Starting phenix.real_space_refine
on Fri Jun  6 19:21:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y8k_39050/06_2025/8y8k_39050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y8k_39050/06_2025/8y8k_39050.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y8k_39050/06_2025/8y8k_39050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y8k_39050/06_2025/8y8k_39050.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y8k_39050/06_2025/8y8k_39050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y8k_39050/06_2025/8y8k_39050.cif"
  }
  resolution = 2.89
  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=   0.001 sd=   0.150
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      34      5.16       5
     C    5352      2.51       5
     N    1330      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8052
  Number of models: 1
  Model: ""
    Number of chains: 2
    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
  Time building chain proxies: 5.42, per 1000 atoms: 0.67
  Number of scatterers: 8052
  At special positions: 0
  Unit cell: (108.9, 106.7, 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      34     16.00
     O    1336      8.00
     N    1330      7.00
     C    5352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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:
      58 helices and 4 sheets defined
      74.3% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  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: 3.702A  pdb=" N   ALA A 710 " --> pdb=" O   SER A 706 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 717 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 3.786A  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: 3.677A  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
    Processing helix  chain 'A' and resid 811 through 819
      removed outlier: 3.823A  pdb=" N   PHE A 814 " --> pdb=" O   GLU A 811 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 850
      removed outlier: 3.575A  pdb=" N   GLN A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL A 846 " --> pdb=" O   LYS A 842 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   PHE A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR A 848 " --> pdb=" O   TYR A 844 " (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: 3.520A  pdb=" N   ILE A 946 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 989
      removed outlier: 3.544A  pdb=" N   MET A 986 " --> pdb=" O   PRO A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1012
      removed outlier: 3.613A  pdb=" N   ALA A 993 " --> pdb=" O   ALA A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1017
      removed outlier: 3.534A  pdb=" N   ARG A1017 " --> pdb=" O   LYS A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1039
      removed outlier: 3.692A  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 1050 through 1060
      removed outlier: 3.600A  pdb=" N   LEU A1060 " --> pdb=" O   HIS A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1095
      removed outlier: 3.575A  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: 4.228A  pdb=" N   LEU A1110 " --> pdb=" O   PRO A1106 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A1122 " --> pdb=" O   GLY A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1136
      removed outlier: 3.697A  pdb=" N   GLN A1129 " --> pdb=" O   ILE A1125 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE A1134 " --> pdb=" O   ARG A1130 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU A1135 " --> pdb=" O   LEU A1131 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   MET A1136 " --> pdb=" O   LEU A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1144 through 1149
      removed outlier: 3.708A  pdb=" N   LYS A1149 " --> pdb=" O   PRO A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1151 through 1175
      removed outlier: 3.731A  pdb=" N   LEU A1157 " --> pdb=" O   TRP A1153 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   PHE A1158 " --> pdb=" O   ARG A1154 " (cutoff:3.500A)
      removed outlier: 3.619A  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
      removed outlier: 3.520A  pdb=" N   LEU A1186 " --> pdb=" O   PRO A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1187 through 1195
      removed outlier: 3.911A  pdb=" N   LEU A1191 " --> pdb=" O   LEU A1187 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG A1192 " --> pdb=" O   THR A1188 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS A1193 " --> pdb=" O   VAL A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1200
      removed outlier: 3.579A  pdb=" N   LEU A1199 " --> pdb=" O   LEU A1195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1209
      removed outlier: 3.508A  pdb=" N   ALA A1207 " --> pdb=" O   ARG A1203 " (cutoff:3.500A)
    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: 3.693A  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: 3.753A  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: 3.815A  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
    Processing helix  chain 'B' and resid 811 through 819
      removed outlier: 3.718A  pdb=" N   PHE B 814 " --> pdb=" O   GLU B 811 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU B 815 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 850
    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: 3.550A  pdb=" N   ILE B 946 " --> pdb=" O   VAL B 942 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 982 through 989
      removed outlier: 3.519A  pdb=" N   MET B 986 " --> pdb=" O   PRO B 982 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 989 through 1012
      removed outlier: 3.583A  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: 3.712A  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: 3.597A  pdb=" N   LEU B1060 " --> pdb=" O   HIS B1056 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1082 through 1095
      removed outlier: 3.541A  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: 4.186A  pdb=" N   LEU B1110 " --> pdb=" O   PRO B1106 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU B1122 " --> pdb=" O   GLY B1118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1125 through 1133
      removed outlier: 3.680A  pdb=" N   GLN B1129 " --> pdb=" O   ILE B1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1144 through 1149
      removed outlier: 3.678A  pdb=" N   LYS B1149 " --> pdb=" O   PRO B1145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1151 through 1175
      removed outlier: 3.902A  pdb=" N   LEU B1157 " --> pdb=" O   TRP B1153 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE B1158 " --> pdb=" O   ARG B1154 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   THR B1159 " --> pdb=" O   MET B1155 " (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
      removed outlier: 3.546A  pdb=" N   LEU B1186 " --> pdb=" O   PRO B1182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1187 through 1195
      removed outlier: 3.862A  pdb=" N   LEU B1191 " --> pdb=" O   LEU B1187 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG B1192 " --> pdb=" O   THR B1188 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   HIS B1193 " --> pdb=" O   VAL B1189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1196 through 1199
    Processing helix  chain 'B' and resid 1201 through 1209
    Processing sheet with id=AA1, first strand: chain 'A' and resid 764 through 766
      removed outlier: 4.874A  pdb=" N   VAL A 764 " --> pdb=" O   ALA A1049 " (cutoff:3.500A)
    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

