Starting phenix.real_space_refine (version: dev)
on Sun Dec 11 19:03:39 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/12_2022/7pd4_13330.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/12_2022/7pd4_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_13330/12_2022/7pd4_13330.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/12_2022/7pd4_13330.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/12_2022/7pd4_13330.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd4_13330/12_2022/7pd4_13330.pdb"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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
Convert atoms to be neutral
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: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 4.19, per 1000 atoms: 0.63
  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: 3.19
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.42
  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: 2.33

  Time building geometry restraints manager: 3.41 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
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.
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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          5.810
  Check model and map are aligned:         0.110
  Convert atoms to be neutral:             0.050
  Process input model:                     22.520
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
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 : 38.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.71 %
    Favored  : 88.29 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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

*********************** 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  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1688
  time to fit residues: 33.8575
Evaluate side-chains
  111 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.807 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1569
-------------------------------------------------------------------------------
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:    9.9990
   chunk 63 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:   20.0000
   overall best weight:    1.9386

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6822  Z= 0.219
  Angle     :  0.742  11.415   9226  Z= 0.376
  Chirality :  0.044   0.180   1057
  Planarity :  0.005   0.056   1145
  Dihedral  :  5.574  22.811    905
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 23.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer Outliers :  0.14 %
  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: -2.72 (0.25), residues: 828
  helix: -1.02 (0.19), residues: 531
  sheet: -2.94 (0.44), residues: 88
  loop : -2.92 (0.38), residues: 209

*********************** 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
  138 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1606
  time to fit residues: 30.5100
Evaluate side-chains
  105 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0970
-------------------------------------------------------------------------------
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:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 82 optimal weight:   20.0000
   chunk 68 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 HIS
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6822  Z= 0.213
  Angle     :  0.709   9.927   9226  Z= 0.361
  Chirality :  0.043   0.181   1057
  Planarity :  0.005   0.060   1145
  Dihedral  :  5.246  21.889    905
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 22.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer Outliers :  0.27 %
  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: -1.62 (0.28), residues: 828
  helix: -0.03 (0.21), residues: 536
  sheet: -2.96 (0.42), residues: 98
  loop : -2.69 (0.43), residues: 194

*********************** 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
  137 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 135
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1421
  time to fit residues: 27.8717
Evaluate side-chains
  103 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1314
-------------------------------------------------------------------------------
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:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 39 optimal weight:   40.0000
   chunk 8 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 515 ASN
A 883 HIS
A1170 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6822  Z= 0.226
  Angle     :  0.721   9.266   9226  Z= 0.368
  Chirality :  0.043   0.183   1057
  Planarity :  0.004   0.051   1145
  Dihedral  :  5.082  21.083    905
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 22.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.28), residues: 828
  helix:  0.22 (0.21), residues: 538
  sheet: -3.03 (0.42), residues: 99
  loop : -2.54 (0.44), residues: 191

*********************** 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
  135 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1426
  time to fit residues: 27.8351
Evaluate side-chains
  103 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.835 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0865
-------------------------------------------------------------------------------
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:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
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: 0.7039
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6822  Z= 0.201
  Angle     :  0.709   9.484   9226  Z= 0.354
  Chirality :  0.043   0.197   1057
  Planarity :  0.004   0.049   1145
  Dihedral  :  4.987  21.167    905
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.29), residues: 828
  helix:  0.53 (0.22), residues: 536
  sheet: -2.79 (0.43), residues: 96
  loop : -2.45 (0.43), residues: 196

*********************** 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
  142 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.824 
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
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1488
  time to fit residues: 30.1869
Evaluate side-chains
  109 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.834 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1177
-------------------------------------------------------------------------------
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:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 81 optimal weight:   20.0000
   chunk 67 optimal weight:    0.4980
   chunk 37 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6822  Z= 0.222
  Angle     :  0.716   9.501   9226  Z= 0.363
  Chirality :  0.043   0.178   1057
  Planarity :  0.005   0.090   1145
  Dihedral  :  4.989  21.184    905
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 23.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.28), residues: 828
  helix:  0.49 (0.21), residues: 529
  sheet: -2.73 (0.46), residues: 97
  loop : -2.33 (0.43), residues: 202

*********************** 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
  140 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1358
  time to fit residues: 27.5655
Evaluate side-chains
  105 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.763 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0753
-------------------------------------------------------------------------------
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:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.5426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6822  Z= 0.181
  Angle     :  0.714  10.332   9226  Z= 0.353
  Chirality :  0.042   0.180   1057
  Planarity :  0.004   0.057   1145
  Dihedral  :  4.866  21.348    905
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.29), residues: 828
  helix:  0.82 (0.22), residues: 531
  sheet: -2.46 (0.46), residues: 97
  loop : -2.40 (0.42), residues: 200

*********************** 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
  140 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1487
  time to fit residues: 29.4797
Evaluate side-chains
  113 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.737 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9999
-------------------------------------------------------------------------------
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:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.5312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6822  Z= 0.291
  Angle     :  0.789   9.477   9226  Z= 0.405
  Chirality :  0.046   0.295   1057
  Planarity :  0.006   0.080   1145
  Dihedral  :  5.266  21.555    905
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 27.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.28), residues: 828
  helix:  0.26 (0.21), residues: 531
  sheet: -2.86 (0.43), residues: 102
  loop : -2.34 (0.44), residues: 195

*********************** 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
  134 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1540
  time to fit residues: 29.3850
Evaluate side-chains
  97 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.814 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0369
-------------------------------------------------------------------------------
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:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.5675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6822  Z= 0.199
  Angle     :  0.738   9.280   9226  Z= 0.377
  Chirality :  0.044   0.199   1057
  Planarity :  0.004   0.045   1145
  Dihedral  :  5.002  21.659    905
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 21.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.29), residues: 828
  helix:  0.69 (0.22), residues: 525
  sheet: -2.73 (0.44), residues: 102
  loop : -2.26 (0.43), residues: 201

*********************** 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
  132 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1433
  time to fit residues: 27.5326
Evaluate side-chains
  105 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.810 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0943
-------------------------------------------------------------------------------
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:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 83 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 70 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1008 HIS
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.6008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6822  Z= 0.181
  Angle     :  0.734   9.491   9226  Z= 0.370
  Chirality :  0.045   0.309   1057
  Planarity :  0.004   0.045   1145
  Dihedral  :  4.798  21.141    905
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 18.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.29), residues: 828
  helix:  0.87 (0.22), residues: 534
  sheet: -2.06 (0.47), residues: 98
  loop : -2.51 (0.42), residues: 196

********************** 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
  139 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1423
  time to fit residues: 28.6304
Evaluate side-chains
  110 residues out of total 733 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0955
-------------------------------------------------------------------------------
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:    0.8980
   chunk 9 optimal weight:    0.3980
   chunk 18 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
** 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**
A1122 ASN
** A1169 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 = 0.3558 r_free = 0.3558 target = 0.070577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.051772 restraints weight = 47413.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.052813 restraints weight = 39269.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.053697 restraints weight = 33246.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.6281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6822  Z= 0.179
  Angle     :  0.740   9.451   9226  Z= 0.370
  Chirality :  0.045   0.231   1057
  Planarity :  0.004   0.045   1145
  Dihedral  :  4.713  20.626    905
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.29), residues: 828
  helix:  0.90 (0.22), residues: 534
  sheet: -1.89 (0.47), residues: 98
  loop : -2.50 (0.41), residues: 196

===============================================================================
Job complete
usr+sys time: 1460.54 seconds
wall clock time: 27 minutes 40.50 seconds (1660.50 seconds total)