Starting phenix.real_space_refine
on Wed Jan 15 08:22:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y85_39034/01_2025/8y85_39034.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y85_39034/01_2025/8y85_39034.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y85_39034/01_2025/8y85_39034.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y85_39034/01_2025/8y85_39034.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y85_39034/01_2025/8y85_39034.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y85_39034/01_2025/8y85_39034.cif"
  }
  resolution = 2.73
  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=   0.154
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      42      5.16       5
     C    5386      2.51       5
     N    1334      2.21       5
     O    1354      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8116
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 4026
          Classifications: {'peptide': 514}
          Link IDs: {'PTRANS': 33, 'TRANS': 480}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 4026
          Classifications: {'peptide': 514}
          Link IDs: {'PTRANS': 33, 'TRANS': 480}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'4KU': 1, 'BCT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'4KU': 1, 'BCT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.26, per 1000 atoms: 0.65
  Number of scatterers: 8116
  At special positions: 0
  Unit cell: (113.3, 102.3, 83.6, 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      42     16.00
     O    1354      8.00
     N    1334      7.00
     C    5386      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 924.8 milliseconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1908

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 4 sheets defined
      75.9% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 682 through 693
    Processing helix  chain 'A' and resid 695 through 702
    Processing helix  chain 'A' and resid 706 through 734
      removed outlier: 3.610A  pdb=" N   ALA A 710 " --> pdb=" O   SER A 706 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE A 717 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER A 721 " --> pdb=" O   PHE A 717 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
    Processing helix  chain 'A' and resid 739 through 758
      removed outlier: 3.642A  pdb=" N   LEU A 743 " --> pdb=" O   GLY A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 785
    Processing helix  chain 'A' and resid 788 through 810
      removed outlier: 3.577A  pdb=" N   GLY A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 819
      removed outlier: 3.562A  pdb=" N   PHE A 814 " --> pdb=" O   GLU A 811 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG A 817 " --> pdb=" O   PHE A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 850
      removed outlier: 3.592A  pdb=" N   THR A 839 " --> pdb=" O   PHE A 835 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE A 840 " --> pdb=" O   ILE A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 913
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 920 through 930
    Processing helix  chain 'A' and resid 930 through 946
      removed outlier: 3.566A  pdb=" N   ILE A 946 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 989
    Processing helix  chain 'A' and resid 989 through 1012
      removed outlier: 3.566A  pdb=" N   ALA A 993 " --> pdb=" O   ALA A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1017
      removed outlier: 3.623A  pdb=" N   ARG A1017 " --> pdb=" O   LYS A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1039
      removed outlier: 3.638A  pdb=" N   GLY A1039 " --> pdb=" O   GLY A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1042
      No H-bonds generated for 'chain 'A' and resid 1040 through 1042'
    Processing helix  chain 'A' and resid 1049 through 1060
      removed outlier: 3.534A  pdb=" N   LEU A1060 " --> pdb=" O   HIS A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1095
      removed outlier: 3.686A  pdb=" N   VAL A1086 " --> pdb=" O   ARG A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1103
    Processing helix  chain 'A' and resid 1106 through 1122
      removed outlier: 4.091A  pdb=" N   LEU A1110 " --> pdb=" O   PRO A1106 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A1122 " --> pdb=" O   GLY A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1136
      removed outlier: 3.709A  pdb=" N   GLN A1129 " --> pdb=" O   ILE A1125 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ILE A1134 " --> pdb=" O   ARG A1130 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   LEU A1135 " --> pdb=" O   LEU A1131 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   MET A1136 " --> pdb=" O   LEU A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1137 through 1141
      removed outlier: 3.859A  pdb=" N   HIS A1141 " --> pdb=" O   ALA A1138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1144 through 1149
      removed outlier: 3.529A  pdb=" N   LYS A1149 " --> pdb=" O   PRO A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1151 through 1175
      removed outlier: 3.737A  pdb=" N   LEU A1157 " --> pdb=" O   TRP A1153 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   PHE A1158 " --> pdb=" O   ARG A1154 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR A1159 " --> pdb=" O   MET A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1179
