Starting phenix.real_space_refine
on Thu Feb 15 17:24:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/02_2024/8f1d_28795_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/02_2024/8f1d_28795.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/02_2024/8f1d_28795.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/02_2024/8f1d_28795.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/02_2024/8f1d_28795_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/02_2024/8f1d_28795_updated.pdb"
  }
  resolution = 2.94
  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=   0.012 sd=   0.042
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: 6
    Type Number    sf(0)   Gaussians
     K       4      8.98       5
     Zn      4      6.06       5
     S      68      5.16       5
     C    8484      2.51       5
     N    2152      2.21       5
     O    2176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE   56": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   56": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   56": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 12888
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3192
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 3192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3192
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "C"
      Number of atoms: 3192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3192
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "D"
      Number of atoms: 3192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3192
          Classifications: {'peptide': 394}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 21, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 33
          Unusual residues: {'  K': 4, ' ZN': 1, 'CLR': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' ZN': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' ZN': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' ZN': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    800  SG  CYS A 104      66.035  80.119  76.719  1.00193.00           S
  ATOM    806  SG  CYS A 105      62.642  78.693  77.855  1.00202.39           S
  ATOM   3823  SG  CYS B  83      65.774  76.456  77.997  1.00207.60           S
  ATOM   3992  SG  CYS B 104      80.119  65.001  76.713  1.00193.69           S
  ATOM   3998  SG  CYS B 105      78.699  68.394  77.855  1.00202.98           S
  ATOM   7015  SG  CYS C  83      76.457  65.265  77.996  1.00206.73           S
  ATOM   7184  SG  CYS C 104      65.002  50.920  76.716  1.00193.64           S
  ATOM   7190  SG  CYS C 105      68.394  52.343  77.858  1.00202.41           S
  ATOM  10207  SG  CYS D  83      65.264  54.584  77.994  1.00206.45           S
  ATOM    631  SG  CYS A  83      54.583  65.775  77.995  1.00206.51           S
  ATOM  10376  SG  CYS D 104      50.921  66.039  76.712  1.00194.05           S
  ATOM  10382  SG  CYS D 105      52.340  62.646  77.854  1.00201.59           S

  Time building chain proxies: 6.96, per 1000 atoms: 0.54
  Number of scatterers: 12888
  At special positions: 0
  Unit cell: (131.88, 131.88, 124.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      4     29.99
     K       4     19.00
     S      68     16.00
     O    2176      8.00
     N    2152      7.00
     C    8484      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  - 3.50
        Amino acid           : False - 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: 5.05
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A  77 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 105 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS B  83 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 104 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" ND1 HIS B  77 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 105 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS C  83 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 104 "
      pdb="  ZN C 601 "
        pdb="ZN    ZN C 601 " - pdb=" ND1 HIS C  77 "
        pdb="ZN    ZN C 601 " - pdb=" SG  CYS C 105 "
        pdb="ZN    ZN C 601 " - pdb=" SG  CYS D  83 "
        pdb="ZN    ZN C 601 " - pdb=" SG  CYS C 104 "
      pdb="  ZN D 601 "
        pdb="ZN    ZN D 601 " - pdb=" ND1 HIS D  77 "
        pdb="ZN    ZN D 601 " - pdb=" SG  CYS D 105 "
        pdb="ZN    ZN D 601 " - pdb=" SG  CYS D 104 "
        pdb="ZN    ZN D 601 " - pdb=" SG  CYS A  83 "
      Number of angles added : 12


  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2976

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      68 helices and 4 sheets defined
      61.4% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 27
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.544A  pdb=" N   TYR A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 94
    Processing helix  chain 'A' and resid 98 through 100
      No H-bonds generated for 'chain 'A' and resid 98 through 100'
    Processing helix  chain 'A' and resid 103 through 105
      No H-bonds generated for 'chain 'A' and resid 103 through 105'
    Processing helix  chain 'A' and resid 109 through 120
      removed outlier: 4.507A  pdb=" N   HIS A 112 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   ARG A 113 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASP A 114 " --> pdb=" O   GLN A 111 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU A 119 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 3.505A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 211
      removed outlier: 4.196A  pdb=" N   THR A 211 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 265
      removed outlier: 3.964A  pdb=" N   GLU A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TRP A 255 " --> pdb=" O   VAL A 251 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 277 through 294
      Proline residue:  A 288  - end of helix
    Processing helix  chain 'A' and resid 300 through 324
      removed outlier: 5.070A  pdb=" N   PHE A 315 " --> pdb=" O   ARG A 311 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   VAL A 316 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ARG A 317 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   ILE A 318 " --> pdb=" O   ARG A 314 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   LEU A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ARG A 320 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   ILE A 321 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   PHE A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   LYS A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU A 324 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'A' and resid 342 through 366
    Processing helix  chain 'A' and resid 388 through 398
      removed outlier: 4.005A  pdb=" N   TRP A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   TRP A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 451
      removed outlier: 3.920A  pdb=" N   LEU A 415 " --> pdb=" O   TRP A 411 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 416 " --> pdb=" O   SER A 412 " (cutoff:3.500A)
      Proline residue:  A 431  - end of helix
      removed outlier: 4.775A  pdb=" N   VAL A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS A 449 " --> pdb=" O   LEU A 445 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLN A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A 451 " --> pdb=" O   MET A 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 27
    Processing helix  chain 'B' and resid 33 through 38
    Processing helix  chain 'B' and resid 64 through 73
