Starting phenix.real_space_refine
on Sun Mar 10 19:38:03 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpe_22286/03_2024/6xpe_22286.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpe_22286/03_2024/6xpe_22286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpe_22286/03_2024/6xpe_22286.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpe_22286/03_2024/6xpe_22286.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpe_22286/03_2024/6xpe_22286.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpe_22286/03_2024/6xpe_22286.pdb"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 144 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      8      6.06       5
     S      32      5.16       5
     C    2806      2.51       5
     N     692      2.21       5
     O     754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR   67": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  131": "NH1" <-> "NH2"
    Residue "B PHE  218": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  248": "OD1" <-> "OD2"
    Residue "B PHE  253": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  284": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  331": "NH1" <-> "NH2"
    Residue "B PHE  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   67": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  131": "NH1" <-> "NH2"
    Residue "A PHE  218": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  248": "OD1" <-> "OD2"
    Residue "A PHE  253": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  284": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  331": "NH1" <-> "NH2"
    Residue "A PHE  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 4292
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2142
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2142
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' ZN': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2158  SG  CYS A  53      34.917  42.485  22.387  1.00140.11           S
  ATOM   2079  SG  CYS B 361      36.563  50.333  26.866  1.00135.63           S
  ATOM   2104  SG  CYS B 364      39.360  48.066  24.716  1.00130.17           S
  ATOM     16  SG  CYS B  53      39.783  23.915  22.387  1.00140.11           S
  ATOM   4221  SG  CYS A 361      38.137  16.067  26.866  1.00135.63           S
  ATOM   4246  SG  CYS A 364      35.340  18.334  24.716  1.00130.17           S

  Time building chain proxies: 2.92, per 1000 atoms: 0.68
  Number of scatterers: 4292
  At special positions: 0
  Unit cell: (75.53, 67.23, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      8     29.99
     S      32     16.00
     O     754      8.00
     N     692      7.00
     C    2806      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: 2.12
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  52 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 361 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 364 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  54 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" NE2 HIS A 301 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS A 318 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS B  53 "
      pdb="  ZN A 403 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS B  52 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 361 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 364 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS B  54 "
      pdb="  ZN A 404 "
        pdb="ZN    ZN A 404 " - pdb=" NE2 HIS A 137 "
        pdb="ZN    ZN A 404 " - pdb=" NE2 HIS A 345 "
      pdb="  ZN A 405 "
        pdb="ZN    ZN A 405 " - pdb=" NE2 HIS A 106 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B 318 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B 301 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A  53 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 137 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 345 "
      pdb="  ZN B 403 "
        pdb="ZN    ZN B 403 " - pdb=" NE2 HIS B 106 "
      Number of angles added : 4


  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 2 sheets defined
      62.5% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'B' and resid 65 through 84
      removed outlier: 3.705A  pdb=" N   ALA B  70 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B  76 " --> pdb=" O   TRP B  72 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ALA B  77 " --> pdb=" O   LYS B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 124
      removed outlier: 4.324A  pdb=" N   LEU B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 116 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 168
      removed outlier: 3.682A  pdb=" N   LEU B 142 " --> pdb=" O   ARG B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 196
      removed outlier: 3.741A  pdb=" N   ILE B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B 181 " --> pdb=" O   VAL B 177 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA B 187 " --> pdb=" O   SER B 183 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 239