      No H-bonds generated for 'chain 'A' and resid 1177 through 1179'
    Processing helix  chain 'A' and resid 1180 through 1187
    Processing helix  chain 'A' and resid 1187 through 1195
      removed outlier: 3.632A  pdb=" N   LEU A1191 " --> pdb=" O   LEU A1187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1200
      removed outlier: 3.706A  pdb=" N   LEU A1199 " --> pdb=" O   LEU A1195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1209
    Processing helix  chain 'B' and resid 682 through 693
    Processing helix  chain 'B' and resid 695 through 702
    Processing helix  chain 'B' and resid 706 through 734
      removed outlier: 3.567A  pdb=" N   ALA B 710 " --> pdb=" O   SER B 706 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE B 717 " --> pdb=" O   LEU B 713 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   SER B 721 " --> pdb=" O   PHE B 717 " (cutoff:3.500A)
      Proline residue:  B 722  - end of helix
    Processing helix  chain 'B' and resid 739 through 758
      removed outlier: 3.676A  pdb=" N   LEU B 743 " --> pdb=" O   GLY B 739 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 768 through 785
    Processing helix  chain 'B' and resid 788 through 810
      removed outlier: 3.663A  pdb=" N   GLY B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 819
      removed outlier: 3.679A  pdb=" N   PHE B 814 " --> pdb=" O   GLU B 811 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU B 815 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG B 817 " --> pdb=" O   PHE B 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 850
      removed outlier: 3.523A  pdb=" N   GLN B 824 " --> pdb=" O   SER B 820 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS B 842 " --> pdb=" O   GLU B 838 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU B 843 " --> pdb=" O   THR B 839 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   HIS B 850 " --> pdb=" O   VAL B 846 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 892 through 913
    Processing helix  chain 'B' and resid 914 through 916
      No H-bonds generated for 'chain 'B' and resid 914 through 916'
    Processing helix  chain 'B' and resid 920 through 930
    Processing helix  chain 'B' and resid 930 through 946
      removed outlier: 3.564A  pdb=" N   ILE B 946 " --> pdb=" O   VAL B 942 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 982 through 989
    Processing helix  chain 'B' and resid 989 through 1012
      removed outlier: 3.554A  pdb=" N   ALA B 993 " --> pdb=" O   ALA B 989 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1013 through 1017
    Processing helix  chain 'B' and resid 1025 through 1039
      removed outlier: 3.657A  pdb=" N   GLY B1039 " --> pdb=" O   GLY B1035 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1040 through 1042
      No H-bonds generated for 'chain 'B' and resid 1040 through 1042'
    Processing helix  chain 'B' and resid 1049 through 1060
      removed outlier: 3.542A  pdb=" N   LEU B1060 " --> pdb=" O   HIS B1056 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1082 through 1095
      removed outlier: 3.662A  pdb=" N   VAL B1086 " --> pdb=" O   ARG B1082 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1098 through 1103
    Processing helix  chain 'B' and resid 1106 through 1122
      removed outlier: 4.079A  pdb=" N   LEU B1110 " --> pdb=" O   PRO B1106 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B1122 " --> pdb=" O   GLY B1118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1125 through 1136
      removed outlier: 3.709A  pdb=" N   GLN B1129 " --> pdb=" O   ILE B1125 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE B1134 " --> pdb=" O   ARG B1130 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU B1135 " --> pdb=" O   LEU B1131 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   MET B1136 " --> pdb=" O   LEU B1132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1137 through 1141
      removed outlier: 3.880A  pdb=" N   HIS B1141 " --> pdb=" O   ALA B1138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1144 through 1149
      removed outlier: 3.506A  pdb=" N   LYS B1149 " --> pdb=" O   PRO B1145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1151 through 1175
      removed outlier: 3.722A  pdb=" N   LEU B1157 " --> pdb=" O   TRP B1153 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   PHE B1158 " --> pdb=" O   ARG B1154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1177 through 1179
      No H-bonds generated for 'chain 'B' and resid 1177 through 1179'
    Processing helix  chain 'B' and resid 1180 through 1187
    Processing helix  chain 'B' and resid 1187 through 1195
      removed outlier: 3.646A  pdb=" N   LEU B1191 " --> pdb=" O   LEU B1187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1195 through 1200
      removed outlier: 3.770A  pdb=" N   LEU B1199 " --> pdb=" O   LEU B1195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1201 through 1209
    Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 766
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1061 through 1063
    Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1061 through 1063

    494 hydrogen bonds defined for protein.