      removed outlier: 3.546A  pdb=" N   TYR B  71 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 94
    Processing helix  chain 'B' and resid 98 through 100
      No H-bonds generated for 'chain 'B' and resid 98 through 100'
    Processing helix  chain 'B' and resid 103 through 105
      No H-bonds generated for 'chain 'B' and resid 103 through 105'
    Processing helix  chain 'B' and resid 109 through 120
      removed outlier: 4.506A  pdb=" N   HIS B 112 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   ARG B 113 " --> pdb=" O   ARG B 110 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP B 114 " --> pdb=" O   GLN B 111 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU B 119 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 181
    Processing helix  chain 'B' and resid 188 through 211
      removed outlier: 4.191A  pdb=" N   THR B 211 " --> pdb=" O   PHE B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 265
      removed outlier: 3.969A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TRP B 255 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 265 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 275
    Processing helix  chain 'B' and resid 277 through 294
      Proline residue:  B 288  - end of helix
    Processing helix  chain 'B' and resid 300 through 324
      removed outlier: 5.066A  pdb=" N   PHE B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   VAL B 316 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   ARG B 317 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   ILE B 318 " --> pdb=" O   ARG B 314 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   LEU B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ARG B 320 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   ILE B 321 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   PHE B 322 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LEU B 324 " --> pdb=" O   ARG B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 339
    Processing helix  chain 'B' and resid 342 through 366
    Processing helix  chain 'B' and resid 388 through 398
      removed outlier: 4.005A  pdb=" N   TRP B 392 " --> pdb=" O   PRO B 388 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   TRP B 393 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 451
      removed outlier: 3.924A  pdb=" N   LEU B 415 " --> pdb=" O   TRP B 411 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL B 416 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
      Proline residue:  B 431  - end of helix
      removed outlier: 4.774A  pdb=" N   VAL B 434 " --> pdb=" O   MET B 430 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS B 449 " --> pdb=" O   LEU B 445 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN B 450 " --> pdb=" O   ALA B 446 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LYS B 451 " --> pdb=" O   MET B 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 27
    Processing helix  chain 'C' and resid 33 through 38
    Processing helix  chain 'C' and resid 64 through 73
      removed outlier: 3.546A  pdb=" N   TYR C  71 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 94
    Processing helix  chain 'C' and resid 98 through 100
      No H-bonds generated for 'chain 'C' and resid 98 through 100'
    Processing helix  chain 'C' and resid 103 through 105
      No H-bonds generated for 'chain 'C' and resid 103 through 105'
    Processing helix  chain 'C' and resid 109 through 120
      removed outlier: 4.507A  pdb=" N   HIS C 112 " --> pdb=" O   TYR C 109 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   ARG C 113 " --> pdb=" O   ARG C 110 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASP C 114 " --> pdb=" O   GLN C 111 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU C 119 " --> pdb=" O   GLU C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 181
      removed outlier: 3.504A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 211
      removed outlier: 4.194A  pdb=" N   THR C 211 " --> pdb=" O   PHE C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 265
      removed outlier: 4.005A  pdb=" N   GLU C 249 " --> pdb=" O   LEU C 245 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TRP C 255 " --> pdb=" O   VAL C 251 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE C 265 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 275
    Processing helix  chain 'C' and resid 277 through 294
      Proline residue:  C 288  - end of helix
    Processing helix  chain 'C' and resid 300 through 324
      removed outlier: 5.067A  pdb=" N   PHE C 315 " --> pdb=" O   ARG C 311 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   VAL C 316 " --> pdb=" O   VAL C 312 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   ARG C 317 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ILE C 318 " --> pdb=" O   ARG C 314 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   LEU C 319 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ARG C 320 " --> pdb=" O   VAL C 316 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   ILE C 321 " --> pdb=" O   ARG C 317 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   PHE C 322 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   LYS C 323 " --> pdb=" O   LEU C 319 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LEU C 324 " --> pdb=" O   ARG C 320 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 339
    Processing helix  chain 'C' and resid 342 through 366
    Processing helix  chain 'C' and resid 388 through 398
      removed outlier: 4.005A  pdb=" N   TRP C 392 " --> pdb=" O   PRO C 388 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   TRP C 393 " --> pdb=" O   ILE C 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 451
      removed outlier: 3.915A  pdb=" N   LEU C 415 " --> pdb=" O   TRP C 411 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL C 416 " --> pdb=" O   SER C 412 " (cutoff:3.500A)
      Proline residue:  C 431  - end of helix
      removed outlier: 4.775A  pdb=" N   VAL C 434 " --> pdb=" O   MET C 430 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS C 449 " --> pdb=" O   LEU C 445 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLN C 450 " --> pdb=" O   ALA C 446 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LYS C 451 " --> pdb=" O   MET C 447 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 27
    Processing helix  chain 'D' and resid 33 through 38
    Processing helix  chain 'D' and resid 64 through 73
      removed outlier: 3.546A  pdb=" N   TYR D  71 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 94
    Processing helix  chain 'D' and resid 98 through 100
      No H-bonds generated for 'chain 'D' and resid 98 through 100'
    Processing helix  chain 'D' and resid 103 through 105
      No H-bonds generated for 'chain 'D' and resid 103 through 105'
    Processing helix  chain 'D' and resid 109 through 120
      removed outlier: 4.511A  pdb=" N   HIS D 112 " --> pdb=" O   TYR D 109 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   ARG D 113 " --> pdb=" O   ARG D 110 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASP D 114 " --> pdb=" O   GLN D 111 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU D 119 " --> pdb=" O   GLU D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 181
      removed outlier: 3.501A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 211
      removed outlier: 4.193A  pdb=" N   THR D 211 " --> pdb=" O   PHE D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 265
