Starting phenix.real_space_refine
on Wed Mar 12 22:51:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ryc_24733/03_2025/7ryc_24733.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ryc_24733/03_2025/7ryc_24733.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ryc_24733/03_2025/7ryc_24733.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ryc_24733/03_2025/7ryc_24733.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ryc_24733/03_2025/7ryc_24733.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ryc_24733/03_2025/7ryc_24733.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.128
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 67 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      55      5.16       5
     C    5321      2.51       5
     N    1409      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8277
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "L"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 68
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "O"
      Number of atoms: 2097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2097
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 204
          Unresolved non-hydrogen angles: 251
          Unresolved non-hydrogen dihedrals: 169
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 133
    Chain: "D"
      Number of atoms: 1973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1973
          Classifications: {'peptide': 263}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 8, 'TRANS': 254}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 160
          Unresolved non-hydrogen angles: 189
          Unresolved non-hydrogen dihedrals: 131
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 103
    Chain: "C"
      Number of atoms: 2442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2442
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 161
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 126
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 108
    Chain: "E"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1695
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "O"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.77, per 1000 atoms: 0.70
  Number of scatterers: 8277
  At special positions: 0
  Unit cell: (89.4705, 124.407, 130.371, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      55     16.00
     Mg      1     11.99
     O    1491      8.00
     N    1409      7.00
     C    5321      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS L   1 " - pdb=" SG  CYS L   6 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 112 " - pdb=" SG  CYS O 187 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 976.3 milliseconds
  

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2114

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      35.8% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'O' and resid 35 through 67
      removed outlier: 3.740A  pdb=" N   GLU O  42 " --> pdb=" O   LEU O  38 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL O  43 " --> pdb=" O   ALA O  39 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA O  44 " --> pdb=" O   ARG O  40 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   CYS O  47 " --> pdb=" O   VAL O  43 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASN O  57 " --> pdb=" O   ALA O  53 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 74 through 92
    Processing helix  chain 'O' and resid 93 through 102
      removed outlier: 3.699A  pdb=" N   ASP O 100 " --> pdb=" O   GLN O  96 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 108 through 143
      removed outlier: 4.071A  pdb=" N   CYS O 112 " --> pdb=" O   PRO O 108 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   TYR O 117 " --> pdb=" O   ARG O 113 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   MET O 123 " --> pdb=" O   GLN O 119 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LEU O 130 " --> pdb=" O   SER O 126 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU O 131 " --> pdb=" O   THR O 127 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 149 through 168
      removed outlier: 4.632A  pdb=" N   VAL O 157 " --> pdb=" O   ASP O 153 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 170 through 174
    Processing helix  chain 'O' and resid 195 through 209
      removed outlier: 3.576A  pdb=" N   ALA O 199 " --> pdb=" O   TRP O 195 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 209 through 235
      removed outlier: 4.025A  pdb=" N   TYR O 220 " --> pdb=" O   LEU O 216 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER O 224 " --> pdb=" O   TYR O 220 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE O 225 " --> pdb=" O   GLY O 221 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   TRP O 228 " --> pdb=" O   SER O 224 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU O 231 " --> pdb=" O   ILE O 227 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ARG O 232 " --> pdb=" O   TRP O 228 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 273 through 299