    488 hydrogen bonds defined for protein.
    1428 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: 2.26

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2466
        1.34 -     1.46: 1559
        1.46 -     1.58: 4179
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 8260
  Sorted by residual:
  bond pdb=" CA  ASP A1209 "
       pdb=" CB  ASP A1209 "
    ideal  model  delta    sigma   weight residual
    1.526  1.553 -0.027 1.53e-02 4.27e+03 3.06e+00
  bond pdb=" CG  ARG B 817 "
       pdb=" CD  ARG B 817 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.01e+00
  bond pdb=" CA  ASP B1209 "
       pdb=" CB  ASP B1209 "
    ideal  model  delta    sigma   weight residual
    1.528  1.553 -0.025 2.61e-02 1.47e+03 9.30e-01
  bond pdb=" N   GLU A 811 "
       pdb=" CA  GLU A 811 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.012 1.29e-02 6.01e+03 8.47e-01
  bond pdb=" C   THR B 839 "
       pdb=" O   THR B 839 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.010 1.15e-02 7.56e+03 8.17e-01
  ... (remaining 8255 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 10923
        1.35 -     2.71: 254
        2.71 -     4.06: 52
        4.06 -     5.42: 15
        5.42 -     6.77: 4
  Bond angle restraints: 11248
  Sorted by residual:
  angle pdb=" CB  ARG B 817 "
        pdb=" CG  ARG B 817 "
        pdb=" CD  ARG B 817 "
      ideal   model   delta    sigma   weight residual
     111.30  118.07   -6.77 2.30e+00 1.89e-01 8.68e+00
  angle pdb=" CG  ARG B 817 "
        pdb=" CD  ARG B 817 "
        pdb=" NE  ARG B 817 "
      ideal   model   delta    sigma   weight residual
     112.00  117.77   -5.77 2.20e+00 2.07e-01 6.88e+00
  angle pdb=" CB  ARG B 917 "
        pdb=" CG  ARG B 917 "
        pdb=" CD  ARG B 917 "
      ideal   model   delta    sigma   weight residual
     111.30  116.76   -5.46 2.30e+00 1.89e-01 5.63e+00
  angle pdb=" CA  GLU A 811 "
        pdb=" CB  GLU A 811 "
        pdb=" CG  GLU A 811 "
      ideal   model   delta    sigma   weight residual
     114.10  118.36   -4.26 2.00e+00 2.50e-01 4.53e+00
  angle pdb=" CG  ARG B 917 "
        pdb=" CD  ARG B 917 "
        pdb=" NE  ARG B 917 "
      ideal   model   delta    sigma   weight residual
     112.00  116.45   -4.45 2.20e+00 2.07e-01 4.10e+00
  ... (remaining 11243 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 4193
       16.46 -    32.92: 508
       32.92 -    49.39: 141
       49.39 -    65.85: 26
       65.85 -    82.31: 12
  Dihedral angle restraints: 4880
    sinusoidal: 1922
      harmonic: 2958
  Sorted by residual:
  dihedral pdb=" CA  THR A 947 "
           pdb=" C   THR A 947 "
           pdb=" N   ASP A 948 "
           pdb=" CA  ASP A 948 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.65   17.35     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  THR B 947 "
           pdb=" C   THR B 947 "
           pdb=" N   ASP B 948 "
           pdb=" CA  ASP B 948 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.33   16.67     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  ASP A1071 "
           pdb=" CB  ASP A1071 "
           pdb=" CG  ASP A1071 "
           pdb=" OD1 ASP A1071 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.16   54.16     1      2.00e+01 2.50e-03 9.95e+00
  ... (remaining 4877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 727
       0.026 -    0.051: 357
       0.051 -    0.077: 175
       0.077 -    0.102: 52
       0.102 -    0.128: 35
  Chirality restraints: 1346
  Sorted by residual:
  chirality pdb=" CA  ILE A 972 "
            pdb=" N   ILE A 972 "
            pdb=" C   ILE A 972 "
            pdb=" CB  ILE A 972 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CA  SER A 721 "
            pdb=" N   SER A 721 "
            pdb=" C   SER A 721 "
            pdb=" CB  SER A 721 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CA  ILE B 972 "
            pdb=" N   ILE B 972 "
            pdb=" C   ILE B 972 "
            pdb=" CB  ILE B 972 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  ... (remaining 1343 not shown)