      removed outlier: 3.963A  pdb=" N   GLU D 249 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TRP D 255 " --> pdb=" O   VAL D 251 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE D 265 " --> pdb=" O   LEU D 261 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 275
    Processing helix  chain 'D' and resid 277 through 294
      Proline residue:  D 288  - end of helix
    Processing helix  chain 'D' and resid 300 through 324
      removed outlier: 5.069A  pdb=" N   PHE D 315 " --> pdb=" O   ARG D 311 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   VAL D 316 " --> pdb=" O   VAL D 312 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   ARG D 317 " --> pdb=" O   VAL D 313 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ILE D 318 " --> pdb=" O   ARG D 314 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LEU D 319 " --> pdb=" O   PHE D 315 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ARG D 320 " --> pdb=" O   VAL D 316 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   ILE D 321 " --> pdb=" O   ARG D 317 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   PHE D 322 " --> pdb=" O   ILE D 318 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LYS D 323 " --> pdb=" O   LEU D 319 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU D 324 " --> pdb=" O   ARG D 320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 339
    Processing helix  chain 'D' and resid 342 through 366
    Processing helix  chain 'D' and resid 388 through 398
      removed outlier: 4.006A  pdb=" N   TRP D 392 " --> pdb=" O   PRO D 388 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   TRP D 393 " --> pdb=" O   ILE D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 451
      removed outlier: 3.924A  pdb=" N   LEU D 415 " --> pdb=" O   TRP D 411 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL D 416 " --> pdb=" O   SER D 412 " (cutoff:3.500A)
      Proline residue:  D 431  - end of helix
      removed outlier: 4.779A  pdb=" N   VAL D 434 " --> pdb=" O   MET D 430 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS D 449 " --> pdb=" O   LEU D 445 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLN D 450 " --> pdb=" O   ALA D 446 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS D 451 " --> pdb=" O   MET D 447 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 17 through 22
    Processing sheet with id=  B, first strand: chain 'B' and resid 17 through 22
      removed outlier: 6.186A  pdb=" N   PHE B  55 " --> pdb=" O   ASN B  13 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 17 through 22
      removed outlier: 6.178A  pdb=" N   PHE C  55 " --> pdb=" O   ASN C  13 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'D' and resid 17 through 22
      removed outlier: 6.169A  pdb=" N   PHE D  55 " --> pdb=" O   ASN D  13 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1728 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.35

  Time building geometry restraints manager: 5.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3978
        1.34 -     1.46: 2748
        1.46 -     1.57: 6446
        1.57 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 13276
  Sorted by residual:
  bond pdb=" C   MET B 430 "
       pdb=" N   PRO B 431 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.031 9.80e-03 1.04e+04 9.70e+00
  bond pdb=" C   MET C 430 "
       pdb=" N   PRO C 431 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.031 9.80e-03 1.04e+04 9.70e+00
  bond pdb=" C   MET A 430 "
       pdb=" N   PRO A 431 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.030 9.80e-03 1.04e+04 9.53e+00
  bond pdb=" C   MET D 430 "
       pdb=" N   PRO D 431 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.030 9.80e-03 1.04e+04 9.45e+00
  bond pdb=" N   LYS A 457 "
       pdb=" CA  LYS A 457 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.012 1.29e-02 6.01e+03 8.17e-01
  ... (remaining 13271 not shown)

  Histogram of bond angle deviations from ideal:
      100.35 -   107.08: 479
      107.08 -   113.81: 7374
      113.81 -   120.54: 5508
      120.54 -   127.27: 4513
      127.27 -   134.00: 198
  Bond angle restraints: 18072
  Sorted by residual:
  angle pdb=" CA  PRO D 431 "
        pdb=" C   PRO D 431 "
        pdb=" O   PRO D 431 "
      ideal   model   delta    sigma   weight residual
     118.78  121.55   -2.77 1.40e+00 5.10e-01 3.92e+00
  angle pdb=" CA  PRO C 431 "
        pdb=" C   PRO C 431 "
        pdb=" O   PRO C 431 "
      ideal   model   delta    sigma   weight residual
     118.78  121.54   -2.76 1.40e+00 5.10e-01 3.88e+00
  angle pdb=" CA  PRO A 431 "
        pdb=" C   PRO A 431 "
        pdb=" O   PRO A 431 "
      ideal   model   delta    sigma   weight residual
     118.78  121.54   -2.76 1.40e+00 5.10e-01 3.88e+00
  angle pdb=" CA  PRO B 431 "
        pdb=" C   PRO B 431 "
        pdb=" O   PRO B 431 "
      ideal   model   delta    sigma   weight residual
     118.78  121.50   -2.72 1.40e+00 5.10e-01 3.77e+00
  angle pdb=" N   LEU B 287 "
        pdb=" CA  LEU B 287 "
        pdb=" C   LEU B 287 "
      ideal   model   delta    sigma   weight residual
     112.75  115.33   -2.58 1.36e+00 5.41e-01 3.60e+00
  ... (remaining 18067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.27: 7392
       16.27 -    32.53: 431
       32.53 -    48.80: 73
       48.80 -    65.07: 8
       65.07 -    81.33: 4
  Dihedral angle restraints: 7908
    sinusoidal: 3300
      harmonic: 4608
  Sorted by residual:
  dihedral pdb=" N   LEU C 245 "
           pdb=" CA  LEU C 245 "
           pdb=" CB  LEU C 245 "
           pdb=" CG  LEU C 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.99   58.99     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   LEU D 245 "
           pdb=" CA  LEU D 245 "
           pdb=" CB  LEU D 245 "
           pdb=" CG  LEU D 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.15   58.15     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   LEU A 245 "
           pdb=" CA  LEU A 245 "
           pdb=" CB  LEU A 245 "
           pdb=" CG  LEU A 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.10   58.10     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 7905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1136
       0.028 -    0.056: 583
       0.056 -    0.085: 174
       0.085 -    0.113: 76
       0.113 -    0.141: 23
  Chirality restraints: 1992
  Sorted by residual:
  chirality pdb=" CA  MET B 430 "
            pdb=" N   MET B 430 "
            pdb=" C   MET B 430 "
            pdb=" CB  MET B 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  MET A 430 "
            pdb=" N   MET A 430 "
            pdb=" C   MET A 430 "
            pdb=" CB  MET A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  MET C 430 "
            pdb=" N   MET C 430 "
            pdb=" C   MET C 430 "
            pdb=" CB  MET C 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.91e-01
  ... (remaining 1989 not shown)

  Planarity restraints: 2244
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D  84 "   -0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO D  85 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO D  85 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D  85 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  84 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.98e+00
        pdb=" N   PRO B  85 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B  85 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  85 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  84 "    0.029 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO A  85 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A  85 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  85 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2241 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.89: 4868
