Starting phenix.real_space_refine
on Sat Jun 14 03:33:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bi4_44558/06_2025/9bi4_44558_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bi4_44558/06_2025/9bi4_44558.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bi4_44558/06_2025/9bi4_44558.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bi4_44558/06_2025/9bi4_44558.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bi4_44558/06_2025/9bi4_44558_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bi4_44558/06_2025/9bi4_44558_neut.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.086
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      50      5.49       5
     Mg      2      5.21       5
     S      75      5.16       5
     C    9861      2.51       5
     N    2729      2.21       5
     O    3148      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15869
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 3620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3620
          Classifications: {'peptide': 453}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 443}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "D"
      Number of atoms: 3676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 3676
          Classifications: {'peptide': 459}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 449}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 3748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3748
          Classifications: {'peptide': 476}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 28, 'TRANS': 447}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "E"
      Number of atoms: 462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 462
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "A"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3855
          Classifications: {'peptide': 493}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 28, 'TRANS': 464}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 38
    Chain: "F"
      Number of atoms: 440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 440
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 9.77, per 1000 atoms: 0.62
  Number of scatterers: 15869
  At special positions: 0
  Unit cell: (93.138, 100.719, 186.276, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      4     24.99
     S      75     16.00
     P      50     15.00
     Mg      2     11.99
     O    3148      8.00
     N    2729      7.00
     C    9861      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.89
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3582