      removed outlier: 4.224A  pdb=" N   ILE O 279 " --> pdb=" O   LYS O 275 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE O 280 " --> pdb=" O   MET O 276 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   PHE O 284 " --> pdb=" O   ILE O 280 " (cutoff:3.500A)
      Proline residue:  O 290  - end of helix
    Processing helix  chain 'O' and resid 308 through 316
      removed outlier: 3.695A  pdb=" N   ILE O 312 " --> pdb=" O   ALA O 308 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU O 316 " --> pdb=" O   ILE O 312 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 320 through 332
      removed outlier: 3.760A  pdb=" N   CYS O 324 " --> pdb=" O   LEU O 320 " (cutoff:3.500A)
      Proline residue:  O 326  - end of helix
    Processing helix  chain 'O' and resid 334 through 345
      removed outlier: 4.622A  pdb=" N   HIS O 338 " --> pdb=" O   GLY O 334 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 24
      removed outlier: 3.959A  pdb=" N   VAL D  16 " --> pdb=" O   ALA D  12 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 34
    Processing helix  chain 'D' and resid 34 through 44
      removed outlier: 3.556A  pdb=" N   ALA D  39 " --> pdb=" O   ALA D  35 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   TYR D  40 " --> pdb=" O   ASP D  36 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   CYS D  41 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLU D  42 " --> pdb=" O   MET D  38 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA D  43 " --> pdb=" O   ALA D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
      removed outlier: 3.794A  pdb=" N   ASP D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 48'
    Processing helix  chain 'D' and resid 1006 through 1031
      removed outlier: 3.849A  pdb=" N   ALA D1011 " --> pdb=" O   ALA D1007 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   MET D1018 " --> pdb=" O   GLU D1014 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ILE D1019 " --> pdb=" O   ARG D1015 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASP D1020 " --> pdb=" O   SER D1016 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LYS D1021 " --> pdb=" O   LYS D1017 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1045 through 1049
      removed outlier: 3.988A  pdb=" N   ILE D1049 " --> pdb=" O   LYS D1046 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1095 through 1099
      removed outlier: 3.706A  pdb=" N   GLN D1098 " --> pdb=" O   LYS D1095 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   CYS D1099 " --> pdb=" O   TRP D1096 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1095 through 1099'
    Processing helix  chain 'D' and resid 1117 through 1130
    Processing helix  chain 'D' and resid 1145 through 1156
      removed outlier: 3.957A  pdb=" N   LEU D1149 " --> pdb=" O   LYS D1145 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA D1150 " --> pdb=" O   GLN D1146 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU D1151 " --> pdb=" O   ASP D1147 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY D1156 " --> pdb=" O   LYS D1152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1159 through 1163
    Processing helix  chain 'D' and resid 1164 through 1169
      removed outlier: 3.685A  pdb=" N   ARG D1169 " --> pdb=" O   GLU D1166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1184 through 1204
      removed outlier: 3.858A  pdb=" N   PHE D1197 " --> pdb=" O   ILE D1193 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE D1200 " --> pdb=" O   GLU D1196 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   SER D1204 " --> pdb=" O   ILE D1200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1223 through 1240
      removed outlier: 4.118A  pdb=" N   ILE D1227 " --> pdb=" O   ASN D1223 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE D1228 " --> pdb=" O   ALA D1224 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP D1233 " --> pdb=" O   ASN D1229 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN D1237 " --> pdb=" O   ASP D1233 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU D1240 " --> pdb=" O   LEU D1236 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 24
      removed outlier: 4.277A  pdb=" N   GLU C  10 " --> pdb=" O   GLN C   6 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA C  11 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLU C  12 " --> pdb=" O   ARG C   8 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA C  24 " --> pdb=" O   ASP C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
      removed outlier: 3.742A  pdb=" N   ILE C  33 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.516A  pdb=" N   PHE E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'O' and resid 175 through 181
      removed outlier: 6.768A  pdb=" N   VAL O 184 " --> pdb=" O   VAL O 180 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 1070 through 1076