        2.89 -     3.45: 14995
        3.45 -     4.01: 22217
        4.01 -     4.58: 32675
        4.58 -     5.14: 45467
  Nonbonded interactions: 120222
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG C  33 "
            pdb=" O   PHE C  93 "
     model   vdw
     2.321 2.520
  nonbonded pdb=" NH1 ARG A  33 "
            pdb=" O   PHE A  93 "
     model   vdw
     2.322 2.520
  nonbonded pdb=" NH1 ARG D  33 "
            pdb=" O   PHE D  93 "
     model   vdw
     2.322 2.520
  nonbonded pdb=" NH1 ARG B  33 "
            pdb=" O   PHE B  93 "
     model   vdw
     2.323 2.520
  nonbonded pdb=" O   THR D 399 "
            pdb=" OG1 THR D 400 "
     model   vdw
     2.416 2.440
  ... (remaining 120217 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 463 or resid 601 through 602))
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:          6.310
  Check model and map are aligned:         0.190
  Set scattering table:                    0.130
  Process input model:                     37.930
  Find NCS groups from input model:        0.810
  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:12.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6169
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13276  Z= 0.280
  Angle     :  0.509   6.258  18072  Z= 0.259
  Chirality :  0.039   0.141   1992
  Planarity :  0.004   0.043   2244
  Dihedral  : 10.401  81.332   4932
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  5.04 %
    Favored  : 94.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.22), residues: 1552
  helix:  1.63 (0.17), residues: 948
  sheet:  1.46 (0.82), residues: 40
  loop : -0.84 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 392 
 HIS   0.002   0.001   HIS C  66 
 PHE   0.007   0.001   PHE D 244 
 TYR   0.008   0.001   TYR B 365 
 ARG   0.002   0.000   ARG C 320 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 223
  time to evaluate  : 1.456 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.7001 (t0) cc_final: 0.6703 (t0)
REVERT: A  213 GLU cc_start: 0.5954 (mp0) cc_final: 0.5674 (mp0)
REVERT: A  275 LYS cc_start: 0.7147 (mttt) cc_final: 0.6472 (tptt)
REVERT: A  295 LEU cc_start: 0.6683 (tp) cc_final: 0.6439 (tt)
REVERT: A  339 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6609 (ttm110)
REVERT: A  437 ASN cc_start: 0.6283 (t0) cc_final: 0.5941 (m-40)
REVERT: A  451 LYS cc_start: 0.6797 (mmpt) cc_final: 0.6411 (mttt)
REVERT: A  457 LYS cc_start: 0.6164 (pttt) cc_final: 0.5791 (tptm)
REVERT: A  458 LYS cc_start: 0.6502 (mmmt) cc_final: 0.6220 (mtmt)
REVERT: B  182 ASP cc_start: 0.7006 (t0) cc_final: 0.6709 (t0)
REVERT: B  213 GLU cc_start: 0.5885 (mp0) cc_final: 0.5565 (mp0)
REVERT: B  275 LYS cc_start: 0.7156 (mttt) cc_final: 0.6481 (tptt)
REVERT: B  295 LEU cc_start: 0.6713 (tp) cc_final: 0.6453 (tt)
REVERT: B  339 ARG cc_start: 0.6807 (ttp-170) cc_final: 0.6597 (ttm110)
REVERT: B  437 ASN cc_start: 0.6269 (t0) cc_final: 0.5928 (m-40)
REVERT: B  451 LYS cc_start: 0.6707 (mmpt) cc_final: 0.6316 (mttt)
REVERT: B  458 LYS cc_start: 0.6551 (mmmt) cc_final: 0.6178 (ttpt)
REVERT: C  182 ASP cc_start: 0.7000 (t0) cc_final: 0.6703 (t0)
REVERT: C  213 GLU cc_start: 0.5875 (mp0) cc_final: 0.5562 (mp0)
REVERT: C  275 LYS cc_start: 0.7116 (mttt) cc_final: 0.6396 (tptt)
REVERT: C  295 LEU cc_start: 0.6699 (tp) cc_final: 0.6444 (tt)
REVERT: C  339 ARG cc_start: 0.6763 (ttp-170) cc_final: 0.6559 (ttm110)
REVERT: C  437 ASN cc_start: 0.6287 (t0) cc_final: 0.5947 (m-40)
REVERT: C  451 LYS cc_start: 0.6786 (mmpt) cc_final: 0.6401 (mttt)
REVERT: C  457 LYS cc_start: 0.6187 (pttt) cc_final: 0.5814 (tmtt)
REVERT: C  458 LYS cc_start: 0.6533 (mmmt) cc_final: 0.6241 (mtmt)
REVERT: D  182 ASP cc_start: 0.7004 (t0) cc_final: 0.6707 (t0)
REVERT: D  213 GLU cc_start: 0.5960 (mp0) cc_final: 0.5677 (mp0)
REVERT: D  275 LYS cc_start: 0.7144 (mttt) cc_final: 0.6471 (tptt)
REVERT: D  295 LEU cc_start: 0.6693 (tp) cc_final: 0.6428 (tt)
REVERT: D  339 ARG cc_start: 0.6771 (ttp-170) cc_final: 0.6568 (ttm110)
REVERT: D  437 ASN cc_start: 0.6314 (t0) cc_final: 0.5970 (m-40)
REVERT: D  451 LYS cc_start: 0.6793 (mmpt) cc_final: 0.6404 (mttt)
REVERT: D  457 LYS cc_start: 0.6301 (pttt) cc_final: 0.5892 (tptm)
REVERT: D  458 LYS cc_start: 0.6463 (mmmt) cc_final: 0.6252 (mtpt)
  outliers start: 8
  outliers final: 0
  residues processed: 231
  average time/residue: 1.1231
  time to fit residues: 284.9181
Evaluate side-chains
  159 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    3.9990
   chunk 118 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:   20.0000
   chunk 63 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 141 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  43 HIS
B  43 HIS
C  43 HIS
D  43 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6238
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  13276  Z= 0.388
  Angle     :  0.647   9.592  18072  Z= 0.322
  Chirality :  0.045   0.149   1992
  Planarity :  0.006   0.052   2244
  Dihedral  :  4.970  37.808   1996
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 10.46 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.22), residues: 1552
  helix:  1.12 (0.17), residues: 952
  sheet:  None (None), residues: 0
  loop : -0.86 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 411 
 HIS   0.004   0.001   HIS B 336 
 PHE   0.014   0.002   PHE A 384 
 TYR   0.015   0.002   TYR C 365 
 ARG   0.004   0.001   ARG C 110 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 1.477 
Fit side-chains
REVERT: A   56 PHE cc_start: 0.7790 (t80) cc_final: 0.7232 (t80)
REVERT: A  182 ASP cc_start: 0.6952 (t70) cc_final: 0.6622 (t0)
REVERT: A  275 LYS cc_start: 0.7149 (mttt) cc_final: 0.6391 (tptp)
REVERT: A  295 LEU cc_start: 0.6727 (tp) cc_final: 0.6509 (tt)
REVERT: A  318 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.7007 (mm)
REVERT: A  437 ASN cc_start: 0.6371 (t0) cc_final: 0.5988 (m-40)
REVERT: A  451 LYS cc_start: 0.6758 (mmpt) cc_final: 0.6379 (mttt)
REVERT: A  457 LYS cc_start: 0.6166 (pttt) cc_final: 0.5811 (tmtt)
REVERT: B  182 ASP cc_start: 0.6840 (t70) cc_final: 0.6519 (t0)
REVERT: B  275 LYS cc_start: 0.7158 (mttt) cc_final: 0.6401 (tptp)
REVERT: B  295 LEU cc_start: 0.6700 (tp) cc_final: 0.6487 (tt)
REVERT: B  318 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7022 (mm)
REVERT: B  437 ASN cc_start: 0.6318 (t0) cc_final: 0.5937 (m-40)
REVERT: B  451 LYS cc_start: 0.6804 (mmpt) cc_final: 0.6414 (mttt)
REVERT: B  458 LYS cc_start: 0.6447 (mmmt) cc_final: 0.6163 (ttmt)
REVERT: C   98 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6986 (pt0)
REVERT: C  182 ASP cc_start: 0.6951 (t70) cc_final: 0.6625 (t0)
REVERT: C  275 LYS cc_start: 0.7149 (mttt) cc_final: 0.6384 (tptp)
REVERT: C  295 LEU cc_start: 0.6747 (tp) cc_final: 0.6515 (tt)
REVERT: C  318 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7028 (mm)
REVERT: C  437 ASN cc_start: 0.6377 (t0) cc_final: 0.5994 (m-40)
REVERT: C  451 LYS cc_start: 0.6733 (mmpt) cc_final: 0.6412 (mttt)
REVERT: C  457 LYS cc_start: 0.6185 (pttt) cc_final: 0.5828 (tmtt)
REVERT: C  458 LYS cc_start: 0.6431 (mmmt) cc_final: 0.6220 (mtmt)
REVERT: D   98 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.7023 (pt0)
REVERT: D  182 ASP cc_start: 0.6960 (t70) cc_final: 0.6630 (t0)
REVERT: D  275 LYS cc_start: 0.7151 (mttt) cc_final: 0.6393 (tptp)
REVERT: D  295 LEU cc_start: 0.6679 (tp) cc_final: 0.6474 (tt)
