (t70)
REVERT: A  888 PHE cc_start: 0.8877 (m-80) cc_final: 0.8567 (m-80)
REVERT: A  987 PHE cc_start: 0.9593 (m-10) cc_final: 0.9201 (m-80)
REVERT: A  996 PHE cc_start: 0.9135 (m-80) cc_final: 0.8805 (m-80)
REVERT: A 1001 PHE cc_start: 0.9252 (m-10) cc_final: 0.9048 (m-10)
REVERT: A 1016 ASP cc_start: 0.9485 (t0) cc_final: 0.9237 (p0)
REVERT: A 1083 TYR cc_start: 0.8823 (m-80) cc_final: 0.8271 (m-80)
REVERT: A 1198 MET cc_start: 0.8975 (mmp) cc_final: 0.8354 (ttm)
REVERT: A 1220 MET cc_start: 0.7500 (mtm) cc_final: 0.7131 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1483
  time to fit residues: 30.5714
Evaluate side-chains
  116 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 37 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.5416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6822  Z= 0.178
  Angle     :  0.717   9.488   9226  Z= 0.362
  Chirality :  0.043   0.190   1057
  Planarity :  0.004   0.045   1145
  Dihedral  :  4.657  20.367    905
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  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: -0.37 (0.29), residues: 828
  helix:  0.91 (0.22), residues: 536
  sheet: -2.31 (0.45), residues: 104
  loop : -2.21 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A1008 
 PHE   0.038   0.002   PHE A 184 
 TYR   0.022   0.001   TYR A 445 
 ARG   0.007   0.000   ARG A1148 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9411 (t80) cc_final: 0.9109 (t80)
REVERT: A  238 MET cc_start: 0.9109 (mmp) cc_final: 0.8731 (mmp)
REVERT: A  243 TYR cc_start: 0.7800 (p90) cc_final: 0.7361 (m-80)
REVERT: A  297 HIS cc_start: 0.9272 (t-90) cc_final: 0.8978 (t-90)
REVERT: A  508 ASP cc_start: 0.9291 (m-30) cc_final: 0.8953 (t70)
REVERT: A  841 MET cc_start: 0.9308 (tmm) cc_final: 0.9017 (ptt)
REVERT: A  888 PHE cc_start: 0.8853 (m-80) cc_final: 0.8530 (m-80)
REVERT: A  987 PHE cc_start: 0.9580 (m-10) cc_final: 0.9153 (m-80)
REVERT: A  996 PHE cc_start: 0.9168 (m-80) cc_final: 0.8815 (m-80)
REVERT: A 1001 PHE cc_start: 0.9247 (m-10) cc_final: 0.9006 (m-10)
REVERT: A 1016 ASP cc_start: 0.9457 (t0) cc_final: 0.9211 (p0)
REVERT: A 1083 TYR cc_start: 0.8753 (m-80) cc_final: 0.8246 (m-10)
REVERT: A 1188 TRP cc_start: 0.8643 (p90) cc_final: 0.8250 (p90)
REVERT: A 1198 MET cc_start: 0.8960 (mmp) cc_final: 0.8304 (ttm)
REVERT: A 1215 ARG cc_start: 0.9420 (ptt-90) cc_final: 0.9145 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7560 (mtm) cc_final: 0.7066 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1492
  time to fit residues: 30.3042
Evaluate side-chains
  118 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 7 optimal weight:    0.1980
   chunk 63 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.5632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6822  Z= 0.180
  Angle     :  0.697   9.442   9226  Z= 0.351
  Chirality :  0.042   0.172   1057
  Planarity :  0.004   0.057   1145
  Dihedral  :  4.577  20.248    905
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  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: -0.24 (0.29), residues: 828
  helix:  0.98 (0.22), residues: 537
  sheet: -2.18 (0.45), residues: 104
  loop : -2.11 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.002   TRP A 130 
 HIS   0.004   0.001   HIS A1008 
 PHE   0.020   0.001   PHE A 798 
 TYR   0.013   0.001   TYR A 538 
 ARG   0.008   0.000   ARG A1148 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9399 (t80) cc_final: 0.9105 (t80)
REVERT: A  130 TRP cc_start: 0.8290 (m-90) cc_final: 0.7941 (m-90)
REVERT: A  243 TYR cc_start: 0.7786 (p90) cc_final: 0.7341 (m-80)
REVERT: A  297 HIS cc_start: 0.9288 (t-90) cc_final: 0.8997 (t-90)
REVERT: A  508 ASP cc_start: 0.9285 (m-30) cc_final: 0.8919 (t70)
REVERT: A  888 PHE cc_start: 0.8892 (m-80) cc_final: 0.8536 (m-80)
REVERT: A  987 PHE cc_start: 0.9580 (m-10) cc_final: 0.9131 (m-80)
REVERT: A  996 PHE cc_start: 0.9180 (m-80) cc_final: 0.8822 (m-80)
REVERT: A 1001 PHE cc_start: 0.9251 (m-10) cc_final: 0.9028 (m-10)
REVERT: A 1016 ASP cc_start: 0.9462 (t0) cc_final: 0.9196 (p0)
REVERT: A 1188 TRP cc_start: 0.8633 (p90) cc_final: 0.8197 (p90)
REVERT: A 1198 MET cc_start: 0.8917 (mmp) cc_final: 0.8245 (ttm)
REVERT: A 1215 ARG cc_start: 0.9427 (ptt-90) cc_final: 0.9140 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7511 (mtm) cc_final: 0.7030 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1596
  time to fit residues: 31.4422
Evaluate side-chains
  119 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 71 optimal weight:   30.0000
   chunk 49 optimal weight:    0.7980
   chunk 79 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
A 239 HIS
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.5773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6822  Z= 0.188
  Angle     :  0.709   9.487   9226  Z= 0.359
  Chirality :  0.042   0.184   1057