    1449 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: 2.23

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 1240
        1.32 -     1.46: 3194
        1.46 -     1.60: 3826
        1.60 -     1.75: 0
        1.75 -     1.89: 64
  Bond restraints: 8324
  Sorted by residual:
  bond pdb=" C   LYS A1173 "
       pdb=" O   LYS A1173 "
    ideal  model  delta    sigma   weight residual
    1.236  1.181  0.055 1.32e-02 5.74e+03 1.75e+01
  bond pdb=" C   LYS B1173 "
       pdb=" O   LYS B1173 "
    ideal  model  delta    sigma   weight residual
    1.236  1.181  0.055 1.32e-02 5.74e+03 1.75e+01
  bond pdb=" C   VAL B1172 "
       pdb=" N   LYS B1173 "
    ideal  model  delta    sigma   weight residual
    1.334  1.283  0.051 1.49e-02 4.50e+03 1.19e+01
  bond pdb=" C   VAL A1172 "
       pdb=" N   LYS A1173 "
    ideal  model  delta    sigma   weight residual
    1.334  1.283  0.051 1.49e-02 4.50e+03 1.19e+01
  bond pdb=" C   BCT B1301 "
       pdb=" O3  BCT B1301 "
    ideal  model  delta    sigma   weight residual
    1.389  1.436 -0.047 2.00e-02 2.50e+03 5.55e+00
  ... (remaining 8319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.92: 11275
        3.92 -     7.84: 49
        7.84 -    11.76: 11
       11.76 -    15.68: 1
       15.68 -    19.59: 2
  Bond angle restraints: 11338
  Sorted by residual:
  angle pdb=" O   VAL A1172 "
        pdb=" C   VAL A1172 "
        pdb=" N   LYS A1173 "
      ideal   model   delta    sigma   weight residual
     121.87  111.80   10.07 9.70e-01 1.06e+00 1.08e+02
  angle pdb=" O   VAL B1172 "
        pdb=" C   VAL B1172 "
        pdb=" N   LYS B1173 "
      ideal   model   delta    sigma   weight residual
     121.87  111.96    9.91 9.70e-01 1.06e+00 1.04e+02
  angle pdb=" C   LYS B1173 "
        pdb=" CA  LYS B1173 "
        pdb=" CB  LYS B1173 "
      ideal   model   delta    sigma   weight residual
     109.99   90.40   19.59 2.09e+00 2.29e-01 8.79e+01
  angle pdb=" C   LYS A1173 "
        pdb=" CA  LYS A1173 "
        pdb=" CB  LYS A1173 "
      ideal   model   delta    sigma   weight residual
     109.99   91.18   18.81 2.09e+00 2.29e-01 8.10e+01
  angle pdb=" CA  VAL A1172 "
        pdb=" C   VAL A1172 "
        pdb=" N   LYS A1173 "
      ideal   model   delta    sigma   weight residual
     117.15  127.23  -10.08 1.14e+00 7.69e-01 7.82e+01
  ... (remaining 11333 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 4201
       16.73 -    33.45: 494
       33.45 -    50.18: 150
       50.18 -    66.91: 36
       66.91 -    83.64: 13
  Dihedral angle restraints: 4894
    sinusoidal: 1936
      harmonic: 2958
  Sorted by residual:
  dihedral pdb=" C   LYS B1173 "
           pdb=" N   LYS B1173 "
           pdb=" CA  LYS B1173 "
           pdb=" CB  LYS B1173 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -99.86  -22.74     0      2.50e+00 1.60e-01 8.28e+01
  dihedral pdb=" C   LYS A1173 "
           pdb=" N   LYS A1173 "
           pdb=" CA  LYS A1173 "
           pdb=" CB  LYS A1173 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -100.90  -21.70     0      2.50e+00 1.60e-01 7.53e+01
  dihedral pdb=" C   LYS A 842 "
           pdb=" N   LYS A 842 "
           pdb=" CA  LYS A 842 "
           pdb=" CB  LYS A 842 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.24   10.64     0      2.50e+00 1.60e-01 1.81e+01
  ... (remaining 4891 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1169
       0.060 -    0.121: 168
       0.121 -    0.181: 5
       0.181 -    0.241: 1
       0.241 -    0.301: 3
  Chirality restraints: 1346
  Sorted by residual:
  chirality pdb=" CA  LYS B1173 "
            pdb=" N   LYS B1173 "
            pdb=" C   LYS B1173 "
            pdb=" CB  LYS B1173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  LYS A1173 "
            pdb=" N   LYS A1173 "
            pdb=" C   LYS A1173 "
            pdb=" CB  LYS A1173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CA  LYS A 842 "
            pdb=" N   LYS A 842 "
            pdb=" C   LYS A 842 "
            pdb=" CB  LYS A 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 1343 not shown)

  Planarity restraints: 1386
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B1173 "    0.019 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   LYS B1173 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   LYS B1173 "    0.026 2.00e-02 2.50e+03
        pdb=" N   SER B1174 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A1173 "   -0.019 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   LYS A1173 "    0.066 2.00e-02 2.50e+03
        pdb=" O   LYS A1173 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   SER A1174 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A1141 "   -0.053 5.00e-02 4.00e+02   8.09e-02 1.05e+01