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 17 sheets defined
      42.2% alpha, 18.8% beta
      17 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 5.26
  Creating SS restraints...
    Processing helix  chain 'C' and resid 39 through 52
      removed outlier: 3.898A  pdb=" N   ILE C  44 " --> pdb=" O   LYS C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 72
    Processing helix  chain 'C' and resid 131 through 144
      removed outlier: 3.938A  pdb=" N   ALA C 137 " --> pdb=" O   LEU C 133 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL C 139 " --> pdb=" O   LEU C 135 " (cutoff:3.500A)
      Proline residue:  C 140  - end of helix
    Processing helix  chain 'C' and resid 146 through 153
      removed outlier: 3.581A  pdb=" N   GLU C 151 " --> pdb=" O   LYS C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 179
      removed outlier: 3.769A  pdb=" N   GLU C 177 " --> pdb=" O   LYS C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 239
      removed outlier: 3.604A  pdb=" N   LYS C 195 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   ASP C 197 " --> pdb=" O   SER C 193 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET C 198 " --> pdb=" O   ILE C 194 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLN C 207 " --> pdb=" O   LYS C 203 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   SER C 219 " --> pdb=" O   ASP C 215 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LYS C 220 " --> pdb=" O   LYS C 216 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ALA C 221 " --> pdb=" O   ASP C 217 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   MET C 222 " --> pdb=" O   ARG C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1090 through 1102
    Processing helix  chain 'C' and resid 1108 through 1145
      removed outlier: 3.810A  pdb=" N   ASP C1125 " --> pdb=" O   SER C1121 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE C1138 " --> pdb=" O   LEU C1134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1146 through 1161
      removed outlier: 3.555A  pdb=" N   ILE C1152 " --> pdb=" O   ASP C1148 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU C1155 " --> pdb=" O   ARG C1151 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ARG C1159 " --> pdb=" O   GLU C1155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1205 through 1222
      removed outlier: 3.581A  pdb=" N   GLU C1222 " --> pdb=" O   LEU C1218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1241 through 1259
    Processing helix  chain 'C' and resid 1273 through 1280
      removed outlier: 4.199A  pdb=" N   LEU C1277 " --> pdb=" O   ASP C1273 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY C1278 " --> pdb=" O   GLU C1274 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   HIS C1279 " --> pdb=" O   LYS C1275 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   MET C1280 " --> pdb=" O   PHE C1276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1273 through 1280'
    Processing helix  chain 'C' and resid 1281 through 1286
      removed outlier: 3.561A  pdb=" N   PHE C1285 " --> pdb=" O   ASN C1281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1308 through 1310
      No H-bonds generated for 'chain 'C' and resid 1308 through 1310'
    Processing helix  chain 'D' and resid 39 through 52
      removed outlier: 3.799A  pdb=" N   ILE D  44 " --> pdb=" O   LYS D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 72
      removed outlier: 3.918A  pdb=" N   THR D  71 " --> pdb=" O   ASP D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 144
      removed outlier: 3.727A  pdb=" N   ALA D 137 " --> pdb=" O   LEU D 133 " (cutoff:3.500A)
      Proline residue:  D 140  - end of helix
    Processing helix  chain 'D' and resid 146 through 153
      removed outlier: 3.663A  pdb=" N   LEU D 150 " --> pdb=" O   PRO D 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 166
      removed outlier: 3.592A  pdb=" N   LEU D 165 " --> pdb=" O   LEU D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 179
      removed outlier: 3.738A  pdb=" N   GLU D 177 " --> pdb=" O   LYS D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 218
      removed outlier: 3.536A  pdb=" N   THR D 185 " --> pdb=" O   ALA D 181 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS D 195 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ASP D 197 " --> pdb=" O   SER D 193 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 239
    Processing helix  chain 'D' and resid 1090 through 1102
    Processing helix  chain 'D' and resid 1106 through 1135
      removed outlier: 3.566A  pdb=" N   TYR D1110 " --> pdb=" O   ILE D1106 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   HIS D1111 " --> pdb=" O   GLU D1107 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR D1130 " --> pdb=" O   ASP D1126 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA D1133 " --> pdb=" O   VAL D1129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1135 through 1146
      removed outlier: 3.932A  pdb=" N   TYR D1141 " --> pdb=" O   ALA D1137 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU D1144 " --> pdb=" O   LYS D1140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1147 through 1159
      removed outlier: 3.567A  pdb=" N   ARG D1151 " --> pdb=" O   GLN D1147 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE D1152 " --> pdb=" O   ASP D1148 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU D1155 " --> pdb=" O   ARG D1151 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS D1158 " --> pdb=" O   ASP D1154 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG D1159 " --> pdb=" O   GLU D1155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1207 through 1224
      removed outlier: 3.595A  pdb=" N   GLU D1222 " --> pdb=" O   LEU D1218 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   THR D1223 " --> pdb=" O   ALA D1219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1241 through 1261
      removed outlier: 3.788A  pdb=" N   HIS D1261 " --> pdb=" O   ASN D1257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1273 through 1281
      removed outlier: 3.850A  pdb=" N   LEU D1277 " --> pdb=" O   ASP D1273 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASN D1281 " --> pdb=" O   LEU D1277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1282 through 1285
    Processing helix  chain 'D' and resid 1308 through 1310
      No H-bonds generated for 'chain 'D' and resid 1308 through 1310'
    Processing helix  chain 'B' and resid 30 through 45
      removed outlier: 3.665A  pdb=" N   LYS B  44 " --> pdb=" O   MET B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 79
      removed outlier: 3.890A  pdb=" N   THR B  74 " --> pdb=" O   GLN B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 96
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 137 through 143
      removed outlier: 3.927A  pdb=" N   THR B 143 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 191
      removed outlier: 3.980A  pdb=" N   ASP B 191 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 276
      removed outlier: 3.627A  pdb=" N   ALA B 275 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN B 276 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 272 through 276'
    Processing helix  chain 'B' and resid 312 through 314
      No H-bonds generated for 'chain 'B' and resid 312 through 314'
    Processing helix  chain 'B' and resid 324 through 349
      removed outlier: 3.750A  pdb=" N   TYR B 328 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   MET B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 392
    Processing helix  chain 'B' and resid 393 through 395
      No H-bonds generated for 'chain 'B' and resid 393 through 395'
    Processing helix  chain 'B' and resid 446 through 451
    Processing helix  chain 'B' and resid 463 through 477
      removed outlier: 3.509A  pdb=" N   PHE B 474 " --> pdb=" O   ALA B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 500
    Processing helix  chain 'B' and resid 501 through 506
      removed outlier: 3.581A  pdb=" N   LEU B 505 " --> pdb=" O   GLU B 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 45
      removed outlier: 3.621A  pdb=" N   THR A  35 " --> pdb=" O   ASP A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 78
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 4.182A  pdb=" N   VAL A  96 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 135 through 143
      removed outlier: 3.755A  pdb=" N   ILE A 139 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 140 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 191
      removed outlier: 4.703A  pdb=" N   ARG A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 276
      removed outlier: 4.094A  pdb=" N   GLN A 276 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 349
      removed outlier: 3.612A  pdb=" N   GLU A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 340 " --> pdb=" O   MET A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 393
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 449 through 458
      removed outlier: 4.343A  pdb=" N   LEU A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   GLN A 458 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 477
      removed outlier: 3.518A  pdb=" N   PHE A 474 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 491
      removed outlier: 4.027A  pdb=" N   PHE A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLU A 490 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 500
      removed outlier: 3.610A  pdb=" N   GLY A 496 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LEU A 498 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 506
      removed outlier: 3.582A  pdb=" N   LEU A 505 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 522
    Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 24
      removed outlier: 6.536A  pdb=" N   ALA C  83 " --> pdb=" O   TYR C   5 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   LEU C   7 " --> pdb=" O   LYS C  81 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LYS C  81 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ILE C   9 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   GLN C  79 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 21 through 24
      removed outlier: 6.536A  pdb=" N   ALA C  83 " --> pdb=" O   TYR C   5 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   LEU C   7 " --> pdb=" O   LYS C  81 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LYS C  81 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ILE C   9 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   GLN C  79 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ASN C  91 " --> pdb=" O   ILE C 119 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   LEU C 116 " --> pdb=" O   LEU C 128 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 1230 through 1234
      removed outlier: 6.351A  pdb=" N   THR C  30 " --> pdb=" O   VAL C1269 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   HIS C1288 " --> pdb=" O   LEU C  29 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   LEU C  31 " --> pdb=" O   HIS C1288 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 1230 through 1234
      removed outlier: 6.351A  pdb=" N   THR C  30 " --> pdb=" O   VAL C1269 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   HIS C1288 " --> pdb=" O   LEU C  29 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   LEU C  31 " --> pdb=" O   HIS C1288 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 1170 through 1173
    Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 24
      removed outlier: 6.693A  pdb=" N   ALA D  83 " --> pdb=" O   TYR D   5 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LEU D   7 " --> pdb=" O   LYS D  81 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LYS D  81 " --> pdb=" O   LEU D   7 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ILE D   9 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   GLN D  79 " --> pdb=" O   ILE D   9 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE D  76 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 21 through 24
      removed outlier: 6.693A  pdb=" N   ALA D  83 " --> pdb=" O   TYR D   5 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LEU D   7 " --> pdb=" O   LYS D  81 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LYS D  81 " --> pdb=" O   LEU D   7 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ILE D   9 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   GLN D  79 " --> pdb=" O   ILE D   9 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE D  76 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU D 116 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 1230 through 1234
      removed outlier: 6.283A  pdb=" N   THR D  30 " --> pdb=" O   VAL D1269 " (cutoff:3.500A)
      removed outlier: 8.594A  pdb=" N   LEU D  29 " --> pdb=" O   HIS D1288 " (cutoff:3.500A)
      removed outlier: 8.473A  pdb=" N   PHE D1290 " --> pdb=" O   LEU D  29 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LEU D  31 " --> pdb=" O   PHE D1290 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   VAL D1292 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL D  33 " --> pdb=" O   VAL D1292 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   ARG D1294 " --> pdb=" O   VAL D  33 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL D1305 " --> pdb=" O   PHE D1289 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 1170 through 1174
    Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 148
      removed outlier: 6.755A  pdb=" N   VAL B 118 " --> pdb=" O   ASN B 147 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   VAL B  51 " --> pdb=" O   PHE B 119 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   MET B  50 " --> pdb=" O   THR B   8 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ARG B  10 " --> pdb=" O   MET B  50 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   VAL B  52 " --> pdb=" O   ARG B  10 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   LEU B  12 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS B 292 " --> pdb=" O   ASP B 284 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 160
    Processing sheet with id=AB3, first strand: chain 'B' and resid 163 through 167
      removed outlier: 8.730A  pdb=" N   MET B 236 " --> pdb=" O   TRP B 206 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ASN B 208 " --> pdb=" O   MET B 236 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   ILE B 238 " --> pdb=" O   ASN B 208 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   MET B 210 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   VAL B 237 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   GLN B 261 " --> pdb=" O   ASN B 248 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ASN B 248 " --> pdb=" O   GLN B 261 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 304 through 310
      removed outlier: 7.809A  pdb=" N   GLN B 407 " --> pdb=" O   ILE B 365 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU B 367 " --> pdb=" O   GLN B 407 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   TYR B 409 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL B 369 " --> pdb=" O   TYR B 409 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 50 through 53
      removed outlier: 8.278A  pdb=" N   MET A  50 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ARG A  10 " --> pdb=" O   MET A  50 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   VAL A  52 " --> pdb=" O   ARG A  10 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LEU A  12 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 88 through 89
      removed outlier: 8.222A  pdb=" N   MET A 236 " --> pdb=" O   TRP A 206 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ASN A 208 " --> pdb=" O   MET A 236 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   ILE A 238 " --> pdb=" O   ASN A 208 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   MET A 210 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE A 257 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   GLN A 261 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ASN A 248 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 158 through 160
    Processing sheet with id=AB8, first strand: chain 'A' and resid 304 through 310