REVERT: D  318 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7031 (mm)
REVERT: D  437 ASN cc_start: 0.6337 (t0) cc_final: 0.5958 (m-40)
REVERT: D  451 LYS cc_start: 0.6692 (mmpt) cc_final: 0.6325 (mttt)
REVERT: D  457 LYS cc_start: 0.6162 (pttt) cc_final: 0.5850 (tmtt)
  outliers start: 28
  outliers final: 15
  residues processed: 185
  average time/residue: 1.0178
  time to fit residues: 208.8965
Evaluate side-chains
  185 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain C residue   98 GLU
Chi-restraints excluded: chain C residue  251 VAL
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  406 MET
Chi-restraints excluded: chain D residue   98 GLU
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  318 ILE
Chi-restraints excluded: chain D residue  406 MET
Chi-restraints excluded: chain D residue  410 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   chunk 117 optimal weight:   20.0000
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 141 optimal weight:    0.9990
   chunk 153 optimal weight:    1.9990
   chunk 126 optimal weight:    5.9990
   chunk 140 optimal weight:   20.0000
   chunk 48 optimal weight:    0.0870
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.8166

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6213
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13276  Z= 0.240
  Angle     :  0.537   6.800  18072  Z= 0.271
  Chirality :  0.040   0.128   1992
  Planarity :  0.005   0.050   2244
  Dihedral  :  4.931  44.553   1996
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.02 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.21), residues: 1552
  helix:  1.13 (0.17), residues: 944
  sheet:  None (None), residues: 0
  loop : -1.05 (0.24), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 411 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.020   0.001   PHE B  56 
 TYR   0.009   0.001   TYR A 365 
 ARG   0.002   0.000   ARG D 110 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 1.426 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.5451 (tp30) cc_final: 0.5034 (pt0)
REVERT: A  182 ASP cc_start: 0.6855 (t70) cc_final: 0.6527 (t0)
REVERT: A  275 LYS cc_start: 0.7121 (mttt) cc_final: 0.6356 (tptp)
REVERT: A  437 ASN cc_start: 0.6334 (t0) cc_final: 0.5941 (m110)
REVERT: A  451 LYS cc_start: 0.6760 (mmpt) cc_final: 0.6426 (mttt)
REVERT: A  457 LYS cc_start: 0.6158 (pttt) cc_final: 0.5778 (tmtt)
REVERT: B  116 GLU cc_start: 0.5427 (tp30) cc_final: 0.5009 (pt0)
REVERT: B  182 ASP cc_start: 0.6795 (t70) cc_final: 0.6462 (t0)
REVERT: B  275 LYS cc_start: 0.7122 (mttt) cc_final: 0.6364 (tptp)
REVERT: B  437 ASN cc_start: 0.6320 (t0) cc_final: 0.5930 (m110)
REVERT: B  451 LYS cc_start: 0.6783 (mmpt) cc_final: 0.6392 (mttt)
REVERT: B  458 LYS cc_start: 0.6433 (mmmt) cc_final: 0.6128 (ttmt)
REVERT: C  116 GLU cc_start: 0.5443 (tp30) cc_final: 0.5034 (pt0)
REVERT: C  182 ASP cc_start: 0.6857 (t70) cc_final: 0.6527 (t0)
REVERT: C  213 GLU cc_start: 0.5840 (mp0) cc_final: 0.5565 (mp0)
REVERT: C  275 LYS cc_start: 0.7146 (mttt) cc_final: 0.6366 (tptp)
REVERT: C  437 ASN cc_start: 0.6338 (t0) cc_final: 0.5946 (m110)
REVERT: C  451 LYS cc_start: 0.6735 (mmpt) cc_final: 0.6410 (mttt)
REVERT: C  457 LYS cc_start: 0.6161 (pttt) cc_final: 0.5794 (tmtt)
REVERT: C  458 LYS cc_start: 0.6382 (mmmt) cc_final: 0.6181 (mtmt)
REVERT: D  116 GLU cc_start: 0.5407 (tp30) cc_final: 0.5001 (pt0)
REVERT: D  182 ASP cc_start: 0.6860 (t70) cc_final: 0.6533 (t0)
REVERT: D  275 LYS cc_start: 0.7123 (mttt) cc_final: 0.6358 (tptp)
REVERT: D  437 ASN cc_start: 0.6393 (t0) cc_final: 0.6008 (m110)
REVERT: D  451 LYS cc_start: 0.6756 (mmpt) cc_final: 0.6381 (mttt)
REVERT: D  457 LYS cc_start: 0.6173 (pttt) cc_final: 0.5828 (tmtt)
  outliers start: 13
  outliers final: 8
  residues processed: 181
  average time/residue: 0.9752
  time to fit residues: 197.2140
Evaluate side-chains
  177 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 169
  time to evaluate  : 1.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  406 MET
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  406 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 142 optimal weight:    0.0970
   chunk 150 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 134 optimal weight:    1.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6177
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  13276  Z= 0.154
  Angle     :  0.531  14.676  18072  Z= 0.253
  Chirality :  0.038   0.136   1992
  Planarity :  0.004   0.047   2244
  Dihedral  :  4.591  44.309   1996
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 14.09 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.22), residues: 1552
  helix:  1.28 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -0.88 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 411 
 HIS   0.001   0.000   HIS A  60 
 PHE   0.020   0.001   PHE B  56 
 TYR   0.006   0.001   TYR A  48 
 ARG   0.001   0.000   ARG B 314 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 1.497 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.5514 (tp30) cc_final: 0.5052 (pt0)
REVERT: A  182 ASP cc_start: 0.6800 (t70) cc_final: 0.6484 (t0)
REVERT: A  275 LYS cc_start: 0.7132 (mttt) cc_final: 0.6364 (tptp)
REVERT: A  437 ASN cc_start: 0.6336 (t0) cc_final: 0.5911 (m110)
REVERT: A  451 LYS cc_start: 0.6772 (mmpt) cc_final: 0.6438 (mttt)
REVERT: A  457 LYS cc_start: 0.6159 (pttt) cc_final: 0.5809 (tmtt)
REVERT: B  116 GLU cc_start: 0.5526 (tp30) cc_final: 0.5044 (pt0)
REVERT: B  182 ASP cc_start: 0.6779 (t70) cc_final: 0.6473 (t0)
REVERT: B  275 LYS cc_start: 0.7127 (mttt) cc_final: 0.6371 (tptp)
REVERT: B  437 ASN cc_start: 0.6322 (t0) cc_final: 0.5900 (m110)
REVERT: B  451 LYS cc_start: 0.6798 (mmpt) cc_final: 0.6407 (mttt)
REVERT: B  458 LYS cc_start: 0.6404 (mmmt) cc_final: 0.6107 (ttmt)
REVERT: C  116 GLU cc_start: 0.5538 (tp30) cc_final: 0.5062 (pt0)
REVERT: C  182 ASP cc_start: 0.6804 (t70) cc_final: 0.6489 (t0)
REVERT: C  213 GLU cc_start: 0.5728 (mp0) cc_final: 0.5511 (mp0)
REVERT: C  275 LYS cc_start: 0.7136 (mttt) cc_final: 0.6345 (tptp)
REVERT: C  437 ASN cc_start: 0.6341 (t0) cc_final: 0.5916 (m110)
REVERT: C  451 LYS cc_start: 0.6761 (mmpt) cc_final: 0.6428 (mttt)
REVERT: C  457 LYS cc_start: 0.6144 (pttt) cc_final: 0.5804 (tmtt)
REVERT: D  116 GLU cc_start: 0.5509 (tp30) cc_final: 0.5044 (pt0)
REVERT: D  182 ASP cc_start: 0.6806 (t70) cc_final: 0.6490 (t0)
REVERT: D  275 LYS cc_start: 0.7132 (mttt) cc_final: 0.6364 (tptp)
REVERT: D  437 ASN cc_start: 0.6343 (t0) cc_final: 0.5921 (m110)
REVERT: D  451 LYS cc_start: 0.6765 (mmpt) cc_final: 0.6394 (mttt)
REVERT: D  457 LYS cc_start: 0.6183 (pttt) cc_final: 0.5831 (tmtt)
  outliers start: 12
  outliers final: 7
  residues processed: 177
  average time/residue: 1.1091
  time to fit residues: 218.8559
Evaluate side-chains
  179 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 172
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  253 VAL
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  271 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 125 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 2 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   chunk 128 optimal weight:    9.9990
   chunk 104 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0040
   overall best weight:    2.2000

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN
B 438 ASN
C 438 ASN
D 438 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6228
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13276  Z= 0.278
  Angle     :  0.610  14.900  18072  Z= 0.288
  Chirality :  0.041   0.134   1992