        pdb=" N   PRO A1142 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A1142 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A1142 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1383 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2473
        2.83 -     3.35: 7484
        3.35 -     3.87: 12831
        3.87 -     4.38: 14056
        4.38 -     4.90: 25734
  Nonbonded interactions: 62578
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 793 "
            pdb=" O   LEU B1043 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" NH2 ARG A 793 "
            pdb=" O   LEU A1043 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" NH2 ARG A1130 "
            pdb=" OE1 GLN A1162 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" NH2 ARG B1130 "
            pdb=" OE1 GLN B1162 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   ALA A1049 "
            pdb=" OG  SER A1053 "
     model   vdw
     2.348 3.040
  ... (remaining 62573 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
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:             0.940
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     21.510
  Find NCS groups from input model:        0.270
  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:13.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
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      :  0.004   0.055   8324  Z= 0.261
  Angle     :  0.763  19.594  11338  Z= 0.408
  Chirality :  0.043   0.301   1346
  Planarity :  0.006   0.081   1386
  Dihedral  : 16.593  83.636   2986
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 19.82 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.42 %
  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:  2.04 (0.27), residues: 1020
  helix:  2.06 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.02 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1153 
 HIS   0.004   0.001   HIS B 850 
 PHE   0.042   0.002   PHE A 840 
 TYR   0.034   0.002   TYR A 841 
 ARG   0.013   0.001   ARG B1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.803 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 106
  average time/residue: 1.3042
  time to fit residues: 146.6498
Evaluate side-chains
  101 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain B residue 1081 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B1081 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.178583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.143319 restraints weight = 8390.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.74
r_work: 0.3531 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.0786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8324  Z= 0.197
  Angle     :  0.564   8.252  11338  Z= 0.278
  Chirality :  0.041   0.150   1346
  Planarity :  0.006   0.060   1386
  Dihedral  :  6.029  70.092   1137
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.34 %
    Favored  : 79.16 %
  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:  1.96 (0.27), residues: 1020
  helix:  1.93 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.01 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 795 
 HIS   0.004   0.001   HIS A 850 
 PHE   0.018   0.002   PHE B 822 
 TYR   0.013   0.001   TYR A 841 
 ARG   0.006   0.000   ARG B1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.7927 (t0) cc_final: 0.7660 (t0)
REVERT: A 1017 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7011 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7639 (pm20)
REVERT: B  817 ARG cc_start: 0.7464 (ptm-80) cc_final: 0.6941 (ptt180)
REVERT: B 1153 TRP cc_start: 0.7771 (p-90) cc_final: 0.7513 (p-90)
  outliers start: 22
  outliers final: 4
  residues processed: 119
  average time/residue: 1.3428
  time to fit residues: 169.2067
Evaluate side-chains
  112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1136 MET
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue 1136 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0470
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.6278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.179452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.144106 restraints weight = 8549.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.76
r_work: 0.3536 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8324  Z= 0.170
  Angle     :  0.518   7.255  11338  Z= 0.257
  Chirality :  0.040   0.125   1346
  Planarity :  0.005   0.047   1386
  Dihedral  :  5.013  62.800   1128
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.00 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.27), residues: 1020
  helix:  2.18 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop :  0.06 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.015   0.001   PHE B 822 