    667 hydrogen bonds defined for protein.
    1896 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      34 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 5.61

  Time building geometry restraints manager: 4.62 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 2628
        1.29 -     1.42: 4121
        1.42 -     1.55: 9241
        1.55 -     1.68: 131
        1.68 -     1.81: 128
  Bond restraints: 16249
  Sorted by residual:
  bond pdb=" CA  LEU A 483 "
       pdb=" C   LEU A 483 "
    ideal  model  delta    sigma   weight residual
    1.524  1.428  0.096 1.29e-02 6.01e+03 5.59e+01
  bond pdb=" C   PHE A 486 "
       pdb=" O   PHE A 486 "
    ideal  model  delta    sigma   weight residual
    1.236  1.162  0.074 1.18e-02 7.18e+03 3.97e+01
  bond pdb=" CA  GLU A 479 "
       pdb=" C   GLU A 479 "
    ideal  model  delta    sigma   weight residual
    1.526  1.453  0.073 1.20e-02 6.94e+03 3.68e+01
  bond pdb=" C4  ATP C1401 "
       pdb=" C5  ATP C1401 "
    ideal  model  delta    sigma   weight residual
    1.388  1.447 -0.059 1.00e-02 1.00e+04 3.52e+01
  bond pdb=" C5  ATP C1401 "
       pdb=" N7  ATP C1401 "
    ideal  model  delta    sigma   weight residual
    1.387  1.328  0.059 1.00e-02 1.00e+04 3.46e+01
  ... (remaining 16244 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.93: 21884
        3.93 -     7.87: 255
        7.87 -    11.80: 14
       11.80 -    15.73: 5
       15.73 -    19.66: 1
  Bond angle restraints: 22159
  Sorted by residual:
  angle pdb=" PA  ATP D1401 "
        pdb=" O3A ATP D1401 "
        pdb=" PB  ATP D1401 "
      ideal   model   delta    sigma   weight residual
     136.83  117.17   19.66 1.00e+00 1.00e+00 3.87e+02
  angle pdb=" PB  ATP D1401 "
        pdb=" O3B ATP D1401 "
        pdb=" PG  ATP D1401 "
      ideal   model   delta    sigma   weight residual
     139.87  124.24   15.63 1.00e+00 1.00e+00 2.44e+02
  angle pdb=" PB  ATP C1401 "
        pdb=" O3B ATP C1401 "
        pdb=" PG  ATP C1401 "
      ideal   model   delta    sigma   weight residual
     139.87  124.95   14.92 1.00e+00 1.00e+00 2.23e+02
  angle pdb=" PA  ATP C1401 "
        pdb=" O3A ATP C1401 "
        pdb=" PB  ATP C1401 "
      ideal   model   delta    sigma   weight residual
     136.83  124.37   12.46 1.00e+00 1.00e+00 1.55e+02
  angle pdb=" N   HIS A 489 "
        pdb=" CA  HIS A 489 "
        pdb=" C   HIS A 489 "
      ideal   model   delta    sigma   weight residual
     111.40   97.81   13.59 1.22e+00 6.72e-01 1.24e+02
  ... (remaining 22154 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 8422
       17.80 -    35.59: 922
       35.59 -    53.39: 381
       53.39 -    71.18: 130
       71.18 -    88.98: 30
  Dihedral angle restraints: 9885
    sinusoidal: 4384
      harmonic: 5501
  Sorted by residual:
  dihedral pdb=" N   TRP B  33 "
           pdb=" C   TRP B  33 "
           pdb=" CA  TRP B  33 "
           pdb=" CB  TRP B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.90  -14.10     0      2.50e+00 1.60e-01 3.18e+01
  dihedral pdb=" C   TRP B  33 "
           pdb=" N   TRP B  33 "
           pdb=" CA  TRP B  33 "
           pdb=" CB  TRP B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.41   13.81     0      2.50e+00 1.60e-01 3.05e+01
  dihedral pdb=" C   SER D 219 "
           pdb=" N   SER D 219 "
           pdb=" CA  SER D 219 "
           pdb=" CB  SER D 219 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.10   11.50     0      2.50e+00 1.60e-01 2.12e+01
  ... (remaining 9882 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 2375
       0.117 -    0.234: 105
       0.234 -    0.351: 18
       0.351 -    0.468: 4
       0.468 -    0.585: 1
  Chirality restraints: 2503
  Sorted by residual:
  chirality pdb=" CA  TRP B  33 "
            pdb=" N   TRP B  33 "
            pdb=" C   TRP B  33 "
            pdb=" CB  TRP B  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.59 2.00e-01 2.50e+01 8.57e+00
  chirality pdb=" CA  ASP A 476 "
            pdb=" N   ASP A 476 "
            pdb=" C   ASP A 476 "
            pdb=" CB  ASP A 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.44 2.00e-01 2.50e+01 4.74e+00
  chirality pdb=" CA  SER A 488 "
            pdb=" N   SER A 488 "
            pdb=" C   SER A 488 "
            pdb=" CB  SER A 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.47e+00
  ... (remaining 2500 not shown)