      removed outlier: 7.190A  pdb=" N   ARG D1035 " --> pdb=" O   ALA D1105 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   ILE D1107 " --> pdb=" O   ARG D1035 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LEU D1037 " --> pdb=" O   ILE D1107 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   VAL D1109 " --> pdb=" O   LEU D1037 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE D1106 " --> pdb=" O   ILE D1140 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   PHE D1142 " --> pdb=" O   ILE D1106 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE D1108 " --> pdb=" O   PHE D1142 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ASN D1144 " --> pdb=" O   PHE D1108 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL D1110 " --> pdb=" O   ASN D1144 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.681A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 7.139A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.844A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153
      removed outlier: 6.850A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.781A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA C 203 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.725A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   CYS C 250 " --> pdb=" O   TYR C 264 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.902A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.151A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ALA E  92 " --> pdb=" O   LEU E 117 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   VAL E  37 " --> pdb=" O   TYR E  95 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER E  99 " --> pdb=" O   GLY E  33 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 5.914A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195
      removed outlier: 5.858A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ILE E 189 " --> pdb=" O   TRP E 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 205 through 207
      removed outlier: 3.954A  pdb=" N   THR E 213 " --> pdb=" O   SER E 206 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    957 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: 2.32

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1849
        1.33 -     1.45: 1916
        1.45 -     1.58: 4613
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 8454
  Sorted by residual:
  bond pdb=" C   TRP O 203 "
       pdb=" N   ILE O 204 "
    ideal  model  delta    sigma   weight residual
    1.335  1.257  0.077 1.26e-02 6.30e+03 3.77e+01
  bond pdb=" C   LEU O 139 "
       pdb=" N   ALA O 140 "
    ideal  model  delta    sigma   weight residual
    1.334  1.423 -0.088 1.49e-02 4.50e+03 3.52e+01
  bond pdb=" C   VAL O 157 "
       pdb=" N   LEU O 158 "
    ideal  model  delta    sigma   weight residual
    1.335  1.256  0.079 1.36e-02 5.41e+03 3.35e+01
  bond pdb=" C   ARG D1117 "
       pdb=" N   LEU D1118 "
    ideal  model  delta    sigma   weight residual
    1.335  1.259  0.076 1.36e-02 5.41e+03 3.13e+01
  bond pdb=" C   LYS O 270 "
       pdb=" N   ILE O 271 "
    ideal  model  delta    sigma   weight residual
    1.332  1.257  0.075 1.36e-02 5.41e+03 3.01e+01
  ... (remaining 8449 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 10863
        1.71 -     3.42: 551
        3.42 -     5.13: 98
        5.13 -     6.84: 15
        6.84 -     8.55: 4
  Bond angle restraints: 11531
  Sorted by residual:
  angle pdb=" N   ILE O 101 "
        pdb=" CA  ILE O 101 "
        pdb=" C   ILE O 101 "
      ideal   model   delta    sigma   weight residual
     110.42  105.48    4.94 9.60e-01 1.09e+00 2.65e+01
  angle pdb=" O   VAL O 157 "
        pdb=" C   VAL O 157 "
        pdb=" N   LEU O 158 "
      ideal   model   delta    sigma   weight residual
     121.87  117.12    4.75 9.70e-01 1.06e+00 2.40e+01
  angle pdb=" N   CYS O 138 "
        pdb=" CA  CYS O 138 "
        pdb=" C   CYS O 138 "
      ideal   model   delta    sigma   weight residual
     111.28  116.47   -5.19 1.09e+00 8.42e-01 2.26e+01
  angle pdb=" O   TRP O 203 "
        pdb=" C   TRP O 203 "
        pdb=" N   ILE O 204 "
      ideal   model   delta    sigma   weight residual
     122.07  117.40    4.67 1.03e+00 9.43e-01 2.05e+01
  angle pdb=" N   ARG O  73 "
        pdb=" CA  ARG O  73 "
        pdb=" C   ARG O  73 "
      ideal   model   delta    sigma   weight residual
     112.97  108.37    4.60 1.06e+00 8.90e-01 1.88e+01
  ... (remaining 11526 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 4411
       15.92 -    31.83: 388
       31.83 -    47.75: 103
       47.75 -    63.66: 23
       63.66 -    79.58: 6
  Dihedral angle restraints: 4931
    sinusoidal: 1668
      harmonic: 3263
  Sorted by residual:
  dihedral pdb=" CB  CYS O 112 "
           pdb=" SG  CYS O 112 "
           pdb=" SG  CYS O 187 "
           pdb=" CB  CYS O 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.54  -68.54     1      1.00e+01 1.00e-02 6.09e+01
  dihedral pdb=" CA  ARG D1032 "
           pdb=" C   ARG D1032 "
           pdb=" N   THR D1033 "
           pdb=" CA  THR D1033 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.44  -25.56     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  ARG D1031 "