 TYR   0.013   0.001   TYR A 841 
 ARG   0.011   0.000   ARG B1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  811 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6874 (tp30)
REVERT: A 1017 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7059 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7673 (pm20)
REVERT: B  780 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6995 (mtpt)
REVERT: B  817 ARG cc_start: 0.7518 (ptm-80) cc_final: 0.6966 (ptt180)
REVERT: B 1080 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7260 (mt-10)
REVERT: B 1081 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.6016 (pp30)
REVERT: B 1209 ASP cc_start: 0.7706 (t0) cc_final: 0.7356 (t70)
  outliers start: 28
  outliers final: 8
  residues processed: 123
  average time/residue: 1.2352
  time to fit residues: 161.5356
Evaluate side-chains
  117 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  780 LYS
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  975 LEU
Chi-restraints excluded: chain B residue 1080 GLU
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 42 optimal weight:    0.1980
   chunk 63 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 68 optimal weight:    0.2980
   chunk 80 optimal weight:    0.0000
   chunk 0 optimal weight:    9.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.4584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.181385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.146345 restraints weight = 8458.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.75
r_work: 0.3566 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8324  Z= 0.151
  Angle     :  0.490   7.625  11338  Z= 0.242
  Chirality :  0.039   0.124   1346
  Planarity :  0.005   0.046   1386
  Dihedral  :  4.819  59.913   1128
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.48 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.27), residues: 1020
  helix:  2.36 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop :  0.12 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 795 
 HIS   0.002   0.001   HIS A 850 
 PHE   0.014   0.001   PHE B 822 
 TYR   0.011   0.001   TYR A 841 
 ARG   0.013   0.000   ARG A1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8104 (t0) cc_final: 0.7689 (t0)
REVERT: A 1017 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7040 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7507 (pm20)
REVERT: B  768 SER cc_start: 0.8338 (p) cc_final: 0.8138 (m)
REVERT: B  817 ARG cc_start: 0.7479 (ptm-80) cc_final: 0.7079 (ptt-90)
REVERT: B 1081 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.6082 (pp30)
REVERT: B 1209 ASP cc_start: 0.7621 (t0) cc_final: 0.7257 (t70)
  outliers start: 19
  outliers final: 6
  residues processed: 122
  average time/residue: 1.2969
  time to fit residues: 167.5681
Evaluate side-chains
  113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue 1081 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 99 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0010
   chunk 11 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.180679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.145553 restraints weight = 8410.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.75
r_work: 0.3556 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8324  Z= 0.159
  Angle     :  0.495   7.865  11338  Z= 0.244
  Chirality :  0.039   0.123   1346
  Planarity :  0.005   0.047   1386
  Dihedral  :  4.736  60.175   1128
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.93 %
    Favored  : 77.90 %
  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:  2.42 (0.27), residues: 1020
  helix:  2.31 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.07 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.014   0.001   PHE B 822 
 TYR   0.011   0.001   TYR A 841 
 ARG   0.015   0.000   ARG B1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A 1017 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7013 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7496 (pm20)
REVERT: B  780 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6983 (mtpt)
REVERT: B  817 ARG cc_start: 0.7463 (ptm-80) cc_final: 0.7062 (ptt-90)
REVERT: B 1081 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.6108 (pp30)
REVERT: B 1209 ASP cc_start: 0.7421 (t0) cc_final: 0.7044 (t0)
  outliers start: 19
  outliers final: 9
  residues processed: 112
  average time/residue: 1.2042
  time to fit residues: 143.5348
Evaluate side-chains
  113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  780 LYS
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  975 LEU
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0370
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.4458