  Planarity restraints: 2705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 486 "   -0.084 2.00e-02 2.50e+03   5.17e-02 4.69e+01
        pdb=" CG  PHE B 486 "    0.082 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 486 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 486 "    0.038 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 486 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 486 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 486 "   -0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 230 "   -0.061 5.00e-02 4.00e+02   9.35e-02 1.40e+01
        pdb=" N   PRO B 231 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO B 231 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 231 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 202 "   -0.016 2.00e-02 2.50e+03   3.25e-02 1.05e+01
        pdb=" C   ILE C 202 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ILE C 202 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LYS C 203 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2702 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.44: 76
        2.44 -     3.05: 9645
        3.05 -     3.67: 23082
        3.67 -     4.28: 35487
        4.28 -     4.90: 59918
  Nonbonded interactions: 128208
  Sorted by model distance:
  nonbonded pdb=" O2B ATP D1401 "
            pdb="MG    MG D1402 "
     model   vdw
     1.821 2.170
  nonbonded pdb=" OG1 THR C  41 "
            pdb="MG    MG C1402 "
     model   vdw
     1.858 2.170
  nonbonded pdb=" OG1 THR D  41 "
            pdb="MG    MG D1402 "
     model   vdw
     1.893 2.170
  nonbonded pdb=" OD1 ASN B 124 "
            pdb="MN    MN B1002 "
     model   vdw
     1.937 2.320
  nonbonded pdb=" OD2 ASP B  56 "
            pdb="MN    MN B1002 "
     model   vdw
     1.974 2.320
  ... (remaining 128203 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 412 or resid 444 through 494 or (resid 495 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 496 through 507 or  \ 
resid 1001 through 1002))
  selection = (chain 'B' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 35 through 69 or (resid 70 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 71 through 137 or (resid 138 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 139 through 254 or \ 
 (resid 255 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 
6 through 306 or (resid 307 and (name N or name CA or name C or name O or name C \ 
B )) or resid 308 through 498 or (resid 499 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 500 through 503 or (resid 504 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 505 through 507 or resid 1001 thro \ 
ugh 1002))
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 211 or (resid 212 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 213 through 1109 or (resid 1110 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 1111 through 1311 or resid \ 
 1401 through 1402))
  selection = (chain 'D' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 34 through 1102 or (resid 1103 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 1104 through 1119 or (resid 1 \ 
120 and (name N or name CA or name C or name O or name CB )) or resid 1121 or (r \ 
esid 1122 and (name N or name CA or name C or name O or name CB )) or resid 1123 \ 
 through 1174 or resid 1184 through 1311 or resid 1401 through 1402))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     40.780
  Find NCS groups from input model:        0.740
  Set up NCS constraints:                  0.070
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
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      :  0.008   0.096  16249  Z= 0.498
  Angle     :  1.033  19.663  22159  Z= 0.714
  Chirality :  0.063   0.585   2503
  Planarity :  0.006   0.093   2705
  Dihedral  : 18.968  88.980   6303
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.43 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 12.52 %
    Favored  : 79.99 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -2.14 (0.18), residues: 1861
  helix: -1.25 (0.18), residues: 672
  sheet: -0.91 (0.28), residues: 363
  loop : -1.68 (0.20), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  33 
 HIS   0.017   0.001   HIS C1111 
 PHE   0.084   0.003   PHE B 486 
 TYR   0.016   0.002   TYR D 236 
 ARG   0.003   0.001   ARG C1159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21581 (  663)
  hydrogen bonds       : angle       8.16980 ( 1964)
  covalent geometry    : bond        0.00816 (16249)
  covalent geometry    : angle       1.03330 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 124
    poor density    : 157
  time to evaluate  : 2.874 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7792 (mmp)
REVERT: C  218 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.5104 (ttp80)
REVERT: C 1132 LYS cc_start: 0.7700 (ttmt) cc_final: 0.7357 (mtpp)
REVERT: D  177 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8274 (pt0)
REVERT: D 1158 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7897 (mtmm)
REVERT: B   16 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8375 (m-30)
REVERT: B  191 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8184 (p0)
REVERT: A   53 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6727 (tt0)
  outliers start: 124
  outliers final: 66
  residues processed: 264
  average time/residue: 0.2886
  time to fit residues: 114.0590
Evaluate side-chains
  201 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 128
  time to evaluate  : 1.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue  218 ARG
Chi-restraints excluded: chain C residue 1117 LEU
Chi-restraints excluded: chain C residue 1124 THR
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1152 ILE
Chi-restraints excluded: chain C residue 1156 LEU
Chi-restraints excluded: chain C residue 1238 THR
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  177 GLU
Chi-restraints excluded: chain D residue  196 LYS
Chi-restraints excluded: chain D residue  206 LYS
Chi-restraints excluded: chain D residue  207 GLN
Chi-restraints excluded: chain D residue  208 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  219 SER
Chi-restraints excluded: chain D residue 1111 HIS
Chi-restraints excluded: chain D residue 1112 LYS
Chi-restraints excluded: chain D residue 1117 LEU
Chi-restraints excluded: chain D residue 1119 THR
Chi-restraints excluded: chain D residue 1123 VAL
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1158 LYS
Chi-restraints excluded: chain D residue 1159 ARG
Chi-restraints excluded: chain D residue 1189 VAL
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   15 THR
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  147 ASN
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  257 PHE
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  476 ASP
Chi-restraints excluded: chain A residue   15 THR
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  293 MET
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  494 GLU
Chi-restraints excluded: chain A residue  497 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    1.9990
   chunk 144 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 148 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 172 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C  36 ASN
C  66 HIS
C  97 ASN
C 211 HIS
C 225 ASN
C 230 GLN
C1235 GLN
C1261 HIS
C1279 HIS
D  36 ASN
D  97 ASN
D 207 GLN
D 225 ASN
D 230 GLN
D1208 GLN
D1239 ASN
D1253 HIS
B 125 HIS
B 214 GLN
B 261 GLN
A  46 ASN
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 HIS
A 148 HIS
A 320 HIS
A 384 GLN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.154557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.113869 restraints weight = 20518.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.25
r_work: 0.3118 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16249  Z= 0.137
  Angle     :  0.554   6.824  22159  Z= 0.307
  Chirality :  0.042   0.138   2503
  Planarity :  0.004   0.060   2705
  Dihedral  : 18.138  89.109   2722
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.25 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.60 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.84 (0.19), residues: 1861
  helix:  0.47 (0.20), residues: 699
  sheet: -0.60 (0.28), residues: 336
  loop : -1.40 (0.20), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  33 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.028   0.001   PHE B 257 
 TYR   0.012   0.001   TYR C   5 
 ARG   0.005   0.000   ARG D1120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05153 (  663)
  hydrogen bonds       : angle       4.70299 ( 1964)
  covalent geometry    : bond        0.00302 (16249)
  covalent geometry    : angle       0.55435 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 158
  time to evaluate  : 1.774 
Fit side-chains
REVERT: C  170 ASN cc_start: 0.8511 (t0) cc_final: 0.8011 (t0)
REVERT: C 1132 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8052 (mtpp)
REVERT: C 1280 MET cc_start: 0.6468 (ttp) cc_final: 0.6190 (ttp)
REVERT: D 1158 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8722 (mtpp)
REVERT: D 1231 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8890 (tp)
REVERT: D 1258 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8260 (tpt)
REVERT: B  184 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7378 (tpp80)
REVERT: B  283 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8759 (tp)
REVERT: B  320 HIS cc_start: 0.7705 (p-80) cc_final: 0.7285 (p-80)
REVERT: A   53 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.6987 (tt0)
REVERT: A  244 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8069 (tt0)
REVERT: A  473 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8287 (mtpt)
REVERT: A  478 ASP cc_start: 0.7758 (t0) cc_final: 0.7491 (t0)
REVERT: A  489 HIS cc_start: 0.6934 (t-90) cc_final: 0.6681 (t-90)
  outliers start: 67
  outliers final: 33
  residues processed: 213
  average time/residue: 0.2722
  time to fit residues: 87.3412
Evaluate side-chains
  182 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 143
  time to evaluate  : 1.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue 1106 ILE
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1261 HIS
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  208 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1119 THR
Chi-restraints excluded: chain D residue 1158 LYS
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1231 ILE
Chi-restraints excluded: chain D residue 1258 MET
Chi-restraints excluded: chain D residue 1267 LEU
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  257 PHE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  494 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 189 optimal weight:    5.9990
   chunk 183 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0050
   chunk 150 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 184 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 124 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    1.4000