  Planarity :  0.005   0.051   2244
  Dihedral  :  5.093  47.519   1996
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.47 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.21), residues: 1552
  helix:  1.12 (0.17), residues: 948
  sheet:  2.01 (0.86), residues: 40
  loop : -1.13 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 411 
 HIS   0.003   0.001   HIS A  60 
 PHE   0.023   0.001   PHE A  56 
 TYR   0.010   0.001   TYR D 365 
 ARG   0.002   0.000   ARG B 339 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 1.578 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.5531 (tp30) cc_final: 0.5039 (pt0)
REVERT: A  182 ASP cc_start: 0.6910 (t70) cc_final: 0.6589 (t0)
REVERT: A  275 LYS cc_start: 0.7145 (mttt) cc_final: 0.6332 (tptp)
REVERT: A  318 ILE cc_start: 0.7267 (tt) cc_final: 0.6939 (mm)
REVERT: A  437 ASN cc_start: 0.6326 (t0) cc_final: 0.5941 (m110)
REVERT: A  451 LYS cc_start: 0.6752 (mmpt) cc_final: 0.6422 (mttt)
REVERT: A  457 LYS cc_start: 0.6145 (pttt) cc_final: 0.5791 (tmtt)
REVERT: B  116 GLU cc_start: 0.5581 (tp30) cc_final: 0.5084 (pt0)
REVERT: B  182 ASP cc_start: 0.6789 (t70) cc_final: 0.6449 (t70)
REVERT: B  275 LYS cc_start: 0.7154 (mttt) cc_final: 0.6307 (tptp)
REVERT: B  318 ILE cc_start: 0.7268 (tt) cc_final: 0.6929 (mm)
REVERT: B  437 ASN cc_start: 0.6312 (t0) cc_final: 0.5930 (m110)
REVERT: B  451 LYS cc_start: 0.6755 (mmpt) cc_final: 0.6421 (mttt)
REVERT: B  458 LYS cc_start: 0.6307 (mmmt) cc_final: 0.6036 (mtmt)
REVERT: C  116 GLU cc_start: 0.5594 (tp30) cc_final: 0.5097 (pt0)
REVERT: C  182 ASP cc_start: 0.6836 (t70) cc_final: 0.6519 (t0)
REVERT: C  213 GLU cc_start: 0.5773 (mp0) cc_final: 0.5539 (mp0)
REVERT: C  275 LYS cc_start: 0.7147 (mttt) cc_final: 0.6320 (tptp)
REVERT: C  318 ILE cc_start: 0.7256 (tt) cc_final: 0.6926 (mm)
REVERT: C  437 ASN cc_start: 0.6331 (t0) cc_final: 0.5948 (m110)
REVERT: C  451 LYS cc_start: 0.6751 (mmpt) cc_final: 0.6424 (mttt)
REVERT: C  457 LYS cc_start: 0.6054 (pttt) cc_final: 0.5743 (tmtt)
REVERT: D  116 GLU cc_start: 0.5545 (tp30) cc_final: 0.5072 (pt0)
REVERT: D  182 ASP cc_start: 0.6912 (t70) cc_final: 0.6591 (t0)
REVERT: D  275 LYS cc_start: 0.7147 (mttt) cc_final: 0.6335 (tptp)
REVERT: D  318 ILE cc_start: 0.7261 (tt) cc_final: 0.6929 (mm)
REVERT: D  437 ASN cc_start: 0.6332 (t0) cc_final: 0.5950 (m110)
REVERT: D  451 LYS cc_start: 0.6736 (mmpt) cc_final: 0.6411 (mttt)
REVERT: D  457 LYS cc_start: 0.6164 (pttt) cc_final: 0.5804 (tmtt)
  outliers start: 18
  outliers final: 7
  residues processed: 183
  average time/residue: 0.9343
  time to fit residues: 192.1765
Evaluate side-chains
  178 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 171
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 135 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 150 optimal weight:    0.5980
   chunk 125 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0570
   chunk 12 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   overall best weight:    1.3100

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6196
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13276  Z= 0.188
  Angle     :  0.548  15.267  18072  Z= 0.260
  Chirality :  0.039   0.137   1992
  Planarity :  0.005   0.049   2244
  Dihedral  :  5.029  51.464   1996
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 13.72 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.21), residues: 1552
  helix:  1.20 (0.17), residues: 948
  sheet:  2.12 (0.89), residues: 40
  loop : -1.09 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 411 
 HIS   0.002   0.001   HIS B  60 
 PHE   0.013   0.001   PHE B  56 
 TYR   0.006   0.001   TYR D 365 
 ARG   0.001   0.000   ARG C 339 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 179
  time to evaluate  : 1.386 
Fit side-chains
REVERT: A   32 THR cc_start: 0.4805 (OUTLIER) cc_final: 0.4554 (p)
REVERT: A  116 GLU cc_start: 0.5494 (tp30) cc_final: 0.5037 (pt0)
REVERT: A  182 ASP cc_start: 0.6782 (t70) cc_final: 0.6474 (t0)
REVERT: A  265 ILE cc_start: 0.7025 (mt) cc_final: 0.6705 (pt)
REVERT: A  275 LYS cc_start: 0.7194 (mttt) cc_final: 0.6361 (tptp)
REVERT: A  318 ILE cc_start: 0.7220 (tt) cc_final: 0.6931 (mm)
REVERT: A  437 ASN cc_start: 0.6338 (t0) cc_final: 0.5963 (m110)
REVERT: A  451 LYS cc_start: 0.6737 (mmpt) cc_final: 0.6417 (mttt)
REVERT: A  457 LYS cc_start: 0.6148 (pttt) cc_final: 0.5790 (tmtt)
REVERT: B   32 THR cc_start: 0.4773 (OUTLIER) cc_final: 0.4524 (p)
REVERT: B  116 GLU cc_start: 0.5785 (tp30) cc_final: 0.5364 (pt0)
REVERT: B  182 ASP cc_start: 0.6713 (t70) cc_final: 0.6402 (t0)
REVERT: B  275 LYS cc_start: 0.7186 (mttt) cc_final: 0.6326 (tptp)
REVERT: B  318 ILE cc_start: 0.7224 (tt) cc_final: 0.6936 (mm)
REVERT: B  437 ASN cc_start: 0.6336 (t0) cc_final: 0.5899 (m110)
REVERT: B  451 LYS cc_start: 0.6760 (mmpt) cc_final: 0.6430 (mttt)
REVERT: B  458 LYS cc_start: 0.6309 (mmmt) cc_final: 0.6047 (mtmt)
REVERT: C   32 THR cc_start: 0.4742 (OUTLIER) cc_final: 0.4492 (p)
REVERT: C  116 GLU cc_start: 0.5796 (tp30) cc_final: 0.5372 (pt0)
REVERT: C  182 ASP cc_start: 0.6792 (t70) cc_final: 0.6479 (t0)
REVERT: C  213 GLU cc_start: 0.5776 (mp0) cc_final: 0.5518 (mp0)
REVERT: C  265 ILE cc_start: 0.7097 (mt) cc_final: 0.6783 (pt)
REVERT: C  275 LYS cc_start: 0.7182 (mttt) cc_final: 0.6322 (tptp)
REVERT: C  318 ILE cc_start: 0.7226 (tt) cc_final: 0.6939 (mm)
REVERT: C  437 ASN cc_start: 0.6344 (t0) cc_final: 0.5904 (m110)
REVERT: C  451 LYS cc_start: 0.6733 (mmpt) cc_final: 0.6416 (mttt)
REVERT: C  457 LYS cc_start: 0.5964 (pttt) cc_final: 0.5694 (tmtt)
REVERT: D   32 THR cc_start: 0.4780 (OUTLIER) cc_final: 0.4535 (p)
REVERT: D  116 GLU cc_start: 0.5509 (tp30) cc_final: 0.5072 (pt0)
REVERT: D  182 ASP cc_start: 0.6787 (t70) cc_final: 0.6478 (t0)
REVERT: D  265 ILE cc_start: 0.7022 (mt) cc_final: 0.6700 (pt)
REVERT: D  275 LYS cc_start: 0.7195 (mttt) cc_final: 0.6363 (tptp)
REVERT: D  318 ILE cc_start: 0.7229 (tt) cc_final: 0.6940 (mm)
REVERT: D  437 ASN cc_start: 0.6347 (t0) cc_final: 0.5971 (m110)
REVERT: D  451 LYS cc_start: 0.6749 (mmpt) cc_final: 0.6422 (mttt)
REVERT: D  457 LYS cc_start: 0.6106 (pttt) cc_final: 0.5754 (tmtt)
  outliers start: 18
  outliers final: 9
  residues processed: 192
  average time/residue: 0.9383
  time to fit residues: 201.4419
Evaluate side-chains
  188 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 175
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue  253 VAL
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 110 optimal weight:    1.9990
   chunk 127 optimal weight:    9.9990
   chunk 84 optimal weight:    0.8980
   chunk 150 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0030
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.0994

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN
B 438 ASN
C 438 ASN
D 438 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6188
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13276  Z= 0.173
  Angle     :  0.544  15.356  18072  Z= 0.257
  Chirality :  0.038   0.141   1992
  Planarity :  0.004   0.049   2244
  Dihedral  :  4.873  50.736   1996
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.98 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.22), residues: 1552
  helix:  1.31 (0.17), residues: 944
  sheet:  2.19 (0.92), residues: 40
  loop : -1.06 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 411 
 HIS   0.002   0.001   HIS A  60 
 PHE   0.017   0.001   PHE A  56 
 TYR   0.006   0.001   TYR C 403 
 ARG   0.001   0.000   ARG D 339 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 174