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.181853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.146812 restraints weight = 8480.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.77
r_work: 0.3570 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8324  Z= 0.149
  Angle     :  0.482   7.870  11338  Z= 0.237
  Chirality :  0.039   0.123   1346
  Planarity :  0.005   0.046   1386
  Dihedral  :  4.649  58.994   1128
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.82 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.27), residues: 1020
  helix:  2.35 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop :  0.08 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.013   0.001   PHE B 909 
 TYR   0.010   0.001   TYR A 841 
 ARG   0.008   0.000   ARG B1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8160 (t0) cc_final: 0.7838 (t0)
REVERT: A 1017 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7005 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7546 (pm20)
REVERT: B  817 ARG cc_start: 0.7472 (ptm-80) cc_final: 0.7080 (ptt-90)
REVERT: B 1081 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.6096 (pp30)
REVERT: B 1209 ASP cc_start: 0.7418 (t0) cc_final: 0.7052 (t0)
  outliers start: 21
  outliers final: 8
  residues processed: 119
  average time/residue: 1.1969
  time to fit residues: 151.5287
Evaluate side-chains
  112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.178258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142684 restraints weight = 8503.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 1.76
r_work: 0.3522 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8324  Z= 0.199
  Angle     :  0.530   8.649  11338  Z= 0.261
  Chirality :  0.040   0.126   1346
  Planarity :  0.005   0.064   1386
  Dihedral  :  4.741  61.694   1128
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.84 %
    Favored  : 77.11 %
  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:  2.26 (0.27), residues: 1020
  helix:  2.13 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop :  0.08 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 795 
 HIS   0.004   0.001   HIS A 850 
 PHE   0.015   0.001   PHE B 822 
 TYR   0.012   0.001   TYR A 841 
 ARG   0.014   0.000   ARG B1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8161 (t0) cc_final: 0.7945 (t0)
REVERT: A 1017 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7067 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7551 (pm20)
REVERT: A 1153 TRP cc_start: 0.7840 (p-90) cc_final: 0.7589 (p-90)
REVERT: B  780 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7061 (mtpt)
REVERT: B  811 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6982 (tp30)
REVERT: B  817 ARG cc_start: 0.7505 (ptm-80) cc_final: 0.6962 (ptt180)
REVERT: B 1081 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.6081 (pp30)
REVERT: B 1129 GLN cc_start: 0.7456 (tp-100) cc_final: 0.7087 (mt0)
  outliers start: 18
  outliers final: 11
  residues processed: 118
  average time/residue: 1.3258
  time to fit residues: 165.8417
Evaluate side-chains
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  780 LYS
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  975 LEU
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 70 optimal weight:    0.0030
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0870
   chunk 71 optimal weight:    0.5980
   chunk 96 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.4170

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.181184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.146090 restraints weight = 8593.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.77
r_work: 0.3562 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8324  Z= 0.150
  Angle     :  0.500   8.537  11338  Z= 0.244
  Chirality :  0.039   0.122   1346
  Planarity :  0.005   0.067   1386
  Dihedral  :  4.630  59.128   1128
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 22.21 %
    Favored  : 76.42 %
  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:  2.45 (0.27), residues: 1020
  helix:  2.31 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop :  0.09 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.002   0.001   HIS A 850 
 PHE   0.016   0.001   PHE B 909 
 TYR   0.011   0.001   TYR A 841 
 ARG   0.016   0.000   ARG A1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8200 (t0) cc_final: 0.7984 (t0)
REVERT: A 1017 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7053 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7525 (pm20)
REVERT: B  702 ASP cc_start: 0.8282 (t0) cc_final: 0.7829 (t0)
REVERT: B  817 ARG cc_start: 0.7418 (ptm-80) cc_final: 0.6995 (ptt-90)
REVERT: B 1081 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.6021 (pp30)
  outliers start: 12
  outliers final: 8