      removed outlier: 4.504A  pdb=" N   VAL B 219 " --> pdb=" O   ARG B 215 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL B 231 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 237 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 274
      removed outlier: 4.342A  pdb=" N   ILE B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE B 257 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   THR B 265 " --> pdb=" O   ALA B 261 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP B 269 " --> pdb=" O   THR B 265 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE B 272 " --> pdb=" O   LYS B 268 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 274 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 293
      removed outlier: 3.550A  pdb=" N   LYS B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU B 289 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 340
      removed outlier: 3.798A  pdb=" N   ARG B 331 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS B 336 " --> pdb=" O   ARG B 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 84
      removed outlier: 3.705A  pdb=" N   ALA A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS A  71 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A  76 " --> pdb=" O   TRP A  72 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ALA A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 124
      removed outlier: 3.821A  pdb=" N   LEU A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU A 116 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 168
      removed outlier: 3.682A  pdb=" N   LEU A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 196
      removed outlier: 3.741A  pdb=" N   ILE A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER A 182 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 187 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 239
      removed outlier: 4.504A  pdb=" N   VAL A 219 " --> pdb=" O   ARG A 215 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL A 231 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 274
      removed outlier: 4.342A  pdb=" N   ILE A 250 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 257 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   THR A 265 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 293
      removed outlier: 3.550A  pdb=" N   LYS A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU A 289 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 3.798A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS A 336 " --> pdb=" O   ARG A 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 301 through 307
      removed outlier: 5.011A  pdb=" N   SER B 302 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   HIS B 318 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 307
      removed outlier: 5.011A  pdb=" N   SER A 302 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   HIS A 318 " --> pdb=" O   SER A 302 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    708 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 2.15 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: 1298
        1.34 -     1.46: 834
        1.46 -     1.57: 2192
        1.57 -     1.69: 2
        1.69 -     1.81: 44
  Bond restraints: 4370
  Sorted by residual:
  bond pdb=" N   HIS B 106 "
       pdb=" CA  HIS B 106 "
    ideal  model  delta    sigma   weight residual
    1.459  1.397  0.062 1.20e-02 6.94e+03 2.68e+01
  bond pdb=" CA  PRO B 354 "
       pdb=" C   PRO B 354 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.065 1.42e-02 4.96e+03 2.08e+01
  bond pdb=" CA  PRO A 354 "
       pdb=" C   PRO A 354 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.065 1.42e-02 4.96e+03 2.08e+01
  bond pdb=" CA  VAL A 355 "
       pdb=" C   VAL A 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.562 -0.039 1.27e-02 6.20e+03 9.57e+00
  bond pdb=" CA  VAL B 355 "
       pdb=" C   VAL B 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.562 -0.039 1.27e-02 6.20e+03 9.57e+00
  ... (remaining 4365 not shown)

  Histogram of bond angle deviations from ideal:
       98.55 -   105.63: 60
      105.63 -   112.72: 2581
      112.72 -   119.81: 1323
      119.81 -   126.89: 1913
      126.89 -   133.98: 63
  Bond angle restraints: 5940
  Sorted by residual:
  angle pdb=" C   VAL A 355 "
        pdb=" N   ASP A 356 "
        pdb=" CA  ASP A 356 "
      ideal   model   delta    sigma   weight residual
     123.00  131.98   -8.98 1.38e+00 5.25e-01 4.24e+01
  angle pdb=" C   VAL B 355 "
        pdb=" N   ASP B 356 "
        pdb=" CA  ASP B 356 "
      ideal   model   delta    sigma   weight residual
     123.00  131.98   -8.98 1.38e+00 5.25e-01 4.24e+01
  angle pdb=" C   PHE A 114 "
        pdb=" N   LEU A 115 "
        pdb=" CA  LEU A 115 "
      ideal   model   delta    sigma   weight residual
     120.82  127.96   -7.14 1.50e+00 4.44e-01 2.26e+01
  angle pdb=" N   PHE A 114 "
        pdb=" CA  PHE A 114 "
        pdb=" C   PHE A 114 "
      ideal   model   delta    sigma   weight residual
     110.80  120.47   -9.67 2.13e+00 2.20e-01 2.06e+01