  Planarity restraints: 1380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1196 "   -0.050 5.00e-02 4.00e+02   7.51e-02 9.04e+00
        pdb=" N   PRO A1197 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A1197 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A1197 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1181 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO A1182 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A1182 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1182 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 820 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO B 821 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 821 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 821 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1377 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1653
        2.78 -     3.31: 7331
        3.31 -     3.84: 12723
        3.84 -     4.37: 14174
        4.37 -     4.90: 26001
  Nonbonded interactions: 61882
  Sorted by model distance:
  nonbonded pdb=" O   ALA A1049 "
            pdb=" OG  SER A1053 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ALA B1049 "
            pdb=" OG  SER B1053 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG A1130 "
            pdb=" OE1 GLN A1162 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" NH2 ARG B1130 "
            pdb=" OE1 GLN B1162 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" NH2 ARG A 793 "
            pdb=" O   LEU A1043 "
     model   vdw
     2.286 3.120
  ... (remaining 61877 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: 0.10
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:             1.090
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.510
  Find NCS groups from input model:        0.260
  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:12.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
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      :  0.003   0.031   8260  Z= 0.144
  Angle     :  0.540   6.775  11248  Z= 0.287
  Chirality :  0.040   0.128   1346
  Planarity :  0.006   0.075   1380
  Dihedral  : 16.016  82.309   2972
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.36 %
    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:  1.68 (0.26), residues: 1020
  helix:  1.80 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -0.30 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 795 
 HIS   0.002   0.001   HIS A1140 
 PHE   0.023   0.001   PHE B 847 
 TYR   0.010   0.001   TYR B 856 
 ARG   0.014   0.000   ARG B 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14188 (  488)
  hydrogen bonds       : angle       4.70945 ( 1428)
  covalent geometry    : bond        0.00326 ( 8260)
  covalent geometry    : angle       0.53986 (11248)

