Starting phenix.real_space_refine
on Wed Sep 17 10:44:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y85_39034/09_2025/8y85_39034.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y85_39034/09_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_39034/09_2025/8y85_39034.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y85_39034/09_2025/8y85_39034.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y85_39034/09_2025/8y85_39034.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y85_39034/09_2025/8y85_39034.cif"
  }
  resolution = 2.73
  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
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.87, per 1000 atoms: 0.23
  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: 0.67
  Conformation dependent library (CDL) restraints added in 386.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.21
  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: 1.26

  Time building geometry restraints manager: 0.87 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: 0.02
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:             1.160
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.160
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  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:9.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.720
-------------------------------------------------------------------------------
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   8326  Z= 0.196
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.013   0.001   ARG B1203 
 TYR   0.034   0.002   TYR A 841 
 PHE   0.042   0.002   PHE A 840 
 TRP   0.019   0.002   TRP A1153 
 HIS   0.004   0.001   HIS B 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8324)
  covalent geometry    : angle       0.76272 (11338)
  hydrogen bonds       : bond        0.14452 (  494)
  hydrogen bonds       : angle       4.95074 ( 1449)
  Misc. bond           : bond        0.01184 (    2)

*********************** 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  : 0.319 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 106
  average time/residue: 0.6032
  time to fit residues: 67.5722
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  : 0.282 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.178447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143065 restraints weight = 8475.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.75
r_work: 0.3526 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.0770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8326  Z= 0.136
  Angle     :  0.567   8.190  11338  Z= 0.280
  Chirality :  0.041   0.149   1346
  Planarity :  0.006   0.059   1386
  Dihedral  :  6.122  71.163   1137
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.22 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.27), residues: 1020
  helix:  1.94 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.06 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B1203 
 TYR   0.015   0.001   TYR A 841 
 PHE   0.017   0.002   PHE B 822 
 TRP   0.011   0.001   TRP A 795 
 HIS   0.004   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8324)
  covalent geometry    : angle       0.56733 (11338)
  hydrogen bonds       : bond        0.06257 (  494)
  hydrogen bonds       : angle       4.00887 ( 1449)
  Misc. bond           : bond        0.00129 (    2)

*********************** 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
  128 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.7923 (t0) cc_final: 0.7656 (t0)
REVERT: A 1017 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7000 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7617 (pm20)
REVERT: B  817 ARG cc_start: 0.7395 (ptm-80) cc_final: 0.7001 (ptt180)
REVERT: B 1153 TRP cc_start: 0.7779 (p-90) cc_final: 0.7541 (p-90)
  outliers start: 24
  outliers final: 6
  residues processed: 120
  average time/residue: 0.5977
  time to fit residues: 75.7086
Evaluate side-chains
  114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  915 ASN
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 86 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0270
   chunk 44 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0970
   chunk 75 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.4236

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.182067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.146343 restraints weight = 8448.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.78
r_work: 0.3569 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8326  Z= 0.107
  Angle     :  0.498   7.279  11338  Z= 0.246
  Chirality :  0.039   0.123   1346
  Planarity :  0.005   0.046   1386
  Dihedral  :  5.118  59.951   1132
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.45 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.27), residues: 1020
  helix:  2.27 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.01 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B1203 
 TYR   0.012   0.001   TYR A 841 
 PHE   0.014   0.001   PHE B 822 
 TRP   0.014   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8324)
  covalent geometry    : angle       0.49801 (11338)
  hydrogen bonds       : bond        0.04753 (  494)
  hydrogen bonds       : angle       3.75519 ( 1449)
  Misc. bond           : bond        0.00009 (    2)