           pdb=" C   ARG D1031 "
           pdb=" N   ARG D1032 "
           pdb=" CA  ARG D1032 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.50  -24.50     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 4928 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1014
       0.052 -    0.104: 248
       0.104 -    0.156: 73
       0.156 -    0.208: 16
       0.208 -    0.260: 6
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CA  ILE O 101 "
            pdb=" N   ILE O 101 "
            pdb=" C   ILE O 101 "
            pdb=" CB  ILE O 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  LEU C 210 "
            pdb=" N   LEU C 210 "
            pdb=" C   LEU C 210 "
            pdb=" CB  LEU C 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  ILE E 216 "
            pdb=" N   ILE E 216 "
            pdb=" C   ILE E 216 "
            pdb=" CB  ILE E 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1354 not shown)

  Planarity restraints: 1454
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS O 270 "   -0.013 2.00e-02 2.50e+03   2.45e-02 6.00e+00
        pdb=" C   LYS O 270 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LYS O 270 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE O 271 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU O 139 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.02e+00
        pdb=" C   LEU O 139 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU O 139 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ALA O 140 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL O 294 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.14e+00
        pdb=" C   VAL O 294 "    0.031 2.00e-02 2.50e+03
        pdb=" O   VAL O 294 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN O 295 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1451 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 659
        2.74 -     3.28: 7570
        3.28 -     3.82: 11897
        3.82 -     4.36: 14432
        4.36 -     4.90: 25748
  Nonbonded interactions: 60306
  Sorted by model distance:
  nonbonded pdb=" O   ASP D1233 "
            pdb=" OD1 ASP D1233 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   ASP C 333 "
            pdb=" OG  SER C 334 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OD1 ASP O 100 "
            pdb="MG    MG O 401 "
     model   vdw
     2.281 2.170
  nonbonded pdb=" O   SER E  52 "
            pdb=" NH1 ARG E  72 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   GLN D1119 "
            pdb=" ND2 ASN D1123 "
     model   vdw
     2.312 3.120
  ... (remaining 60301 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.930
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  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:14.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
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      :  0.006   0.088   8454  Z= 0.408
  Angle     :  0.864   8.554  11531  Z= 0.575
  Chirality :  0.053   0.260   1357
  Planarity :  0.004   0.044   1454
  Dihedral  : 13.762  79.578   2808
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 13.50 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -2.98 (0.22), residues: 1099
  helix: -1.76 (0.25), residues: 346
  sheet: -1.30 (0.31), residues: 247
  loop : -2.44 (0.22), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  36 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.018   0.002   PHE C 235 
 TYR   0.018   0.002   TYR L   2 
 ARG   0.002   0.000   ARG O 104 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 140
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 LYS cc_start: 0.5538 (mttt) cc_final: 0.5282 (tmmt)
REVERT: D 1018 MET cc_start: 0.6654 (mtp) cc_final: 0.6424 (mtt)
REVERT: C  154 ASP cc_start: 0.7708 (m-30) cc_final: 0.7445 (m-30)
REVERT: C  188 MET cc_start: 0.8859 (mmp) cc_final: 0.8581 (mmm)
REVERT: C  258 ASP cc_start: 0.7636 (t0) cc_final: 0.7231 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 143
  average time/residue: 1.3133
  time to fit residues: 198.6706
Evaluate side-chains
  96 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue  296 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.2980
   chunk 84 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0040
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    0.4980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
O 171 GLN
D  59 ASN
C 176 GLN
E 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.133094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.109952 restraints weight = 14133.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 3.04
r_work: 0.3332 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8454  Z= 0.158
  Angle     :  0.577   9.035  11531  Z= 0.303
  Chirality :  0.042   0.153   1357
  Planarity :  0.004   0.033   1454
  Dihedral  :  4.763  51.546   1198
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 18.38 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.83 (0.24), residues: 1099