  time to evaluate  : 1.443 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.5774 (tp30) cc_final: 0.5332 (pt0)
REVERT: A  182 ASP cc_start: 0.6793 (t70) cc_final: 0.6476 (t70)
REVERT: A  265 ILE cc_start: 0.7048 (mt) cc_final: 0.6722 (pt)
REVERT: A  275 LYS cc_start: 0.7238 (mttt) cc_final: 0.6360 (tptp)
REVERT: A  318 ILE cc_start: 0.7170 (tt) cc_final: 0.6881 (mm)
REVERT: A  437 ASN cc_start: 0.6342 (t0) cc_final: 0.5960 (m110)
REVERT: A  451 LYS cc_start: 0.6759 (mmpt) cc_final: 0.6432 (mttt)
REVERT: A  457 LYS cc_start: 0.6171 (pttt) cc_final: 0.5803 (tmtt)
REVERT: B  116 GLU cc_start: 0.5766 (tp30) cc_final: 0.5338 (pt0)
REVERT: B  182 ASP cc_start: 0.6716 (t70) cc_final: 0.6407 (t0)
REVERT: B  275 LYS cc_start: 0.7248 (mttt) cc_final: 0.6371 (tptp)
REVERT: B  318 ILE cc_start: 0.7175 (tt) cc_final: 0.6890 (mm)
REVERT: B  437 ASN cc_start: 0.6330 (t0) cc_final: 0.5948 (m110)
REVERT: B  451 LYS cc_start: 0.6759 (mmpt) cc_final: 0.6428 (mttt)
REVERT: B  458 LYS cc_start: 0.6334 (mmmt) cc_final: 0.6080 (mtmt)
REVERT: C   41 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6316 (p0)
REVERT: C  116 GLU cc_start: 0.5791 (tp30) cc_final: 0.5373 (pt0)
REVERT: C  182 ASP cc_start: 0.6785 (t70) cc_final: 0.6467 (t0)
REVERT: C  213 GLU cc_start: 0.5752 (mp0) cc_final: 0.5462 (mp0)
REVERT: C  265 ILE cc_start: 0.7122 (mt) cc_final: 0.6801 (pt)
REVERT: C  275 LYS cc_start: 0.7273 (mttt) cc_final: 0.6378 (tptp)
REVERT: C  318 ILE cc_start: 0.7176 (tt) cc_final: 0.6889 (mm)
REVERT: C  437 ASN cc_start: 0.6346 (t0) cc_final: 0.5964 (m110)
REVERT: C  451 LYS cc_start: 0.6759 (mmpt) cc_final: 0.6433 (mttt)
REVERT: C  457 LYS cc_start: 0.5890 (pttt) cc_final: 0.5635 (tmtt)
REVERT: D   41 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6245 (p0)
REVERT: D  116 GLU cc_start: 0.5768 (tp30) cc_final: 0.5350 (pt0)
REVERT: D  182 ASP cc_start: 0.6792 (t70) cc_final: 0.6494 (t0)
REVERT: D  265 ILE cc_start: 0.7050 (mt) cc_final: 0.6721 (pt)
REVERT: D  275 LYS cc_start: 0.7241 (mttt) cc_final: 0.6362 (tptp)
REVERT: D  318 ILE cc_start: 0.7178 (tt) cc_final: 0.6889 (mm)
REVERT: D  437 ASN cc_start: 0.6349 (t0) cc_final: 0.5967 (m110)
REVERT: D  451 LYS cc_start: 0.6750 (mmpt) cc_final: 0.6422 (mttt)
REVERT: D  457 LYS cc_start: 0.6047 (pttt) cc_final: 0.5701 (tmtt)
  outliers start: 30
  outliers final: 16
  residues processed: 196
  average time/residue: 0.9294
  time to fit residues: 203.9132
Evaluate side-chains
  190 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 172
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue   41 ASP
Chi-restraints excluded: chain C residue  253 VAL
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  406 MET
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue   41 ASP
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  389 ILE
Chi-restraints excluded: chain D residue  406 MET
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 118 optimal weight:    9.9990
   chunk 136 optimal weight:    0.7980
   chunk 144 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN
B 438 ASN
C 438 ASN
D 438 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6202
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13276  Z= 0.211
  Angle     :  0.567  15.661  18072  Z= 0.267
  Chirality :  0.039   0.136   1992
  Planarity :  0.004   0.050   2244
  Dihedral  :  4.976  51.970   1996
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.76 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.22), residues: 1552
  helix:  1.13 (0.17), residues: 964
  sheet:  2.16 (0.91), residues: 40
  loop : -1.12 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 411 
 HIS   0.002   0.001   HIS A  60 
 PHE   0.010   0.001   PHE B  56 
 TYR   0.007   0.001   TYR D 365 
 ARG   0.001   0.000   ARG D 339 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 1.342 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.5710 (tp30) cc_final: 0.5273 (pt0)
REVERT: A  182 ASP cc_start: 0.6794 (t70) cc_final: 0.6494 (t0)
REVERT: A  265 ILE cc_start: 0.7093 (mt) cc_final: 0.6736 (pt)
REVERT: A  275 LYS cc_start: 0.7234 (mttt) cc_final: 0.6378 (tptp)
REVERT: A  318 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6899 (mm)
REVERT: A  437 ASN cc_start: 0.6318 (t0) cc_final: 0.5926 (m110)
REVERT: A  451 LYS cc_start: 0.6755 (mmpt) cc_final: 0.6431 (mttt)
REVERT: A  457 LYS cc_start: 0.5973 (pttt) cc_final: 0.5726 (tmtt)
REVERT: B   41 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6203 (p0)
REVERT: B  182 ASP cc_start: 0.6738 (t70) cc_final: 0.6429 (t0)
REVERT: B  275 LYS cc_start: 0.7235 (mttt) cc_final: 0.6377 (tptp)
REVERT: B  318 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6890 (mm)
REVERT: B  437 ASN cc_start: 0.6304 (t0) cc_final: 0.5913 (m110)
REVERT: B  451 LYS cc_start: 0.6748 (mmpt) cc_final: 0.6427 (mttt)
REVERT: B  458 LYS cc_start: 0.6321 (mmmt) cc_final: 0.6063 (mtmt)
REVERT: C   41 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.6288 (p0)
REVERT: C  182 ASP cc_start: 0.6800 (t70) cc_final: 0.6491 (t0)
REVERT: C  213 GLU cc_start: 0.5764 (mp0) cc_final: 0.5471 (mp0)
REVERT: C  265 ILE cc_start: 0.7096 (mt) cc_final: 0.6741 (pt)
REVERT: C  275 LYS cc_start: 0.7249 (mttt) cc_final: 0.6362 (tptp)
REVERT: C  318 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6903 (mm)
REVERT: C  437 ASN cc_start: 0.6323 (t0) cc_final: 0.5931 (m110)
REVERT: C  451 LYS cc_start: 0.6733 (mmpt) cc_final: 0.6416 (mttt)
REVERT: C  457 LYS cc_start: 0.5982 (pttt) cc_final: 0.5671 (tmtt)
REVERT: D   41 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.6232 (p0)
REVERT: D  182 ASP cc_start: 0.6798 (t70) cc_final: 0.6499 (t0)
REVERT: D  265 ILE cc_start: 0.7099 (mt) cc_final: 0.6737 (pt)
REVERT: D  275 LYS cc_start: 0.7234 (mttt) cc_final: 0.6378 (tptp)
REVERT: D  318 ILE cc_start: 0.7220 (tt) cc_final: 0.6903 (mm)
REVERT: D  437 ASN cc_start: 0.6327 (t0) cc_final: 0.5936 (m110)
REVERT: D  451 LYS cc_start: 0.6737 (mmpt) cc_final: 0.6419 (mttt)
REVERT: D  457 LYS cc_start: 0.5939 (pttt) cc_final: 0.5647 (tmtt)
  outliers start: 29
  outliers final: 20
  residues processed: 189
  average time/residue: 0.9453
  time to fit residues: 199.6210
Evaluate side-chains
  199 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue   41 ASP
Chi-restraints excluded: chain C residue  253 VAL
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  406 MET
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue   41 ASP
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  389 ILE
Chi-restraints excluded: chain D residue  406 MET
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    3.9990
   chunk 140 optimal weight:   20.0000
   chunk 144 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   chunk 126 optimal weight:    8.9990
   chunk 132 optimal weight:    1.9990
   chunk 139 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6211
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13276  Z= 0.235
  Angle     :  0.585  16.006  18072  Z= 0.274
  Chirality :  0.040   0.145   1992
  Planarity :  0.005   0.050   2244
  Dihedral  :  5.162  54.405   1996
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.83 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.21), residues: 1552
  helix:  1.09 (0.17), residues: 964
  sheet:  2.13 (0.91), residues: 40
  loop : -1.18 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 411 
 HIS   0.003   0.001   HIS A  60 
 PHE   0.018   0.001   PHE A  56 
 TYR   0.008   0.001   TYR C 365 
 ARG   0.001   0.000   ARG A  59 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 176
  time to evaluate  : 1.366 
Fit side-chains
REVERT: A   41 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6307 (p0)