*********************** 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
  131 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  811 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6894 (tp30)
REVERT: A 1017 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7056 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7515 (pm20)
REVERT: B  817 ARG cc_start: 0.7506 (ptm-80) cc_final: 0.6969 (ptt180)
REVERT: B 1081 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.6096 (pp30)
  outliers start: 23
  outliers final: 6
  residues processed: 121
  average time/residue: 0.5505
  time to fit residues: 70.6783
Evaluate side-chains
  114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 69 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3986 r_free = 0.3986 target = 0.175107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.139019 restraints weight = 8678.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.77
r_work: 0.3468 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8326  Z= 0.173
  Angle     :  0.587   7.760  11338  Z= 0.294
  Chirality :  0.043   0.139   1346
  Planarity :  0.006   0.052   1386
  Dihedral  :  5.083  64.953   1128
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.68 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.27), residues: 1020
  helix:  1.86 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.09 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1203 
 TYR   0.013   0.002   TYR A 841 
 PHE   0.016   0.002   PHE B 822 
 TRP   0.011   0.001   TRP A 795 
 HIS   0.006   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8324)
  covalent geometry    : angle       0.58723 (11338)
  hydrogen bonds       : bond        0.07303 (  494)
  hydrogen bonds       : angle       4.00057 ( 1449)
  Misc. bond           : bond        0.00081 (    2)

*********************** 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
  135 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8149 (t0) cc_final: 0.7776 (t0)
REVERT: A  811 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6987 (tp30)
REVERT: A 1017 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7061 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7588 (pm20)
REVERT: B  780 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7046 (mtpt)
REVERT: B  811 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6956 (tp30)
REVERT: B 1081 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.6132 (pp30)
REVERT: B 1153 TRP cc_start: 0.7745 (p-90) cc_final: 0.7511 (p-90)
  outliers start: 27
  outliers final: 7
  residues processed: 124
  average time/residue: 0.5789
  time to fit residues: 75.9463
Evaluate side-chains
  116 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 78 optimal weight:    0.1980
   chunk 47 optimal weight:    5.9990
   chunk 95 optimal weight:    0.3980
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.179155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.143811 restraints weight = 8493.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.76
r_work: 0.3535 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8326  Z= 0.115
  Angle     :  0.503   7.586  11338  Z= 0.251
  Chirality :  0.039   0.124   1346
  Planarity :  0.005   0.047   1386
  Dihedral  :  4.878  60.460   1128
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 19.36 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.27), residues: 1020
  helix:  2.19 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop :  0.09 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1203 
 TYR   0.012   0.001   TYR A 841 
 PHE   0.015   0.001   PHE B 822 
 TRP   0.014   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8324)
  covalent geometry    : angle       0.50306 (11338)
  hydrogen bonds       : bond        0.05239 (  494)
  hydrogen bonds       : angle       3.79590 ( 1449)
  Misc. bond           : bond        0.00032 (    2)

*********************** 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
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  811 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7080 (tp30)
REVERT: A 1017 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7090 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7529 (pm20)
REVERT: B  702 ASP cc_start: 0.8203 (t0) cc_final: 0.7766 (t0)
REVERT: B  780 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6944 (mtpt)
REVERT: B  811 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6969 (tp30)
REVERT: B 1081 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.6068 (pp30)
  outliers start: 26
  outliers final: 9
  residues processed: 122
  average time/residue: 0.5589
  time to fit residues: 72.2175
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  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue 1136 MET
Chi-restraints excluded: chain B residue  675 LEU
Chi-restraints excluded: chain B residue  780 LYS
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue 1081 GLN
Chi-restraints excluded: chain B residue 1119 VAL
Chi-restraints excluded: chain B residue 1136 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.177595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141959 restraints weight = 8494.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.76
r_work: 0.3512 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8326  Z= 0.129
  Angle     :  0.524   8.012  11338  Z= 0.261
  Chirality :  0.040   0.126   1346
  Planarity :  0.005   0.054   1386
  Dihedral  :  4.858  61.489   1128
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.16 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.27), residues: 1020
  helix:  2.08 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.00 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A1203 
 TYR   0.012   0.001   TYR A 841 
 PHE   0.014   0.001   PHE B 909 
 TRP   0.012   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8324)
  covalent geometry    : angle       0.52373 (11338)
  hydrogen bonds       : bond        0.05891 (  494)
  hydrogen bonds       : angle       3.82107 ( 1449)
  Misc. bond           : bond        0.00034 (    2)