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

Flipped N/Q/H residues before XYZ refinement:
C1098 GLN
C1254 ASN
C1261 HIS
D1257 ASN
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 320 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.151993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.109796 restraints weight = 20262.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.24
r_work: 0.3100 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16249  Z= 0.169
  Angle     :  0.546   7.304  22159  Z= 0.297
  Chirality :  0.043   0.148   2503
  Planarity :  0.004   0.048   2705
  Dihedral  : 17.528  88.041   2632
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.67 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.81 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.42 (0.19), residues: 1861
  helix:  1.02 (0.20), residues: 699
  sheet: -0.58 (0.28), residues: 349
  loop : -1.26 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  33 
 HIS   0.014   0.001   HIS C1261 
 PHE   0.026   0.002   PHE B 257 
 TYR   0.010   0.001   TYR A 279 
 ARG   0.004   0.000   ARG C1260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04668 (  663)
  hydrogen bonds       : angle       4.31742 ( 1964)
  covalent geometry    : bond        0.00397 (16249)
  covalent geometry    : angle       0.54613 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 151
  time to evaluate  : 1.885 
Fit side-chains
REVERT: C  170 ASN cc_start: 0.8598 (t0) cc_final: 0.8040 (t0)
REVERT: C 1132 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8017 (mtpp)
REVERT: D 1158 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8848 (mtpp)
REVERT: D 1231 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8885 (tp)
REVERT: D 1306 ASP cc_start: 0.8652 (t0) cc_final: 0.8133 (t0)
REVERT: B  184 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7248 (tpp80)
REVERT: B  320 HIS cc_start: 0.7743 (p-80) cc_final: 0.7372 (p-80)
REVERT: B  348 LEU cc_start: 0.7699 (tt) cc_final: 0.7439 (tp)
REVERT: A   53 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7068 (tt0)
REVERT: A  244 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8134 (tt0)
REVERT: A  478 ASP cc_start: 0.7644 (t0) cc_final: 0.7330 (t0)
REVERT: A  489 HIS cc_start: 0.7218 (t-90) cc_final: 0.6999 (t-90)
  outliers start: 65
  outliers final: 46
  residues processed: 206
  average time/residue: 0.4217
  time to fit residues: 132.4526
Evaluate side-chains
  188 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 138
  time to evaluate  : 2.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue 1106 ILE
Chi-restraints excluded: chain C residue 1124 THR
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1238 THR
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   19 ASP
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1158 LYS
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1231 ILE
Chi-restraints excluded: chain D residue 1267 LEU
Chi-restraints excluded: chain D residue 1292 VAL
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  137 MET
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  494 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 23 optimal weight:   30.0000
   chunk 135 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 151 optimal weight:    5.9990
   chunk 167 optimal weight:    5.9990
   chunk 175 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN
A 214 GLN
A 320 HIS
A 501 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.151451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109162 restraints weight = 20332.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.10
r_work: 0.3054 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16249  Z= 0.180
  Angle     :  0.544   7.144  22159  Z= 0.296
  Chirality :  0.043   0.157   2503
  Planarity :  0.004   0.036   2705
  Dihedral  : 17.179  89.558   2621
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.46 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 16.87 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.15 (0.20), residues: 1861
  helix:  1.28 (0.20), residues: 696
  sheet: -0.44 (0.27), residues: 360
  loop : -1.14 (0.21), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  33 
 HIS   0.006   0.001   HIS B 316 
 PHE   0.023   0.002   PHE B 257 
 TYR   0.016   0.001   TYR C   5 
 ARG   0.005   0.000   ARG D1309 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  663)
  hydrogen bonds       : angle       4.10865 ( 1964)
  covalent geometry    : bond        0.00429 (16249)
  covalent geometry    : angle       0.54447 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 155
  time to evaluate  : 1.567 
Fit side-chains
   revert: symmetry clash
REVERT: C  170 ASN cc_start: 0.8591 (t0) cc_final: 0.8063 (t0)
REVERT: C 1132 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8015 (mtpp)
REVERT: C 1172 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7955 (ptm-80)
REVERT: D  177 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.9055 (pt0)
REVERT: D 1158 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8840 (mtpp)
REVERT: D 1231 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8878 (tp)
REVERT: D 1306 ASP cc_start: 0.8545 (t0) cc_final: 0.8193 (t0)
REVERT: B  191 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8429 (p0)
REVERT: B  320 HIS cc_start: 0.7745 (p-80) cc_final: 0.7417 (p-80)
REVERT: A   53 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.6960 (tt0)
REVERT: A  244 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8171 (tt0)
REVERT: A  478 ASP cc_start: 0.7724 (t0) cc_final: 0.7430 (t0)
  outliers start: 86
  outliers final: 63
  residues processed: 226
  average time/residue: 0.3818
  time to fit residues: 130.6040
Evaluate side-chains
  217 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 147
  time to evaluate  : 2.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  171 LEU
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue 1106 ILE
Chi-restraints excluded: chain C residue 1124 THR
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1155 GLU
Chi-restraints excluded: chain C residue 1172 ARG
Chi-restraints excluded: chain C residue 1189 VAL
Chi-restraints excluded: chain C residue 1238 THR
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   19 ASP
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  177 GLU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1158 LYS
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1231 ILE
Chi-restraints excluded: chain D residue 1267 LEU
Chi-restraints excluded: chain D residue 1292 VAL
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  137 MET
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  472 LYS
Chi-restraints excluded: chain A residue  494 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 178 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 175 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 125 optimal weight:    4.9990
   chunk 181 optimal weight:    0.5980
   chunk 150 optimal weight:    3.9990
   chunk 137 optimal weight:    8.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 320 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.151370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.106331 restraints weight = 20368.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.40
r_work: 0.2999 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16249  Z= 0.155
  Angle     :  0.522   7.568  22159  Z= 0.283
  Chirality :  0.042   0.171   2503
  Planarity :  0.003   0.043   2705
  Dihedral  : 16.884  89.691   2616
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.46 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 17.78 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.06 (0.20), residues: 1861
  helix:  1.48 (0.20), residues: 695
  sheet: -0.33 (0.27), residues: 380
  loop : -1.04 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  33 
 HIS   0.008   0.001   HIS C1253 
 PHE   0.018   0.001   PHE A 257 
 TYR   0.010   0.001   TYR A 279 
 ARG   0.002   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  663)
  hydrogen bonds       : angle       3.97632 ( 1964)
  covalent geometry    : bond        0.00366 (16249)
  covalent geometry    : angle       0.52222 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 152
  time to evaluate  : 1.758 
Fit side-chains
   revert: symmetry clash
REVERT: C  170 ASN cc_start: 0.8657 (t0) cc_final: 0.8121 (t0)
REVERT: C 1132 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8014 (mtpp)
REVERT: C 1154 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8545 (t0)
REVERT: C 1172 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7959 (ptm-80)
REVERT: D 1158 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8899 (mtpp)
REVERT: D 1231 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8910 (tp)
REVERT: D 1306 ASP cc_start: 0.8547 (t0) cc_final: 0.8233 (t0)
REVERT: B  184 ARG cc_start: 0.7737 (tpp80) cc_final: 0.7344 (tpp80)
REVERT: B  320 HIS cc_start: 0.7777 (p-80) cc_final: 0.7473 (p-80)
REVERT: A   53 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7255 (tt0)
REVERT: A  244 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8196 (tt0)
REVERT: A  477 LYS cc_start: 0.8428 (mptt) cc_final: 0.8069 (mmtm)
REVERT: A  478 ASP cc_start: 0.7844 (t0) cc_final: 0.7592 (t0)
  outliers start: 73
  outliers final: 54
  residues processed: 215
  average time/residue: 0.2600
  time to fit residues: 85.0186
Evaluate side-chains
  207 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 147
  time to evaluate  : 1.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue 1106 ILE
Chi-restraints excluded: chain C residue 1124 THR
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1154 ASP
Chi-restraints excluded: chain C residue 1155 GLU
Chi-restraints excluded: chain C residue 1156 LEU
Chi-restraints excluded: chain C residue 1172 ARG
Chi-restraints excluded: chain C residue 1189 VAL
Chi-restraints excluded: chain C residue 1238 THR
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   19 ASP
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1158 LYS
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1231 ILE
Chi-restraints excluded: chain D residue 1267 LEU
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  494 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 188 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 168 optimal weight:    2.9990
   chunk 166 optimal weight:    0.0000
   chunk 51 optimal weight:    2.9990
   chunk 136 optimal weight:   20.0000
   chunk 152 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0770
   chunk 125 optimal weight:    0.0980
   overall best weight:    0.3944