REVERT: A  182 ASP cc_start: 0.6809 (t70) cc_final: 0.6494 (t70)
REVERT: A  275 LYS cc_start: 0.7257 (mttt) cc_final: 0.6286 (tptp)
REVERT: A  318 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6915 (mm)
REVERT: A  437 ASN cc_start: 0.6351 (t0) cc_final: 0.5966 (m110)
REVERT: A  451 LYS cc_start: 0.6715 (mmpt) cc_final: 0.6408 (mttt)
REVERT: A  457 LYS cc_start: 0.5928 (pttt) cc_final: 0.5685 (tmtt)
REVERT: B   41 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6232 (p0)
REVERT: B  182 ASP cc_start: 0.6724 (t70) cc_final: 0.6423 (t0)
REVERT: B  275 LYS cc_start: 0.7239 (mttt) cc_final: 0.6312 (tptp)
REVERT: B  318 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6917 (mm)
REVERT: B  437 ASN cc_start: 0.6338 (t0) cc_final: 0.5954 (m110)
REVERT: B  451 LYS cc_start: 0.6738 (mmpt) cc_final: 0.6425 (mttt)
REVERT: B  458 LYS cc_start: 0.6340 (mmmt) cc_final: 0.6115 (mtmt)
REVERT: C   41 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6346 (p0)
REVERT: C  182 ASP cc_start: 0.6802 (t70) cc_final: 0.6491 (t0)
REVERT: C  213 GLU cc_start: 0.5799 (mp0) cc_final: 0.5512 (mp0)
REVERT: C  275 LYS cc_start: 0.7277 (mttt) cc_final: 0.6307 (tptp)
REVERT: C  318 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6916 (mm)
REVERT: C  437 ASN cc_start: 0.6358 (t0) cc_final: 0.5971 (m110)
REVERT: C  451 LYS cc_start: 0.6629 (mmpt) cc_final: 0.6342 (mttt)
REVERT: C  457 LYS cc_start: 0.6047 (pttt) cc_final: 0.5744 (tmtt)
REVERT: D   41 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6300 (p0)
REVERT: D  116 GLU cc_start: 0.5801 (tp30) cc_final: 0.5377 (pt0)
REVERT: D  182 ASP cc_start: 0.6813 (t70) cc_final: 0.6498 (t70)
REVERT: D  275 LYS cc_start: 0.7257 (mttt) cc_final: 0.6286 (tptp)
REVERT: D  318 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6920 (mm)
REVERT: D  437 ASN cc_start: 0.6361 (t0) cc_final: 0.5975 (m110)
REVERT: D  451 LYS cc_start: 0.6730 (mmpt) cc_final: 0.6418 (mttt)
REVERT: D  457 LYS cc_start: 0.5983 (pttt) cc_final: 0.5672 (tmtt)
  outliers start: 31
  outliers final: 19
  residues processed: 193
  average time/residue: 0.8844
  time to fit residues: 191.8304
Evaluate side-chains
  202 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue   41 ASP
Chi-restraints excluded: chain C residue  253 VAL
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  389 ILE
Chi-restraints excluded: chain C residue  406 MET
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue   41 ASP
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  318 ILE
Chi-restraints excluded: chain D residue  389 ILE
Chi-restraints excluded: chain D residue  406 MET
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 70 optimal weight:    0.3980
   chunk 102 optimal weight:    3.9990
   chunk 155 optimal weight:    9.9990
   chunk 143 optimal weight:    3.9990
   chunk 123 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    2.2788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6226
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13276  Z= 0.287
  Angle     :  0.620  16.136  18072  Z= 0.292
  Chirality :  0.041   0.149   1992
  Planarity :  0.005   0.051   2244
  Dihedral  :  5.434  59.579   1996
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.72 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.21), residues: 1552
  helix:  0.93 (0.17), residues: 968
  sheet:  2.11 (0.89), residues: 40
  loop : -1.23 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 411 
 HIS   0.003   0.001   HIS A  60 
 PHE   0.014   0.001   PHE B  56 
 TYR   0.009   0.001   TYR C 365 
 ARG   0.002   0.000   ARG A 339 

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

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

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3104 Ramachandran restraints generated.
    1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 171
  time to evaluate  : 1.409 
Fit side-chains
REVERT: A  116 GLU cc_start: 0.5794 (tp30) cc_final: 0.5375 (pt0)
REVERT: A  182 ASP cc_start: 0.6811 (t70) cc_final: 0.6495 (t70)
REVERT: A  275 LYS cc_start: 0.7283 (mttt) cc_final: 0.6330 (tptp)
REVERT: A  318 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6916 (mm)
REVERT: A  437 ASN cc_start: 0.6363 (t0) cc_final: 0.5971 (m110)
REVERT: A  451 LYS cc_start: 0.6634 (mmpt) cc_final: 0.6348 (mtmt)
REVERT: B   41 ASP cc_start: 0.6649 (OUTLIER) cc_final: 0.6356 (p0)
REVERT: B  182 ASP cc_start: 0.6773 (t70) cc_final: 0.6456 (t70)
REVERT: B  275 LYS cc_start: 0.7259 (mttt) cc_final: 0.6319 (tptp)
REVERT: B  318 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6923 (mm)
REVERT: B  437 ASN cc_start: 0.6348 (t0) cc_final: 0.5961 (m110)
REVERT: B  451 LYS cc_start: 0.6644 (mmpt) cc_final: 0.6349 (mttt)
REVERT: B  458 LYS cc_start: 0.6331 (mmmt) cc_final: 0.6107 (mtmt)
REVERT: C   41 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6267 (p0)
REVERT: C  182 ASP cc_start: 0.6835 (t70) cc_final: 0.6517 (t70)
REVERT: C  213 GLU cc_start: 0.5801 (mp0) cc_final: 0.5516 (mp0)
REVERT: C  275 LYS cc_start: 0.7296 (mttt) cc_final: 0.6318 (tptp)
REVERT: C  318 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6933 (mm)
REVERT: C  437 ASN cc_start: 0.6367 (t0) cc_final: 0.5980 (m110)
REVERT: C  451 LYS cc_start: 0.6619 (mmpt) cc_final: 0.6339 (mtmt)
REVERT: D  182 ASP cc_start: 0.6814 (t70) cc_final: 0.6498 (t70)
REVERT: D  275 LYS cc_start: 0.7283 (mttt) cc_final: 0.6330 (tptp)
REVERT: D  318 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6934 (mm)
REVERT: D  437 ASN cc_start: 0.6369 (t0) cc_final: 0.5980 (m110)
REVERT: D  451 LYS cc_start: 0.6639 (mmpt) cc_final: 0.6347 (mttt)
REVERT: D  457 LYS cc_start: 0.6035 (pttt) cc_final: 0.5733 (tmtt)
  outliers start: 28
  outliers final: 12
  residues processed: 184
  average time/residue: 0.9365
  time to fit residues: 193.4783
Evaluate side-chains
  188 residues out of total 1364 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  412 SER
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain C residue   41 ASP
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  406 MET
Chi-restraints excluded: chain C residue  412 SER
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  318 ILE
Chi-restraints excluded: chain D residue  406 MET
Chi-restraints excluded: chain D residue  412 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 123 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 127 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0870
   chunk 108 optimal weight:    0.0870
   overall best weight:    0.5738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.198972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.137371 restraints weight = 14551.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.93
r_work: 0.3045 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
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      :  0.002   0.050  13276  Z= 0.137
  Angle     :  0.533  16.023  18072  Z= 0.249
  Chirality :  0.038   0.154   1992
  Planarity :  0.004   0.048   2244
  Dihedral  :  5.025  58.199   1996
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.32 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.22), residues: 1552
  helix:  1.39 (0.17), residues: 940
  sheet:  2.18 (0.93), residues: 40
  loop : -1.06 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 411 
 HIS   0.002   0.000   HIS A  60 
 PHE   0.019   0.001   PHE A  56 
 TYR   0.006   0.001   TYR A  48 
 ARG   0.001   0.000   ARG A 314 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4170.50 seconds
wall clock time: 75 minutes 5.97 seconds (4505.97 seconds total)