  residues processed: 108
  average time/residue: 1.2489
  time to fit residues: 143.5192
Evaluate side-chains
  110 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0010
   chunk 85 optimal weight:    0.0980
   overall best weight:    0.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.180873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145640 restraints weight = 8698.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.78
r_work: 0.3559 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8324  Z= 0.156
  Angle     :  0.503   8.924  11338  Z= 0.244
  Chirality :  0.039   0.122   1346
  Planarity :  0.005   0.052   1386
  Dihedral  :  4.568  59.551   1128
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 22.44 %
    Favored  : 76.20 %
  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:  2.49 (0.27), residues: 1020
  helix:  2.31 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop :  0.18 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 795 
 HIS   0.002   0.001   HIS B 850 
 PHE   0.015   0.001   PHE A 909 
 TYR   0.010   0.001   TYR A 841 
 ARG   0.011   0.000   ARG A1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8221 (t0) cc_final: 0.8003 (t0)
REVERT: A 1017 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7031 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7583 (pm20)
REVERT: A 1129 GLN cc_start: 0.7407 (tp-100) cc_final: 0.7063 (mt0)
REVERT: B  702 ASP cc_start: 0.8290 (t0) cc_final: 0.7840 (t0)
REVERT: B  817 ARG cc_start: 0.7420 (ptm-80) cc_final: 0.7002 (ptt-90)
REVERT: B 1081 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6035 (pp30)
REVERT: B 1129 GLN cc_start: 0.7429 (tp-100) cc_final: 0.7059 (mt0)
  outliers start: 12
  outliers final: 8
  residues processed: 111
  average time/residue: 1.2529
  time to fit residues: 147.8057
Evaluate side-chains
  112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 95 optimal weight:    0.0670
   chunk 15 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.6718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.179658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144331 restraints weight = 8447.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 1.75
r_work: 0.3545 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8324  Z= 0.174
  Angle     :  0.521   9.838  11338  Z= 0.254
  Chirality :  0.040   0.138   1346
  Planarity :  0.005   0.050   1386
  Dihedral  :  4.616  60.644   1128
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.87 %
    Favored  : 76.31 %
  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:  2.41 (0.27), residues: 1020
  helix:  2.24 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop :  0.16 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.017   0.001   PHE A 909 
 TYR   0.011   0.001   TYR A 841 
 ARG   0.011   0.000   ARG A1203 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8270 (t0) cc_final: 0.8055 (t0)
REVERT: A 1017 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7094 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7612 (pm20)
REVERT: A 1129 GLN cc_start: 0.7424 (tp-100) cc_final: 0.7081 (mt0)
REVERT: B  702 ASP cc_start: 0.8298 (t0) cc_final: 0.7913 (t0)
REVERT: B  817 ARG cc_start: 0.7431 (ptm-80) cc_final: 0.7018 (ptt-90)
REVERT: B 1081 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.6074 (pp30)
REVERT: B 1129 GLN cc_start: 0.7440 (tp-100) cc_final: 0.7070 (mt0)
  outliers start: 16
  outliers final: 10
  residues processed: 114
  average time/residue: 1.2860
  time to fit residues: 155.3579
Evaluate side-chains
  116 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  947 THR
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1017 ARG
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 45 optimal weight:    0.2980
   chunk 14 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.179877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.144450 restraints weight = 8577.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 1.77
r_work: 0.3542 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8324  Z= 0.171
  Angle     :  0.532  10.008  11338  Z= 0.257
  Chirality :  0.039   0.135   1346
  Planarity :  0.005   0.066   1386
  Dihedral  :  4.617  60.264   1128
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.75 %
    Favored  : 76.42 %
  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:  2.43 (0.27), residues: 1020
  helix:  2.26 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop :  0.16 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A 850 
 PHE   0.014   0.001   PHE B 822 
 TYR   0.011   0.001   TYR A 841 
 ARG   0.018   0.001   ARG B1203 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5996.48 seconds
wall clock time: 106 minutes 43.63 seconds (6403.63 seconds total)