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

Flipped N/Q/H residues before XYZ refinement:
C  91 ASN
D1235 GLN
A 320 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.154294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.111863 restraints weight = 20217.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.36
r_work: 0.3099 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  16249  Z= 0.100
  Angle     :  0.472   8.062  22159  Z= 0.259
  Chirality :  0.040   0.149   2503
  Planarity :  0.003   0.042   2705
  Dihedral  : 16.500  86.716   2611
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.82 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.92 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.37 (0.20), residues: 1861
  helix:  1.76 (0.20), residues: 700
  sheet: -0.14 (0.27), residues: 380
  loop : -0.93 (0.21), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  33 
 HIS   0.005   0.001   HIS B 316 
 PHE   0.015   0.001   PHE A 257 
 TYR   0.008   0.001   TYR B 107 
 ARG   0.002   0.000   ARG B 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  663)
  hydrogen bonds       : angle       3.79852 ( 1964)
  covalent geometry    : bond        0.00215 (16249)
  covalent geometry    : angle       0.47223 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 168
  time to evaluate  : 1.583 
Fit side-chains
   revert: symmetry clash
REVERT: C  170 ASN cc_start: 0.8563 (t0) cc_final: 0.8056 (t0)
REVERT: C 1132 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7939 (mtpp)
REVERT: D    1 MET cc_start: 0.5740 (mtp) cc_final: 0.5519 (mtm)
REVERT: D   92 MET cc_start: 0.9250 (mtp) cc_final: 0.8981 (mtp)
REVERT: D 1231 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8892 (tp)
REVERT: D 1306 ASP cc_start: 0.8436 (t0) cc_final: 0.8226 (t0)
REVERT: B  191 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8503 (p0)
REVERT: B  306 MET cc_start: 0.9198 (tpt) cc_final: 0.8814 (tpt)
REVERT: B  320 HIS cc_start: 0.7737 (p-80) cc_final: 0.7475 (p-80)
REVERT: A  116 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8922 (mt)
REVERT: A  244 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8071 (tt0)
REVERT: A  477 LYS cc_start: 0.8412 (mptt) cc_final: 0.8068 (mmtm)
REVERT: A  478 ASP cc_start: 0.7825 (t0) cc_final: 0.7611 (t0)
REVERT: A  484 LYS cc_start: 0.7844 (tptp) cc_final: 0.7628 (tptp)
REVERT: A  489 HIS cc_start: 0.7196 (t-90) cc_final: 0.6989 (t-90)
  outliers start: 54
  outliers final: 36
  residues processed: 211
  average time/residue: 0.2612
  time to fit residues: 84.7142
Evaluate side-chains
  192 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 1.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1155 GLU
Chi-restraints excluded: chain C residue 1156 LEU
Chi-restraints excluded: chain C residue 1189 VAL
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1147 GLN
Chi-restraints excluded: chain D residue 1231 ILE
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   78 CYS
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  494 GLU
Chi-restraints excluded: chain A residue  513 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 170 optimal weight:    0.3980
   chunk 92 optimal weight:    0.6980
   chunk 90 optimal weight:    7.9990
   chunk 142 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 163 optimal weight:    0.0170
   chunk 20 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 144 optimal weight:    2.9990
   overall best weight:    0.6222