*********************** 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
  137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8217 (t0) cc_final: 0.8005 (t0)
REVERT: A  811 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7067 (tp30)
REVERT: A  825 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6994 (mm-30)
REVERT: A 1017 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7089 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7568 (pm20)
REVERT: B  780 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6942 (mtpt)
REVERT: B  817 ARG cc_start: 0.7465 (ptm-80) cc_final: 0.7003 (ptt180)
REVERT: B 1081 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.6070 (pp30)
REVERT: B 1153 TRP cc_start: 0.7698 (p-90) cc_final: 0.7473 (p-90)
  outliers start: 26
  outliers final: 12
  residues processed: 126
  average time/residue: 0.5948
  time to fit residues: 79.1553
Evaluate side-chains
  117 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue 1136 MET
Chi-restraints excluded: chain B residue  675 LEU
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
Chi-restraints excluded: chain B residue 1136 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.174747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.138814 restraints weight = 8613.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.76
r_work: 0.3455 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
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      :  0.004   0.034   8326  Z= 0.163
  Angle     :  0.576   8.483  11338  Z= 0.288
  Chirality :  0.042   0.129   1346
  Planarity :  0.006   0.054   1386
  Dihedral  :  5.036  63.846   1128
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.27), residues: 1020
  helix:  1.85 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.09 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A1203 
 TYR   0.010   0.001   TYR A 841 
 PHE   0.016   0.002   PHE B 909 
 TRP   0.010   0.001   TRP B 795 
 HIS   0.005   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8324)
  covalent geometry    : angle       0.57612 (11338)
  hydrogen bonds       : bond        0.07072 (  494)
  hydrogen bonds       : angle       3.99298 ( 1449)
  Misc. bond           : bond        0.00060 (    2)

*********************** 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
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A 1017 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7133 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7613 (pm20)
REVERT: A 1129 GLN cc_start: 0.7496 (tp-100) cc_final: 0.7135 (mt0)
REVERT: B  780 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6967 (mtpt)
REVERT: B 1081 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6125 (pp30)
REVERT: B 1129 GLN cc_start: 0.7508 (tp-100) cc_final: 0.7135 (mt0)
REVERT: B 1153 TRP cc_start: 0.7750 (p-90) cc_final: 0.7533 (p-90)
  outliers start: 29
  outliers final: 14
  residues processed: 124
  average time/residue: 0.5885
  time to fit residues: 77.1474
Evaluate side-chains
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  915 ASN
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 1081 GLN
Chi-restraints excluded: chain A residue 1119 VAL
Chi-restraints excluded: chain A residue 1136 MET
Chi-restraints excluded: chain B residue  675 LEU
Chi-restraints excluded: chain B residue  780 LYS
Chi-restraints excluded: chain B residue  805 LEU
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
Chi-restraints excluded: chain B residue 1136 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0030
   chunk 28 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0000
   chunk 92 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.3994

-------------------------------------------------------------------------------
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 = 0.179563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.144444 restraints weight = 8526.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 1.77
r_work: 0.3541 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8326  Z= 0.110
  Angle     :  0.504   8.463  11338  Z= 0.250
  Chirality :  0.039   0.126   1346
  Planarity :  0.005   0.068   1386
  Dihedral  :  4.757  59.389   1128
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.87 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.27), residues: 1020
  helix:  2.26 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop :  0.06 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1203 
 TYR   0.013   0.001   TYR A 841 
 PHE   0.017   0.001   PHE B 909 
 TRP   0.017   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8324)
  covalent geometry    : angle       0.50406 (11338)
  hydrogen bonds       : bond        0.04908 (  494)
  hydrogen bonds       : angle       3.75677 ( 1449)
  Misc. bond           : bond        0.00015 (    2)

*********************** 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
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8216 (t0) cc_final: 0.7980 (t0)
REVERT: A 1017 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7103 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7631 (pm20)
REVERT: B  780 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6918 (mtpt)
REVERT: B  817 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.6876 (ptt180)
REVERT: B 1081 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.5894 (pp30)
  outliers start: 19
  outliers final: 8
  residues processed: 116
  average time/residue: 0.5544
  time to fit residues: 68.2135
Evaluate side-chains
  111 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  675 LEU
Chi-restraints excluded: chain B residue  780 LYS
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 1 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0050
   chunk 88 optimal weight:    0.0670
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.7536