*********************** 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
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.972 
Fit side-chains
REVERT: B  817 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7329 (ptm-80)
REVERT: B  917 ARG cc_start: 0.6917 (mtp-110) cc_final: 0.6549 (tpp-160)
  outliers start: 20
  outliers final: 15
  residues processed: 117
  average time/residue: 1.3926
  time to fit residues: 171.6980
Evaluate side-chains
  113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  804 VAL
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1022 SER
Chi-restraints excluded: chain A residue 1076 GLN
Chi-restraints excluded: chain A residue 1150 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  755 SER
Chi-restraints excluded: chain B residue 1022 SER
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1172 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.0980
   chunk 77 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0670
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
B1076 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.175196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137613 restraints weight = 8344.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.89
r_work: 0.3352 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.0651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8260  Z= 0.144
  Angle     :  0.512   5.407  11248  Z= 0.264
  Chirality :  0.041   0.126   1346
  Planarity :  0.006   0.061   1380
  Dihedral  :  4.594  36.678   1129
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.11 %
    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 (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:  1.79 (0.27), residues: 1020
  helix:  1.94 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.40 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 795 
 HIS   0.002   0.001   HIS A1025 
 PHE   0.020   0.001   PHE B 847 
 TYR   0.007   0.001   TYR B 856 
 ARG   0.008   0.000   ARG B 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06695 (  488)
  hydrogen bonds       : angle       3.95309 ( 1428)
  covalent geometry    : bond        0.00337 ( 8260)
  covalent geometry    : angle       0.51221 (11248)

*********************** 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
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A 1063 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7787 (mtm)
REVERT: A 1067 ILE cc_start: 0.3775 (OUTLIER) cc_final: 0.3337 (mt)
REVERT: A 1206 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7337 (tp-100)
REVERT: B  688 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6587 (m-30)
REVERT: B  732 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6760 (tt0)
REVERT: B  917 ARG cc_start: 0.7371 (mtp180) cc_final: 0.6748 (tpp-160)
  outliers start: 32
  outliers final: 17
  residues processed: 122
  average time/residue: 1.2981
  time to fit residues: 167.6269
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  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  939 MET
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain A residue 1206 GLN
Chi-restraints excluded: chain B residue  688 ASP
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  846 VAL
Chi-restraints excluded: chain B residue  939 MET
Chi-restraints excluded: chain B residue  948 ASP
Chi-restraints excluded: chain B residue 1096 ILE
Chi-restraints excluded: chain B residue 1155 MET
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1186 LEU
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
A1076 GLN
B1076 GLN
B1140 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.173827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.141394 restraints weight = 8531.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.82
r_work: 0.3395 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.0928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8260  Z= 0.155
  Angle     :  0.524   5.557  11248  Z= 0.267
  Chirality :  0.041   0.127   1346
  Planarity :  0.006   0.057   1380
  Dihedral  :  3.707  17.825   1110
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 17.54 %
    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 (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:  1.59 (0.26), residues: 1020
  helix:  1.78 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.57 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 795 
 HIS   0.002   0.001   HIS B 850 
 PHE   0.018   0.001   PHE B 822 
 TYR   0.010   0.001   TYR B 856 
 ARG   0.010   0.000   ARG B1203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07004 (  488)
  hydrogen bonds       : angle       3.91424 ( 1428)
  covalent geometry    : bond        0.00372 ( 8260)
  covalent geometry    : angle       0.52370 (11248)