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

Flipped N/Q/H residues before XYZ refinement:
A 320 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.154034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110715 restraints weight = 20343.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.22
r_work: 0.3083 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16249  Z= 0.109
  Angle     :  0.481   7.905  22159  Z= 0.261
  Chirality :  0.040   0.150   2503
  Planarity :  0.003   0.042   2705
  Dihedral  : 16.409  85.440   2600
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.87 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.80 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.53 (0.20), residues: 1861
  helix:  1.91 (0.20), residues: 698
  sheet: -0.03 (0.27), residues: 380
  loop : -0.87 (0.21), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  33 
 HIS   0.008   0.001   HIS C1253 
 PHE   0.024   0.001   PHE A 474 
 TYR   0.009   0.001   TYR B 107 
 ARG   0.003   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03584 (  663)
  hydrogen bonds       : angle       3.73897 ( 1964)
  covalent geometry    : bond        0.00244 (16249)
  covalent geometry    : angle       0.48053 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 158
  time to evaluate  : 1.659 
Fit side-chains
   revert: symmetry clash
REVERT: C  170 ASN cc_start: 0.8469 (t0) cc_final: 0.7947 (t0)
REVERT: C 1172 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7903 (ptm-80)
REVERT: D   92 MET cc_start: 0.9251 (mtp) cc_final: 0.8985 (mtp)
REVERT: D 1306 ASP cc_start: 0.8376 (t0) cc_final: 0.8155 (t0)
REVERT: B  184 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7250 (tpp80)
REVERT: B  191 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8434 (p0)
REVERT: B  306 MET cc_start: 0.9211 (tpt) cc_final: 0.8825 (tpt)
REVERT: B  320 HIS cc_start: 0.7717 (p-80) cc_final: 0.7473 (p-80)
REVERT: A  116 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8898 (mt)
REVERT: A  244 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8072 (tt0)
REVERT: A  477 LYS cc_start: 0.8422 (mptt) cc_final: 0.8088 (mmtm)
REVERT: A  484 LYS cc_start: 0.7756 (tptp) cc_final: 0.7517 (tptp)
REVERT: A  489 HIS cc_start: 0.7189 (t-90) cc_final: 0.6956 (t-90)
  outliers start: 56
  outliers final: 45
  residues processed: 201
  average time/residue: 0.2611
  time to fit residues: 79.4538
Evaluate side-chains
  201 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 152
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1155 GLU
Chi-restraints excluded: chain C residue 1156 LEU
Chi-restraints excluded: chain C residue 1172 ARG
Chi-restraints excluded: chain C residue 1189 VAL
Chi-restraints excluded: chain C residue 1286 THR
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1147 GLN
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   78 CYS
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  494 GLU
Chi-restraints excluded: chain A residue  513 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 121 optimal weight:    0.0070
   chunk 61 optimal weight:    1.9990
   chunk 178 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 138 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 104 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 129 optimal weight:    3.9990
   chunk 176 optimal weight:    7.9990
   overall best weight:    1.6006

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

Flipped N/Q/H residues before XYZ refinement:
D1253 HIS
A 320 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.153318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111197 restraints weight = 20323.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.14
r_work: 0.3074 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16249  Z= 0.177
  Angle     :  0.528   9.065  22159  Z= 0.285
  Chirality :  0.043   0.152   2503
  Planarity :  0.003   0.043   2705
  Dihedral  : 16.606  89.180   2600
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.41 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 18.56 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.43 (0.20), residues: 1861
  helix:  1.80 (0.20), residues: 700
  sheet: -0.11 (0.27), residues: 382
  loop : -0.90 (0.22), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  33 
 HIS   0.007   0.001   HIS B 316 
 PHE   0.022   0.002   PHE B 257 
 TYR   0.011   0.001   TYR A 279 
 ARG   0.002   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  663)
  hydrogen bonds       : angle       3.84449 ( 1964)
  covalent geometry    : bond        0.00426 (16249)
  covalent geometry    : angle       0.52788 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 152
  time to evaluate  : 1.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  170 ASN cc_start: 0.8608 (t0) cc_final: 0.8075 (t0)
REVERT: C 1132 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8017 (mtpp)
REVERT: C 1172 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7935 (ptm-80)
REVERT: B  184 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7324 (tpp80)
REVERT: B  191 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8436 (p0)
REVERT: B  201 MET cc_start: 0.7200 (pmm) cc_final: 0.6988 (pmm)
REVERT: B  306 MET cc_start: 0.9206 (tpt) cc_final: 0.8794 (tpt)
REVERT: B  320 HIS cc_start: 0.7733 (p-80) cc_final: 0.7486 (p-80)
REVERT: A  244 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8127 (tt0)
REVERT: A  477 LYS cc_start: 0.8422 (mptt) cc_final: 0.8059 (mmtm)
REVERT: A  489 HIS cc_start: 0.7192 (t-90) cc_final: 0.6970 (t-90)
  outliers start: 65
  outliers final: 57
  residues processed: 206
  average time/residue: 0.2669
  time to fit residues: 83.7068
Evaluate side-chains
  205 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 145
  time to evaluate  : 1.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1155 GLU
Chi-restraints excluded: chain C residue 1156 LEU
Chi-restraints excluded: chain C residue 1172 ARG
Chi-restraints excluded: chain C residue 1189 VAL
Chi-restraints excluded: chain C residue 1238 THR
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1147 GLN
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1310 VAL
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   78 CYS
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  513 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 169 optimal weight:    0.9990
   chunk 128 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 104 optimal weight:    0.6980
   chunk 153 optimal weight:    0.3980
   chunk 109 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 125 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
D1253 HIS
D1257 ASN
A 320 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.109524 restraints weight = 20413.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.90
r_work: 0.2984 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16249  Z= 0.115
  Angle     :  0.493   8.321  22159  Z= 0.268
  Chirality :  0.041   0.148   2503
  Planarity :  0.003   0.044   2705
  Dihedral  : 16.399  87.646   2597
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.03 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.29 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.61 (0.20), residues: 1861
  helix:  2.04 (0.20), residues: 698
  sheet: -0.06 (0.27), residues: 380
  loop : -0.86 (0.22), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  33 
 HIS   0.008   0.001   HIS C1253 
 PHE   0.022   0.001   PHE A 474 
 TYR   0.009   0.001   TYR B 107 
 ARG   0.003   0.000   ARG C1309 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03580 (  663)
  hydrogen bonds       : angle       3.74136 ( 1964)
  covalent geometry    : bond        0.00260 (16249)
  covalent geometry    : angle       0.49325 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 158
  time to evaluate  : 1.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  170 ASN cc_start: 0.8474 (t0) cc_final: 0.7958 (t0)
REVERT: C 1172 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7891 (ptm-80)
REVERT: B  184 ARG cc_start: 0.7637 (tpp80) cc_final: 0.7252 (tpp80)
REVERT: B  191 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8465 (p0)
REVERT: B  306 MET cc_start: 0.9168 (tpt) cc_final: 0.8739 (tpt)
REVERT: B  320 HIS cc_start: 0.7704 (p-80) cc_final: 0.7464 (p-80)
REVERT: A  116 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8890 (mt)
REVERT: A  244 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8127 (tt0)
REVERT: A  477 LYS cc_start: 0.8473 (mptt) cc_final: 0.8159 (mmtm)
REVERT: A  489 HIS cc_start: 0.7184 (t-90) cc_final: 0.6962 (t-90)
  outliers start: 54
  outliers final: 47
  residues processed: 201
  average time/residue: 0.2708
  time to fit residues: 82.9977
Evaluate side-chains
  205 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 154
  time to evaluate  : 1.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   94 VAL
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  215 ASP
Chi-restraints excluded: chain C residue 1128 ASP
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1155 GLU
Chi-restraints excluded: chain C residue 1156 LEU
Chi-restraints excluded: chain C residue 1172 ARG
Chi-restraints excluded: chain C residue 1189 VAL
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1147 GLN
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1292 VAL
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   78 CYS
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 131 optimal weight:    9.9990
   chunk 148 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 141 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 145 optimal weight:    0.0470
   overall best weight:    0.5680