  helix: -0.29 (0.28), residues: 341
  sheet: -0.68 (0.30), residues: 278
  loop : -2.21 (0.24), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP O 300 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.009   0.001   PHE C 151 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.003   0.000   ARG C  49 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
REVERT: O  123 MET cc_start: 0.6671 (ttm) cc_final: 0.6376 (mtp)
REVERT: D   29 LYS cc_start: 0.5249 (mttt) cc_final: 0.4908 (tmmt)
REVERT: D 1018 MET cc_start: 0.6318 (mtp) cc_final: 0.6096 (mtt)
REVERT: C  154 ASP cc_start: 0.7638 (m-30) cc_final: 0.7381 (m-30)
REVERT: C  258 ASP cc_start: 0.7685 (t0) cc_final: 0.7122 (t0)
REVERT: E   69 THR cc_start: 0.6185 (OUTLIER) cc_final: 0.5854 (m)
  outliers start: 11
  outliers final: 3
  residues processed: 113
  average time/residue: 1.9332
  time to fit residues: 231.2396
Evaluate side-chains
  112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain E residue   69 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 54 optimal weight:    0.0020
   chunk 14 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
O 295 GLN
D  59 ASN
C 183 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.129796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.106482 restraints weight = 14433.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 3.05
r_work: 0.3271 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8454  Z= 0.269
  Angle     :  0.628   9.279  11531  Z= 0.328
  Chirality :  0.043   0.151   1357
  Planarity :  0.004   0.045   1454
  Dihedral  :  4.700  47.822   1195
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.62 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.58 (0.24), residues: 1099
  helix: -0.10 (0.27), residues: 350
  sheet: -0.74 (0.30), residues: 290
  loop : -1.95 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  82 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.016   0.002   PHE O  76 
 TYR   0.018   0.002   TYR L   2 
 ARG   0.006   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 LYS cc_start: 0.5296 (mttt) cc_final: 0.4899 (ttmt)
REVERT: D 1229 ASN cc_start: 0.7609 (t0) cc_final: 0.7291 (t0)
REVERT: D 1244 ASN cc_start: 0.8718 (t0) cc_final: 0.8453 (t0)
REVERT: C  154 ASP cc_start: 0.7651 (m-30) cc_final: 0.7412 (m-30)
REVERT: C  188 MET cc_start: 0.8879 (mmp) cc_final: 0.8647 (mmm)
REVERT: C  226 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7170 (mp0)
REVERT: C  258 ASP cc_start: 0.7720 (t0) cc_final: 0.7166 (t0)
REVERT: E   69 THR cc_start: 0.6261 (OUTLIER) cc_final: 0.5936 (m)
REVERT: E  158 SER cc_start: 0.7751 (t) cc_final: 0.7479 (m)
  outliers start: 27
  outliers final: 11
  residues processed: 128
  average time/residue: 1.1810
  time to fit residues: 161.1651
Evaluate side-chains
  118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 CYS
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue   66 THR
Chi-restraints excluded: chain O residue  299 VAL
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain D residue 1201 SER
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  192 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 75 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0050
   chunk 81 optimal weight:    0.2980
   chunk 56 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 74 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.2594

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

Flipped N/Q/H residues before XYZ refinement:
D  59 ASN
D1080 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.133853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.110801 restraints weight = 14356.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 3.14
r_work: 0.3347 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8454  Z= 0.128
  Angle     :  0.511   7.787  11531  Z= 0.265
  Chirality :  0.040   0.138   1357
  Planarity :  0.003   0.033   1454
  Dihedral  :  4.238  45.881   1195
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.75 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.25), residues: 1099
  helix:  0.57 (0.28), residues: 348
  sheet: -0.39 (0.30), residues: 291
  loop : -1.75 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  36 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.009   0.001   PHE D1074 
 TYR   0.016   0.001   TYR L   2 
 ARG   0.006   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 LYS cc_start: 0.5212 (mttt) cc_final: 0.4868 (ttmt)
REVERT: D 1018 MET cc_start: 0.6444 (mtp) cc_final: 0.6218 (mtt)
REVERT: D 1024 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6999 (ttp80)
REVERT: D 1229 ASN cc_start: 0.7541 (t0) cc_final: 0.7249 (t0)
REVERT: C  154 ASP cc_start: 0.7595 (m-30) cc_final: 0.7382 (m-30)
REVERT: C  226 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7137 (mp0)
REVERT: C  258 ASP cc_start: 0.7629 (t0) cc_final: 0.7047 (t0)
REVERT: E   69 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.5736 (m)
REVERT: E  158 SER cc_start: 0.7588 (t) cc_final: 0.7384 (m)
  outliers start: 22
  outliers final: 5