  angle pdb=" N   VAL B 355 "
        pdb=" CA  VAL B 355 "
        pdb=" C   VAL B 355 "
      ideal   model   delta    sigma   weight residual
     109.34  116.94   -7.60 2.08e+00 2.31e-01 1.33e+01
  ... (remaining 5935 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.89: 2155
       11.89 -    23.79: 264
       23.79 -    35.68: 120
       35.68 -    47.57: 41
       47.57 -    59.47: 10
  Dihedral angle restraints: 2590
    sinusoidal: 952
      harmonic: 1638
  Sorted by residual:
  dihedral pdb=" CA  LEU B 308 "
           pdb=" C   LEU B 308 "
           pdb=" N   THR B 309 "
           pdb=" CA  THR B 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  LEU A 308 "
           pdb=" C   LEU A 308 "
           pdb=" N   THR A 309 "
           pdb=" CA  THR A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  PRO A 354 "
           pdb=" C   PRO A 354 "
           pdb=" N   VAL A 355 "
           pdb=" CA  VAL A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.06   23.94     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 2587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 666
       0.067 -    0.135: 73
       0.135 -    0.202: 2
       0.202 -    0.269: 0
       0.269 -    0.337: 1
  Chirality restraints: 742
  Sorted by residual:
  chirality pdb=" CA  PHE A 114 "
            pdb=" N   PHE A 114 "
            pdb=" C   PHE A 114 "
            pdb=" CB  PHE A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CB  ILE B 305 "
            pdb=" CA  ILE B 305 "
            pdb=" CG1 ILE B 305 "
            pdb=" CG2 ILE B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CB  ILE A 305 "
            pdb=" CA  ILE A 305 "
            pdb=" CG1 ILE A 305 "
            pdb=" CG2 ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.83e-01
  ... (remaining 739 not shown)

  Planarity restraints: 706
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 105 "   -0.021 2.00e-02 2.50e+03   4.31e-02 1.86e+01
        pdb=" C   ALA B 105 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ALA B 105 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   HIS B 106 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 106 "   -0.019 2.00e-02 2.50e+03   2.17e-02 7.08e+00
        pdb=" CG  HIS B 106 "    0.019 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 106 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 106 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 106 "    0.014 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 106 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 248 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 249 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 249 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 249 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 703 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.17: 9
        2.17 -     2.86: 1745
        2.86 -     3.54: 6492
        3.54 -     4.22: 9384
        4.22 -     4.90: 15752
  Nonbonded interactions: 33382
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.492 2.230
  nonbonded pdb=" OD2 ASP B 224 "
            pdb="ZN    ZN B 403 "
     model   vdw
     1.514 2.230
  nonbonded pdb=" OD1 ASP B 224 "
            pdb="ZN    ZN B 403 "
     model   vdw
     1.590 2.230
  nonbonded pdb=" CG  ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.615 2.460
  nonbonded pdb=" OD1 ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.619 2.230
  ... (remaining 33377 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 52 through 369 or resid 401 through 403))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.830
  Check model and map are aligned:         0.070
  Set scattering table:                    0.040
  Process input model:                     17.580
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   4370  Z= 0.410
  Angle     :  0.819   9.670   5940  Z= 0.461
  Chirality :  0.044   0.337    742
  Planarity :  0.004   0.043    706
  Dihedral  : 14.302  59.467   1510
  Min Nonbonded Distance : 1.492

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  : 10.57 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.08 %
    Favored  : 85.83 %
  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: -5.36 (0.30), residues: 530
  helix: -3.29 (0.21), residues: 332
  sheet: -4.09 (0.59), residues: 44
  loop : -3.38 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 122 
 HIS   0.025   0.002   HIS B 106 
 PHE   0.012   0.001   PHE B 218 
 TYR   0.007   0.001   TYR B 160 
 ARG   0.002   0.000   ARG B 131 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 GLN cc_start: 0.9142 (tp40) cc_final: 0.8608 (tm-30)
REVERT: B  310 MET cc_start: 0.7366 (mmm) cc_final: 0.7068 (mtp)
REVERT: A  227 GLN cc_start: 0.9131 (tp40) cc_final: 0.8593 (tm-30)
REVERT: A  310 MET cc_start: 0.7360 (mmm) cc_final: 0.7074 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 75
  average time/residue: 0.1918
  time to fit residues: 17.8113
Evaluate side-chains
  52 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 27 optimal weight:   30.0000