*********************** 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
  148 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 106
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A  917 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7611 (tpp-160)
REVERT: A  943 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7450 (t70)
REVERT: A 1063 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7806 (mtm)
REVERT: A 1067 ILE cc_start: 0.3788 (OUTLIER) cc_final: 0.3294 (mt)
REVERT: A 1081 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7028 (pm20)
REVERT: B  917 ARG cc_start: 0.7569 (mtp180) cc_final: 0.6962 (tpp-160)
REVERT: B  943 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7450 (t70)
REVERT: B 1203 ARG cc_start: 0.5860 (ttp-110) cc_final: 0.5227 (ptt-90)
  outliers start: 42
  outliers final: 22
  residues processed: 129
  average time/residue: 1.2418
  time to fit residues: 169.4012
Evaluate side-chains
  127 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  917 ARG
Chi-restraints excluded: chain A residue  943 ASP
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1081 GLN
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  738 MET
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  900 MET
Chi-restraints excluded: chain B residue  943 ASP
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue 1096 ILE
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1152 THR
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1186 LEU
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0770
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
A1076 GLN
B1076 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.174694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141061 restraints weight = 8429.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.76
r_work: 0.3345 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8260  Z= 0.139
  Angle     :  0.497   5.541  11248  Z= 0.254
  Chirality :  0.040   0.124   1346
  Planarity :  0.005   0.053   1380
  Dihedral  :  3.628  18.057   1110
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 18.34 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.27), residues: 1020
  helix:  1.90 (0.20), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.60 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 795 
 HIS   0.002   0.001   HIS B 850 
 PHE   0.016   0.001   PHE B 822 
 TYR   0.007   0.001   TYR A 844 
 ARG   0.005   0.000   ARG B 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06432 (  488)
  hydrogen bonds       : angle       3.81680 ( 1428)
  covalent geometry    : bond        0.00329 ( 8260)
  covalent geometry    : angle       0.49716 (11248)

*********************** 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
  143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 99
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A  917 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7561 (tpp-160)
REVERT: A  943 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7411 (t70)
REVERT: A 1063 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7796 (mtm)
REVERT: A 1067 ILE cc_start: 0.3835 (OUTLIER) cc_final: 0.3332 (mt)
REVERT: A 1206 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7641 (tt0)
REVERT: B  688 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6735 (m-30)
REVERT: B  917 ARG cc_start: 0.7533 (mtp180) cc_final: 0.6970 (tpp-160)
REVERT: B 1063 MET cc_start: 0.7996 (mmm) cc_final: 0.7304 (mtm)
REVERT: B 1203 ARG cc_start: 0.5866 (ttp-110) cc_final: 0.5246 (ptt-90)
  outliers start: 44
  outliers final: 27
  residues processed: 124
  average time/residue: 1.2867
  time to fit residues: 168.8545
Evaluate side-chains
  131 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  732 GLU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  917 ARG
Chi-restraints excluded: chain A residue  943 ASP
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  688 ASP
Chi-restraints excluded: chain B residue  738 MET
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  900 MET
Chi-restraints excluded: chain B residue  943 ASP
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  998 ILE
Chi-restraints excluded: chain B residue  999 LEU
Chi-restraints excluded: chain B residue 1096 ILE
Chi-restraints excluded: chain B residue 1126 GLN
Chi-restraints excluded: chain B residue 1152 THR
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1186 LEU
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 99 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.175941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139095 restraints weight = 8314.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.84
r_work: 0.3399 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8260  Z= 0.125
  Angle     :  0.480   5.430  11248  Z= 0.244
  Chirality :  0.040   0.125   1346
  Planarity :  0.005   0.051   1380
  Dihedral  :  3.530  17.802   1110
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 17.65 %
    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 (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:  1.82 (0.27), residues: 1020
  helix:  2.00 (0.20), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.55 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 795 
 HIS   0.002   0.001   HIS A1025 
 PHE   0.015   0.001   PHE B 822 
 TYR   0.007   0.001   TYR A 844 
 ARG   0.011   0.000   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05879 (  488)
  hydrogen bonds       : angle       3.72780 ( 1428)
  covalent geometry    : bond        0.00286 ( 8260)
  covalent geometry    : angle       0.48015 (11248)