  residues processed: 136
  average time/residue: 1.2516
  time to fit residues: 180.6987
Evaluate side-chains
  114 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 CYS
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   69 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D1131 ASN
C  75 GLN
C 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.131401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.107973 restraints weight = 14217.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.99
r_work: 0.3304 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8454  Z= 0.205
  Angle     :  0.572   9.923  11531  Z= 0.296
  Chirality :  0.042   0.138   1357
  Planarity :  0.003   0.039   1454
  Dihedral  :  4.322  45.988   1195
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 19.50 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.25), residues: 1099
  helix:  0.56 (0.28), residues: 358
  sheet: -0.31 (0.31), residues: 290
  loop : -1.68 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  82 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.014   0.002   PHE O  76 
 TYR   0.014   0.001   TYR L   2 
 ARG   0.006   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 LYS cc_start: 0.5186 (mttt) cc_final: 0.4923 (ttpt)
REVERT: D 1018 MET cc_start: 0.6625 (mtp) cc_final: 0.6193 (mtt)
REVERT: D 1229 ASN cc_start: 0.7540 (t0) cc_final: 0.7246 (t0)
REVERT: C  154 ASP cc_start: 0.7622 (m-30) cc_final: 0.7413 (m-30)
REVERT: C  226 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7136 (mp0)
REVERT: C  258 ASP cc_start: 0.7719 (t0) cc_final: 0.7219 (t0)
REVERT: E   69 THR cc_start: 0.6224 (OUTLIER) cc_final: 0.5978 (m)
  outliers start: 33
  outliers final: 13
  residues processed: 135
  average time/residue: 1.2188
  time to fit residues: 175.0206
Evaluate side-chains
  124 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 CYS
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue   66 THR
Chi-restraints excluded: chain O residue  299 VAL
Chi-restraints excluded: chain O residue  313 ILE
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain D residue 1201 SER
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  186 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0010
   chunk 37 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0970
   chunk 7 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 105 optimal weight:    0.2980
   overall best weight:    0.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.133242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.110036 restraints weight = 14213.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 3.08
r_work: 0.3333 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8454  Z= 0.144
  Angle     :  0.524   8.202  11531  Z= 0.271
  Chirality :  0.041   0.132   1357
  Planarity :  0.003   0.036   1454
  Dihedral  :  4.148  44.449   1195
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.88 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1099
  helix:  0.88 (0.28), residues: 354
  sheet: -0.01 (0.32), residues: 279
  loop : -1.56 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  36 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.010   0.001   PHE O  76 
 TYR   0.014   0.001   TYR L   2 
 ARG   0.005   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: D   29 LYS cc_start: 0.5157 (mttt) cc_final: 0.4926 (ttpt)
REVERT: D   36 ASP cc_start: 0.7987 (t70) cc_final: 0.7603 (t0)
REVERT: D 1018 MET cc_start: 0.6493 (mtp) cc_final: 0.6171 (mtt)
REVERT: D 1024 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6871 (ttp80)
REVERT: D 1229 ASN cc_start: 0.7553 (t0) cc_final: 0.7271 (t0)
REVERT: C   78 LYS cc_start: 0.9080 (mmtp) cc_final: 0.8842 (mmtt)
REVERT: C  226 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7146 (mp0)
REVERT: C  258 ASP cc_start: 0.7616 (t0) cc_final: 0.7159 (t0)
REVERT: E   69 THR cc_start: 0.6123 (OUTLIER) cc_final: 0.5872 (m)
  outliers start: 19
  outliers final: 8
  residues processed: 126
  average time/residue: 1.2519
  time to fit residues: 167.5828
Evaluate side-chains
  113 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 CYS
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   69 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 106 optimal weight:    0.2980
   chunk 82 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D1244 ASN
C 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.132403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.109100 restraints weight = 14379.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 3.05
r_work: 0.3319 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8454  Z= 0.171
  Angle     :  0.548  10.206  11531  Z= 0.283
  Chirality :  0.041   0.135   1357
  Planarity :  0.003   0.038   1454
  Dihedral  :  4.164  42.281   1195
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 22.12 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.25), residues: 1099
  helix:  0.91 (0.28), residues: 356
  sheet: -0.08 (0.32), residues: 285