  Planarity :  0.004   0.046   1145
  Dihedral  :  4.558  20.153    905
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  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: -0.29 (0.29), residues: 828
  helix:  0.94 (0.22), residues: 533
  sheet: -2.25 (0.45), residues: 107
  loop : -2.00 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A 297 
 PHE   0.026   0.002   PHE A 121 
 TYR   0.013   0.001   TYR A 538 
 ARG   0.008   0.000   ARG A1148 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9376 (t80) cc_final: 0.9058 (t80)
REVERT: A  243 TYR cc_start: 0.7767 (p90) cc_final: 0.7320 (m-80)
REVERT: A  297 HIS cc_start: 0.9329 (t-90) cc_final: 0.9040 (t-90)
REVERT: A  508 ASP cc_start: 0.9310 (m-30) cc_final: 0.8919 (t70)
REVERT: A  888 PHE cc_start: 0.8902 (m-80) cc_final: 0.8585 (m-80)
REVERT: A  987 PHE cc_start: 0.9583 (m-10) cc_final: 0.9137 (m-80)
REVERT: A  996 PHE cc_start: 0.9202 (m-80) cc_final: 0.8839 (m-80)
REVERT: A 1001 PHE cc_start: 0.9248 (m-10) cc_final: 0.8937 (m-10)
REVERT: A 1016 ASP cc_start: 0.9464 (t0) cc_final: 0.9188 (p0)
REVERT: A 1115 TYR cc_start: 0.9074 (t80) cc_final: 0.8730 (t80)
REVERT: A 1188 TRP cc_start: 0.8635 (p90) cc_final: 0.8153 (p90)
REVERT: A 1198 MET cc_start: 0.8914 (mmp) cc_final: 0.8220 (ttm)
REVERT: A 1215 ARG cc_start: 0.9417 (ptt-90) cc_final: 0.9126 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7477 (mtm) cc_final: 0.6985 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1542
  time to fit residues: 29.6860
Evaluate side-chains
  118 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 66 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
A 239 HIS
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.5843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6822  Z= 0.196
  Angle     :  0.727   9.504   9226  Z= 0.368
  Chirality :  0.043   0.181   1057
  Planarity :  0.004   0.046   1145
  Dihedral  :  4.583  20.434    905
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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: -0.32 (0.29), residues: 828
  helix:  0.89 (0.22), residues: 531
  sheet: -2.26 (0.46), residues: 100
  loop : -1.96 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 130 
 HIS   0.005   0.001   HIS A 297 
 PHE   0.041   0.002   PHE A 184 
 TYR   0.012   0.001   TYR A 538 
 ARG   0.008   0.000   ARG A1148 

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 PHE cc_start: 0.9400 (t80) cc_final: 0.9018 (t80)
REVERT: A  243 TYR cc_start: 0.7669 (p90) cc_final: 0.7205 (m-80)
REVERT: A  297 HIS cc_start: 0.9330 (t-90) cc_final: 0.9030 (t-90)
REVERT: A  508 ASP cc_start: 0.9315 (m-30) cc_final: 0.8946 (t70)
REVERT: A  888 PHE cc_start: 0.8918 (m-80) cc_final: 0.8599 (m-80)
REVERT: A  987 PHE cc_start: 0.9583 (m-10) cc_final: 0.9134 (m-80)
REVERT: A  996 PHE cc_start: 0.9222 (m-80) cc_final: 0.8881 (m-80)
REVERT: A 1001 PHE cc_start: 0.9285 (m-10) cc_final: 0.8963 (m-10)
REVERT: A 1016 ASP cc_start: 0.9458 (t0) cc_final: 0.9181 (p0)
REVERT: A 1115 TYR cc_start: 0.9084 (t80) cc_final: 0.8768 (t80)
REVERT: A 1188 TRP cc_start: 0.8654 (p90) cc_final: 0.8136 (p90)
REVERT: A 1198 MET cc_start: 0.8860 (mmp) cc_final: 0.8152 (ttm)
REVERT: A 1215 ARG cc_start: 0.9418 (ptt-90) cc_final: 0.9119 (tpp-160)
REVERT: A 1220 MET cc_start: 0.7496 (mtm) cc_final: 0.7018 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1552
  time to fit residues: 28.8359
Evaluate side-chains
  111 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 48 optimal weight:    8.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 ASN
** A1122 ASN ** 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 = 0.3516 r_free = 0.3516 target = 0.068516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.051263 restraints weight = 50210.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.052230 restraints weight = 41056.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.053045 restraints weight = 34838.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.5719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6822  Z= 0.281
  Angle     :  0.793   9.598   9226  Z= 0.410
  Chirality :  0.046   0.180   1057
  Planarity :  0.005   0.050   1145
  Dihedral  :  5.006  20.932    905
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 24.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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: -0.78 (0.29), residues: 828
  helix:  0.37 (0.22), residues: 530
  sheet: -2.04 (0.53), residues: 83
  loop : -1.92 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 130 
 HIS   0.007   0.001   HIS A 297 
 PHE   0.032   0.003   PHE A 798 
 TYR   0.016   0.002   TYR A 252 
 ARG   0.007   0.001   ARG A1148 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1661.28 seconds
wall clock time: 31 minutes 25.61 seconds (1885.61 seconds total)