*********************** 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
  148 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 100
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  817 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7873 (ttm110)
REVERT: A  917 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7558 (tpp-160)
REVERT: A 1063 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7780 (mtm)
REVERT: A 1067 ILE cc_start: 0.3823 (OUTLIER) cc_final: 0.3327 (mt)
REVERT: A 1157 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7461 (mt)
REVERT: A 1206 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7684 (tt0)
REVERT: B  688 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6661 (m-30)
REVERT: B  917 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7061 (tpp-160)
REVERT: B  952 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8078 (tt0)
REVERT: B 1203 ARG cc_start: 0.5911 (ttp-110) cc_final: 0.5291 (ptt-90)
  outliers start: 48
  outliers final: 31
  residues processed: 128
  average time/residue: 1.2182
  time to fit residues: 165.3290
Evaluate side-chains
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  917 ARG
Chi-restraints excluded: chain A residue  943 ASP
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  688 ASP
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  732 GLU
Chi-restraints excluded: chain B residue  738 MET
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  900 MET
Chi-restraints excluded: chain B residue  943 ASP
Chi-restraints excluded: chain B residue  952 GLN
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  998 ILE
Chi-restraints excluded: chain B residue  999 LEU
Chi-restraints excluded: chain B residue 1096 ILE
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1186 LEU
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0050
   chunk 40 optimal weight:    0.7980
   chunk 88 optimal weight:    0.0470
   chunk 32 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.5292

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.177855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141336 restraints weight = 8302.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.83
r_work: 0.3451 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
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      :  0.002   0.028   8260  Z= 0.109
  Angle     :  0.462   5.527  11248  Z= 0.233
  Chirality :  0.039   0.123   1346
  Planarity :  0.005   0.048   1380
  Dihedral  :  3.413  17.464   1110
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.02 %
    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 (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:  2.14 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.62 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 795 
 HIS   0.002   0.000   HIS A1025 
 PHE   0.013   0.001   PHE B 822 
 TYR   0.007   0.001   TYR A 844 
 ARG   0.009   0.000   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05135 (  488)
  hydrogen bonds       : angle       3.63353 ( 1428)
  covalent geometry    : bond        0.00240 ( 8260)
  covalent geometry    : angle       0.46171 (11248)

*********************** 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
  133 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A 1063 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7806 (mtm)
REVERT: A 1067 ILE cc_start: 0.3828 (OUTLIER) cc_final: 0.3393 (mt)
REVERT: A 1157 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7397 (mt)
REVERT: A 1198 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7279 (mtt180)
REVERT: A 1206 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7679 (tt0)
REVERT: B  688 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6586 (m-30)
REVERT: B  917 ARG cc_start: 0.7531 (mtp180) cc_final: 0.7106 (tpp-160)
  outliers start: 36
  outliers final: 25
  residues processed: 118
  average time/residue: 1.2092
  time to fit residues: 151.4314
Evaluate side-chains
  125 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  688 ASP
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  845 LYS
Chi-restraints excluded: chain B residue  943 ASP
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  999 LEU
Chi-restraints excluded: chain B residue 1096 ILE
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1186 LEU
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0670
   chunk 51 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
B1076 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.177162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.140447 restraints weight = 8400.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.86
r_work: 0.3442 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8260  Z= 0.116
  Angle     :  0.472   5.732  11248  Z= 0.239
  Chirality :  0.039   0.125   1346
  Planarity :  0.005   0.049   1380
  Dihedral  :  3.402  16.788   1110
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 19.02 %
    Favored  : 76.54 %
  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:  2.00 (0.27), residues: 1020
  helix:  2.14 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.55 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 795 
 HIS   0.002   0.001   HIS A1025 
 PHE   0.014   0.001   PHE A 855 
 TYR   0.006   0.001   TYR A 844 
 ARG   0.012   0.000   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05425 (  488)
  hydrogen bonds       : angle       3.62627 ( 1428)
  covalent geometry    : bond        0.00263 ( 8260)
  covalent geometry    : angle       0.47222 (11248)