  loop : -1.47 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 332 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.015   0.001   PHE E  68 
 TYR   0.014   0.001   TYR L   2 
 ARG   0.007   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.955 
Fit side-chains
REVERT: D   29 LYS cc_start: 0.5186 (mttt) cc_final: 0.4946 (ttpt)
REVERT: D   36 ASP cc_start: 0.7967 (t70) cc_final: 0.7581 (t0)
REVERT: D 1018 MET cc_start: 0.6596 (mtp) cc_final: 0.6227 (mtt)
REVERT: D 1229 ASN cc_start: 0.7560 (t0) cc_final: 0.7268 (t0)
REVERT: C   78 LYS cc_start: 0.9111 (mmtp) cc_final: 0.8839 (mmtt)
REVERT: C  226 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7172 (mp0)
REVERT: C  258 ASP cc_start: 0.7597 (t0) cc_final: 0.7247 (t0)
REVERT: E   69 THR cc_start: 0.6244 (OUTLIER) cc_final: 0.5985 (m)
REVERT: E   87 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8224 (mtp180)
  outliers start: 22
  outliers final: 9
  residues processed: 124
  average time/residue: 1.3033
  time to fit residues: 171.7830
Evaluate side-chains
  115 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue  299 VAL
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain D residue 1118 LEU
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  186 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
D1244 ASN
C  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.130472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.101340 restraints weight = 14445.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.44
r_work: 0.3316 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8454  Z= 0.249
  Angle     :  0.603   9.253  11531  Z= 0.315
  Chirality :  0.043   0.136   1357
  Planarity :  0.004   0.043   1454
  Dihedral  :  4.364  40.398   1195
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 23.00 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1099
  helix:  0.76 (0.28), residues: 360
  sheet: -0.22 (0.31), residues: 297
  loop : -1.50 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 332 
 HIS   0.005   0.002   HIS C 225 
 PHE   0.016   0.002   PHE E  68 
 TYR   0.015   0.002   TYR L   2 
 ARG   0.007   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.879 
Fit side-chains
REVERT: D   29 LYS cc_start: 0.5183 (mttt) cc_final: 0.4826 (mptt)
REVERT: D   36 ASP cc_start: 0.7995 (t70) cc_final: 0.7627 (t0)
REVERT: D 1229 ASN cc_start: 0.7678 (t0) cc_final: 0.7405 (t0)
REVERT: C  226 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7367 (mp0)
REVERT: C  258 ASP cc_start: 0.7829 (t0) cc_final: 0.7510 (t0)
REVERT: E   69 THR cc_start: 0.6394 (OUTLIER) cc_final: 0.6054 (m)
REVERT: E   87 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7963 (mtp180)
  outliers start: 21
  outliers final: 13
  residues processed: 121
  average time/residue: 1.3181
  time to fit residues: 169.2267
Evaluate side-chains
  119 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue  204 ILE
Chi-restraints excluded: chain O residue  206 LEU
Chi-restraints excluded: chain O residue  299 VAL
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain D residue 1118 LEU
Chi-restraints excluded: chain D residue 1198 VAL
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  186 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 101 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D1244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.131337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.107963 restraints weight = 14343.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 3.01
r_work: 0.3307 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8454  Z= 0.193
  Angle     :  0.565   9.082  11531  Z= 0.295
  Chirality :  0.041   0.133   1357
  Planarity :  0.003   0.041   1454
  Dihedral  :  4.248  38.090   1195
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 23.75 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1099
  helix:  0.98 (0.28), residues: 355
  sheet: -0.16 (0.31), residues: 297
  loop : -1.43 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 332 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.014   0.002   PHE E  68 
 TYR   0.018   0.001   TYR L   2 
 ARG   0.007   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.850 
Fit side-chains
REVERT: D   29 LYS cc_start: 0.5225 (mttt) cc_final: 0.4866 (mptt)
REVERT: D   36 ASP cc_start: 0.7967 (t70) cc_final: 0.7603 (t0)
REVERT: D 1018 MET cc_start: 0.6549 (mtp) cc_final: 0.6163 (mtt)
REVERT: D 1229 ASN cc_start: 0.7609 (t0) cc_final: 0.7326 (t0)
REVERT: C  226 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7259 (mp0)
REVERT: C  258 ASP cc_start: 0.7734 (t0) cc_final: 0.7328 (t0)
REVERT: E   69 THR cc_start: 0.6255 (OUTLIER) cc_final: 0.5985 (m)
REVERT: E   87 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7860 (mtp180)
REVERT: E  158 SER cc_start: 0.7702 (t) cc_final: 0.7356 (m)
  outliers start: 19
  outliers final: 12
  residues processed: 121
  average time/residue: 1.2756
  time to fit residues: 164.0403
Evaluate side-chains
  117 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 ASN
Chi-restraints excluded: chain L residue    6 CYS