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

Flipped N/Q/H residues before XYZ refinement:
D1253 HIS
D1257 ASN
A 228 GLN
A 320 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.109901 restraints weight = 20443.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.77
r_work: 0.2965 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  16249  Z= 0.107
  Angle     :  0.490  11.193  22159  Z= 0.264
  Chirality :  0.041   0.164   2503
  Planarity :  0.003   0.045   2705
  Dihedral  : 16.312  86.561   2596
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.82 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.71 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.74 (0.20), residues: 1861
  helix:  2.15 (0.20), residues: 698
  sheet:  0.02 (0.27), residues: 386
  loop : -0.80 (0.22), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  33 
 HIS   0.007   0.001   HIS C1253 
 PHE   0.023   0.001   PHE B 474 
 TYR   0.010   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03451 (  663)
  hydrogen bonds       : angle       3.69172 ( 1964)
  covalent geometry    : bond        0.00239 (16249)
  covalent geometry    : angle       0.48975 (22159)

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

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

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3722 Ramachandran restraints generated.
    1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 160
  time to evaluate  : 1.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  170 ASN cc_start: 0.8412 (t0) cc_final: 0.7925 (t0)
REVERT: C 1172 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7858 (ptm-80)
REVERT: D   92 MET cc_start: 0.9188 (mtp) cc_final: 0.8952 (mtp)
REVERT: B  184 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7308 (tpp80)
REVERT: B  191 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8423 (p0)
REVERT: B  306 MET cc_start: 0.9149 (tpt) cc_final: 0.8770 (tpt)
REVERT: B  320 HIS cc_start: 0.7694 (p-80) cc_final: 0.7469 (p-80)
REVERT: A  244 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8074 (tt0)
REVERT: A  477 LYS cc_start: 0.8391 (mptt) cc_final: 0.8109 (mmtm)
REVERT: A  489 HIS cc_start: 0.7264 (t-90) cc_final: 0.7028 (t-90)
  outliers start: 47
  outliers final: 41
  residues processed: 197
  average time/residue: 0.2739
  time to fit residues: 81.3062
Evaluate side-chains
  204 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 160
  time to evaluate  : 1.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue 1128 ASP
Chi-restraints excluded: chain C residue 1139 MET
Chi-restraints excluded: chain C residue 1145 LYS
Chi-restraints excluded: chain C residue 1148 ASP
Chi-restraints excluded: chain C residue 1155 GLU
Chi-restraints excluded: chain C residue 1156 LEU
Chi-restraints excluded: chain C residue 1172 ARG
Chi-restraints excluded: chain C residue 1189 VAL
Chi-restraints excluded: chain D residue    2 SER
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   88 ASN
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  211 HIS
Chi-restraints excluded: chain D residue 1124 THR
Chi-restraints excluded: chain D residue 1147 GLN
Chi-restraints excluded: chain D residue 1164 THR
Chi-restraints excluded: chain D residue 1292 VAL
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   46 ASN
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  289 GLU
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   78 CYS
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  244 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  347 LYS
Chi-restraints excluded: chain A residue  377 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 176 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 122 optimal weight:    3.9990
   chunk 183 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 171 optimal weight:    4.9990
   chunk 22 optimal weight:   20.0000
   chunk 6 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
D1253 HIS
D1257 ASN
A 228 GLN
A 320 HIS
A 346 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.152455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.111933 restraints weight = 20310.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.22
r_work: 0.3086 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  16249  Z= 0.295
  Angle     :  0.629  10.713  22159  Z= 0.335
  Chirality :  0.047   0.181   2503
  Planarity :  0.004   0.043   2705
  Dihedral  : 16.871  84.756   2594
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.37 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.29 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.22 (0.20), residues: 1861
  helix:  1.57 (0.20), residues: 708
  sheet: -0.22 (0.26), residues: 392
  loop : -1.00 (0.22), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  33 
 HIS   0.009   0.001   HIS C1253 
 PHE   0.033   0.002   PHE B 257 
 TYR   0.024   0.002   TYR B 107 
 ARG   0.004   0.001   ARG C1188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04569 (  663)
  hydrogen bonds       : angle       4.02699 ( 1964)
  covalent geometry    : bond        0.00724 (16249)
  covalent geometry    : angle       0.62950 (22159)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9307.47 seconds
wall clock time: 162 minutes 52.11 seconds (9772.11 seconds total)