-------------------------------------------------------------------------------
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 = 0.178140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.142631 restraints weight = 8530.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 1.77
r_work: 0.3521 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8326  Z= 0.124
  Angle     :  0.527   8.868  11338  Z= 0.261
  Chirality :  0.040   0.126   1346
  Planarity :  0.005   0.048   1386
  Dihedral  :  4.744  60.798   1128
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.75 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.27), residues: 1020
  helix:  2.15 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.01 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1203 
 TYR   0.011   0.001   TYR A 841 
 PHE   0.017   0.001   PHE B 909 
 TRP   0.030   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8324)
  covalent geometry    : angle       0.52719 (11338)
  hydrogen bonds       : bond        0.05569 (  494)
  hydrogen bonds       : angle       3.76619 ( 1449)
  Misc. bond           : bond        0.00027 (    2)

*********************** 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
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A 1017 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7111 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7564 (pm20)
REVERT: B  780 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6907 (mtpt)
REVERT: B  817 ARG cc_start: 0.7425 (ptm-80) cc_final: 0.6882 (ptt180)
REVERT: B 1081 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.5912 (pp30)
REVERT: B 1129 GLN cc_start: 0.7409 (tp-100) cc_final: 0.7038 (mt0)
REVERT: B 1209 ASP cc_start: 0.7463 (t0) cc_final: 0.7185 (t70)
  outliers start: 21
  outliers final: 13
  residues processed: 117
  average time/residue: 0.5685
  time to fit residues: 70.3161
Evaluate side-chains
  118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  675 LEU
Chi-restraints excluded: chain B residue  780 LYS
Chi-restraints excluded: chain B residue  805 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3987 r_free = 0.3987 target = 0.175319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.139516 restraints weight = 8567.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.76
r_work: 0.3482 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8326  Z= 0.159
  Angle     :  0.590   9.963  11338  Z= 0.292
  Chirality :  0.042   0.126   1346
  Planarity :  0.006   0.056   1386
  Dihedral  :  4.936  63.887   1128
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.53 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.27), residues: 1020
  helix:  1.91 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.09 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG B1203 
 TYR   0.010   0.001   TYR A 841 
 PHE   0.018   0.002   PHE B 909 
 TRP   0.032   0.002   TRP A1153 
 HIS   0.004   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8324)
  covalent geometry    : angle       0.59024 (11338)
  hydrogen bonds       : bond        0.06829 (  494)
  hydrogen bonds       : angle       3.93427 ( 1449)
  Misc. bond           : bond        0.00054 (    2)

********************** 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
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.8275 (t0) cc_final: 0.8035 (t0)
REVERT: A 1017 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7140 (mmt90)
REVERT: A 1081 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7586 (pm20)
REVERT: A 1129 GLN cc_start: 0.7494 (tp-100) cc_final: 0.7119 (mt0)
REVERT: B  780 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6898 (mtpt)
REVERT: B  817 ARG cc_start: 0.7443 (ptm-80) cc_final: 0.7030 (ptt180)
REVERT: B 1081 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.6032 (pp30)
REVERT: B 1129 GLN cc_start: 0.7460 (tp-100) cc_final: 0.7082 (mt0)
REVERT: B 1153 TRP cc_start: 0.7749 (p-90) cc_final: 0.7399 (p-90)
  outliers start: 21
  outliers final: 14
  residues processed: 114
  average time/residue: 0.5989
  time to fit residues: 72.3215
Evaluate side-chains
  115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  915 ASN
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  675 LEU
Chi-restraints excluded: chain B residue  780 LYS
Chi-restraints excluded: chain B residue  805 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0870
   chunk 90 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 55 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.179334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144257 restraints weight = 8529.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 1.76
r_work: 0.3543 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8326  Z= 0.114
  Angle     :  0.531   9.983  11338  Z= 0.261
  Chirality :  0.039   0.129   1346
  Planarity :  0.005   0.061   1386
  Dihedral  :  4.748  59.723   1128
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 22.32 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.27), residues: 1020
  helix:  2.26 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop :  0.05 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B1203 
 TYR   0.013   0.001   TYR A 841 
 PHE   0.019   0.001   PHE B 909 
 TRP   0.033   0.001   TRP A1153 
 HIS   0.003   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8324)
  covalent geometry    : angle       0.53147 (11338)
  hydrogen bonds       : bond        0.05019 (  494)
  hydrogen bonds       : angle       3.74173 ( 1449)
  Misc. bond           : bond        0.00021 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2978.08 seconds
wall clock time: 51 minutes 19.01 seconds (3079.01 seconds total)