*********************** 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
  135 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 96
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A  817 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7809 (ttm110)
REVERT: A  917 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7627 (tpp-160)
REVERT: A 1063 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7814 (mtm)
REVERT: A 1067 ILE cc_start: 0.3821 (OUTLIER) cc_final: 0.3333 (mt)
REVERT: A 1157 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7390 (mt)
REVERT: A 1198 ARG cc_start: 0.7509 (mmm160) cc_final: 0.7270 (mtt180)
REVERT: A 1206 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7643 (tt0)
REVERT: B  688 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6765 (m-30)
REVERT: B  917 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7120 (tpp-160)
REVERT: B 1203 ARG cc_start: 0.6127 (ttp-110) cc_final: 0.5216 (ptt-90)
  outliers start: 39
  outliers final: 28
  residues processed: 121
  average time/residue: 1.2652
  time to fit residues: 162.1403
Evaluate side-chains
  130 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  732 GLU
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  917 ARG
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1150 VAL
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain A residue 1206 GLN
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  688 ASP
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  845 LYS
Chi-restraints excluded: chain B residue  900 MET
Chi-restraints excluded: chain B residue  943 ASP
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  998 ILE
Chi-restraints excluded: chain B residue  999 LEU
Chi-restraints excluded: chain B residue 1096 ILE
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1186 LEU
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 99 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
B1076 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.175981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139141 restraints weight = 8456.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.86
r_work: 0.3427 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8260  Z= 0.126
  Angle     :  0.484   5.561  11248  Z= 0.245
  Chirality :  0.040   0.127   1346
  Planarity :  0.005   0.048   1380
  Dihedral  :  3.431  16.886   1110
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 19.13 %
    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:  1.97 (0.27), residues: 1020
  helix:  2.08 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.44 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.002   0.001   HIS B1025 
 PHE   0.015   0.001   PHE B 822 
 TYR   0.007   0.001   TYR A1146 
 ARG   0.011   0.000   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05827 (  488)
  hydrogen bonds       : angle       3.67118 ( 1428)
  covalent geometry    : bond        0.00292 ( 8260)
  covalent geometry    : angle       0.48429 (11248)

*********************** 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
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  917 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7616 (tpp-160)
REVERT: A 1063 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7799 (mtm)
REVERT: A 1067 ILE cc_start: 0.3802 (OUTLIER) cc_final: 0.3301 (mt)
REVERT: A 1157 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7451 (mt)
REVERT: A 1198 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7267 (mtt180)
REVERT: A 1206 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7710 (tt0)
REVERT: B  917 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7130 (tpp-160)
REVERT: B 1203 ARG cc_start: 0.6105 (ttp-110) cc_final: 0.5180 (ptt-90)
  outliers start: 39
  outliers final: 30
  residues processed: 126
  average time/residue: 1.2903
  time to fit residues: 172.2962
Evaluate side-chains
  131 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  732 GLU
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  917 ARG
Chi-restraints excluded: chain A residue  939 MET
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1150 VAL
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  732 GLU
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  900 MET
Chi-restraints excluded: chain B residue  943 ASP
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  998 ILE
Chi-restraints excluded: chain B residue  999 LEU
Chi-restraints excluded: chain B residue 1126 GLN
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 88 optimal weight:    0.0040
   chunk 59 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0770
   chunk 70 optimal weight:    0.0770
   chunk 57 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0070
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.4328

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
B1076 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.179142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.142372 restraints weight = 8508.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.89
r_work: 0.3473 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8260  Z= 0.104
  Angle     :  0.458   6.009  11248  Z= 0.232
  Chirality :  0.038   0.122   1346
  Planarity :  0.005   0.047   1380
  Dihedral  :  3.314  16.837   1110
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.27 %
    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:  2.20 (0.27), residues: 1020
  helix:  2.30 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.46 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 795 
 HIS   0.002   0.000   HIS A1025 
 PHE   0.017   0.001   PHE A 855 
 TYR   0.007   0.001   TYR A 789 
 ARG   0.015   0.000   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  488)
  hydrogen bonds       : angle       3.56475 ( 1428)
  covalent geometry    : bond        0.00225 ( 8260)
  covalent geometry    : angle       0.45832 (11248)