Chi-restraints excluded: chain O residue  299 VAL
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain D residue 1118 LEU
Chi-restraints excluded: chain D residue 1198 VAL
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  186 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    0.0170
   chunk 73 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
D1244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.132361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.109153 restraints weight = 14232.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 3.03
r_work: 0.3326 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8454  Z= 0.168
  Angle     :  0.544   8.921  11531  Z= 0.283
  Chirality :  0.041   0.137   1357
  Planarity :  0.003   0.038   1454
  Dihedral  :  4.093  34.938   1195
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 24.25 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.25), residues: 1099
  helix:  1.12 (0.28), residues: 357
  sheet: -0.05 (0.31), residues: 291
  loop : -1.39 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 332 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.012   0.001   PHE E  68 
 TYR   0.024   0.001   TYR L   2 
 ARG   0.007   0.000   ARG C 137 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.890 
Fit side-chains
REVERT: D   29 LYS cc_start: 0.5241 (mttt) cc_final: 0.4863 (mptt)
REVERT: D   42 GLU cc_start: 0.7786 (tt0) cc_final: 0.7494 (tp30)
REVERT: D 1018 MET cc_start: 0.6498 (mtp) cc_final: 0.6154 (mtt)
REVERT: D 1229 ASN cc_start: 0.7590 (t0) cc_final: 0.7303 (t0)
REVERT: C  226 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7265 (mp0)
REVERT: C  258 ASP cc_start: 0.7662 (t0) cc_final: 0.7300 (t0)
REVERT: E   69 THR cc_start: 0.6198 (OUTLIER) cc_final: 0.5948 (m)
REVERT: E   87 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7848 (mtp180)
REVERT: E  158 SER cc_start: 0.7667 (t) cc_final: 0.7346 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 119
  average time/residue: 1.2620
  time to fit residues: 159.5223
Evaluate side-chains
  119 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 ASN
Chi-restraints excluded: chain O residue  204 ILE
Chi-restraints excluded: chain O residue  206 LEU
Chi-restraints excluded: chain O residue  315 MET
Chi-restraints excluded: chain D residue 1082 HIS
Chi-restraints excluded: chain D residue 1198 VAL
Chi-restraints excluded: chain D residue 1246 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  186 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7486 > 50:
  distance: 75 - 157:  28.556
  distance: 78 - 154:  28.169
  distance: 89 - 142:  34.203
  distance: 92 - 139:  31.504
  distance: 115 - 120:  34.028
  distance: 120 - 121:  40.597
  distance: 121 - 122:  56.573
  distance: 121 - 124:  15.514
  distance: 122 - 123:  40.187
  distance: 122 - 125:  40.694
  distance: 125 - 126:   5.540
  distance: 126 - 127:  32.958
  distance: 126 - 129:  28.062
  distance: 127 - 128:  21.208
  distance: 127 - 133:  39.120
  distance: 129 - 130:  43.607
  distance: 130 - 131:  18.798
  distance: 130 - 132:  34.790
  distance: 133 - 134:  14.249
  distance: 134 - 135:  31.947
  distance: 134 - 137:  13.407
  distance: 135 - 136:  24.530
  distance: 135 - 139:  36.357
  distance: 137 - 138:  18.578
  distance: 139 - 140:   9.983
  distance: 140 - 141:  13.786
  distance: 140 - 143:   9.792
  distance: 141 - 142:  21.621
  distance: 141 - 147:  15.310
  distance: 143 - 144:  37.432
  distance: 144 - 145:  28.274
  distance: 144 - 146:  14.727
  distance: 147 - 148:  33.188
  distance: 148 - 149:  25.364
  distance: 148 - 151:  23.662
  distance: 149 - 150:   7.005
  distance: 149 - 154:  24.042
  distance: 150 - 218:  33.450
  distance: 151 - 152:  27.377
  distance: 154 - 155:   9.557
  distance: 155 - 156:  19.787
  distance: 155 - 158:   7.194
  distance: 156 - 157:  13.156
  distance: 156 - 168:  12.757
  distance: 158 - 159:  16.660
  distance: 159 - 160:  12.473
  distance: 160 - 162:   3.826
  distance: 161 - 163:  10.444
  distance: 161 - 164:   9.048
  distance: 162 - 163:   6.284
  distance: 163 - 165:   9.653
  distance: 164 - 166:  23.954
  distance: 165 - 167:  24.334
  distance: 166 - 167:  18.832
  distance: 168 - 169:  11.992
  distance: 169 - 170:  22.160
  distance: 169 - 172:  19.177
  distance: 170 - 171:   8.757
  distance: 170 - 176:  37.361
  distance: 172 - 173:  19.621
  distance: 173 - 174:  19.616
  distance: 173 - 175:  15.403
  distance: 176 - 177:  15.239
  distance: 177 - 178:  37.418
  distance: 177 - 180:  16.275
  distance: 178 - 179:   4.211
  distance: 178 - 181:  40.758
  distance: 181 - 182:  34.093
  distance: 182 - 183:  45.614
  distance: 182 - 185:  21.842
  distance: 183 - 184:   7.296
  distance: 183 - 189:  47.499
  distance: 186 - 188:  37.194
  distance: 189 - 190:  14.764
  distance: 190 - 191:  42.977
  distance: 190 - 193:  21.261
  distance: 191 - 198:  34.039
  distance: 193 - 194:  33.341
  distance: 194 - 195:  39.468
  distance: 195 - 196:  41.870
  distance: 196 - 197:  13.190