*********************** 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
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A 1063 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7785 (mtm)
REVERT: A 1157 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7322 (mt)
REVERT: A 1198 ARG cc_start: 0.7485 (mmm160) cc_final: 0.7234 (mtt180)
REVERT: A 1204 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6840 (mt-10)
REVERT: A 1206 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7713 (tt0)
REVERT: B  917 ARG cc_start: 0.7487 (mtp180) cc_final: 0.7115 (tpp-160)
REVERT: B 1203 ARG cc_start: 0.6094 (ttp-110) cc_final: 0.5181 (ptt-90)
  outliers start: 30
  outliers final: 20
  residues processed: 124
  average time/residue: 1.7444
  time to fit residues: 228.7686
Evaluate side-chains
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  939 MET
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1150 VAL
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  845 LYS
Chi-restraints excluded: chain B residue  939 MET
Chi-restraints excluded: chain B residue  999 LEU
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 99 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0670
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
B1076 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.168166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.132238 restraints weight = 8640.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.79
r_work: 0.3267 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8260  Z= 0.110
  Angle     :  0.464   5.794  11248  Z= 0.235
  Chirality :  0.039   0.131   1346
  Planarity :  0.005   0.047   1380
  Dihedral  :  3.295  16.080   1110
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.50 %
    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:  2.21 (0.27), residues: 1020
  helix:  2.29 (0.20), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.44 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 795 
 HIS   0.002   0.000   HIS A1025 
 PHE   0.014   0.001   PHE A 908 
 TYR   0.007   0.001   TYR A 844 
 ARG   0.010   0.000   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05043 (  488)
  hydrogen bonds       : angle       3.57900 ( 1428)
  covalent geometry    : bond        0.00246 ( 8260)
  covalent geometry    : angle       0.46443 (11248)

********************** 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
  124 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  817 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7826 (ttp-110)
REVERT: A 1063 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7652 (mtm)
REVERT: A 1067 ILE cc_start: 0.3772 (OUTLIER) cc_final: 0.3344 (mt)
REVERT: A 1157 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7123 (mt)
REVERT: A 1198 ARG cc_start: 0.7291 (mmm160) cc_final: 0.7021 (mtt180)
REVERT: A 1206 GLN cc_start: 0.7772 (tp-100) cc_final: 0.7564 (tt0)
REVERT: B  917 ARG cc_start: 0.7506 (mtp180) cc_final: 0.6971 (tpp-160)
REVERT: B 1203 ARG cc_start: 0.5957 (ttp-110) cc_final: 0.5078 (ptt-90)
  outliers start: 27
  outliers final: 21
  residues processed: 117
  average time/residue: 1.3121
  time to fit residues: 162.6563
Evaluate side-chains
  119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  755 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  939 MET
Chi-restraints excluded: chain A residue 1063 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1150 VAL
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1178 SER
Chi-restraints excluded: chain A residue 1195 LEU
Chi-restraints excluded: chain B residue  706 SER
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  845 LYS
Chi-restraints excluded: chain B residue  939 MET
Chi-restraints excluded: chain B residue  961 SER
Chi-restraints excluded: chain B residue  999 LEU
Chi-restraints excluded: chain B residue 1150 VAL
Chi-restraints excluded: chain B residue 1168 LEU
Chi-restraints excluded: chain B residue 1178 SER
Chi-restraints excluded: chain B residue 1195 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0010
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
A1074 GLN
B1076 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.166597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.130054 restraints weight = 8649.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.88
r_work: 0.3267 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8260  Z= 0.120
  Angle     :  0.477   5.919  11248  Z= 0.242
  Chirality :  0.039   0.125   1346
  Planarity :  0.005   0.048   1380
  Dihedral  :  3.352  15.917   1110
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.39 %
    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:  2.11 (0.27), residues: 1020
  helix:  2.18 (0.20), residues: 706
  sheet:  None (None), residues: 0
  loop : -0.41 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 795 
 HIS   0.002   0.000   HIS A1025 
 PHE   0.015   0.001   PHE B 822 
 TYR   0.007   0.001   TYR A 844 
 ARG   0.011   0.000   ARG A 817 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05553 (  488)
  hydrogen bonds       : angle       3.62730 ( 1428)
  covalent geometry    : bond        0.00275 ( 8260)
  covalent geometry    : angle       0.47739 (11248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6847.63 seconds
wall clock time: 118 minutes 20.88 seconds (7100.88 seconds total)