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 211 ASN
** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4370  Z= 0.254
  Angle     :  0.628   6.570   5940  Z= 0.324
  Chirality :  0.042   0.234    742
  Planarity :  0.004   0.035    706
  Dihedral  :  4.995  28.814    572
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  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: -2.76 (0.36), residues: 530
  helix: -1.12 (0.27), residues: 342
  sheet: -2.78 (0.71), residues: 40
  loop : -2.90 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 122 
 HIS   0.004   0.001   HIS A 318 
 PHE   0.017   0.002   PHE A 114 
 TYR   0.009   0.001   TYR B  67 
 ARG   0.002   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  140 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8521 (mt-10)
REVERT: B  310 MET cc_start: 0.7237 (mmm) cc_final: 0.6815 (mtp)
REVERT: A  140 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8539 (mt-10)
REVERT: A  310 MET cc_start: 0.7236 (mmm) cc_final: 0.6825 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1298
  time to fit residues: 12.5256
Evaluate side-chains
  41 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:   30.0000
   chunk 15 optimal weight:   20.0000
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4370  Z= 0.282
  Angle     :  0.642   7.253   5940  Z= 0.326
  Chirality :  0.042   0.177    742
  Planarity :  0.004   0.039    706
  Dihedral  :  4.901  28.992    572
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  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: -1.77 (0.38), residues: 530
  helix: -0.28 (0.28), residues: 342
  sheet: -2.50 (0.72), residues: 42
  loop : -2.69 (0.58), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 122 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.020   0.002   PHE B 114 
 TYR   0.016   0.002   TYR B  69 
 ARG   0.002   0.000   ARG B 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 LEU cc_start: 0.8906 (tp) cc_final: 0.8701 (tp)
REVERT: B  310 MET cc_start: 0.7142 (mmm) cc_final: 0.6708 (mtp)
REVERT: A  310 MET cc_start: 0.7133 (mmm) cc_final: 0.6694 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1438
  time to fit residues: 12.2006
Evaluate side-chains
  45 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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: 0.8175
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4370  Z= 0.155
  Angle     :  0.532   6.709   5940  Z= 0.272
  Chirality :  0.039   0.137    742
  Planarity :  0.004   0.041    706
  Dihedral  :  4.464  26.212    572
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.38), residues: 530
  helix:  0.45 (0.29), residues: 342
  sheet: -2.05 (0.73), residues: 48
  loop : -2.75 (0.53), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.009   0.001   PHE A 119 
 TYR   0.013   0.001   TYR B  69 
 ARG   0.001   0.000   ARG B 138 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8867 (t) cc_final: 0.8274 (p)
REVERT: B  275 MET cc_start: 0.8751 (mmm) cc_final: 0.8264 (mmt)
REVERT: B  309 THR cc_start: 0.8070 (p) cc_final: 0.7809 (p)
REVERT: B  365 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: A   75 CYS cc_start: 0.8875 (t) cc_final: 0.8298 (p)
REVERT: A  109 ILE cc_start: 0.9030 (mt) cc_final: 0.8677 (tp)
REVERT: A  227 GLN cc_start: 0.8871 (tp40) cc_final: 0.8520 (tm-30)
REVERT: A  275 MET cc_start: 0.8812 (mmm) cc_final: 0.8292 (mmt)
REVERT: A  309 THR cc_start: 0.8071 (p) cc_final: 0.7803 (p)
REVERT: A  365 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7745 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1311
  time to fit residues: 14.6745
Evaluate side-chains
  56 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0060
   chunk 26 optimal weight:   20.0000
   chunk 46 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    2.4004

-------------------------------------------------------------------------------
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: 0.8162
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4370  Z= 0.198
  Angle     :  0.560   5.533   5940  Z= 0.291
  Chirality :  0.041   0.239    742
  Planarity :  0.004   0.037    706
  Dihedral  :  4.351  22.299    572
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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: -0.82 (0.39), residues: 530
  helix:  0.60 (0.30), residues: 344
  sheet: -2.14 (0.73), residues: 48
  loop : -2.80 (0.52), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 152 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.018   0.002   PHE A 114 
 TYR   0.012   0.001   TYR B  69 
 ARG   0.009   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8869 (t) cc_final: 0.8301 (p)
REVERT: B  111 LEU cc_start: 0.8881 (tp) cc_final: 0.8676 (tp)
REVERT: B  227 GLN cc_start: 0.8789 (tp40) cc_final: 0.8550 (tm-30)
REVERT: B  331 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8810 (ttp80)
REVERT: B  365 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7621 (tm-30)
REVERT: A   75 CYS cc_start: 0.8868 (t) cc_final: 0.8289 (p)
REVERT: A  109 ILE cc_start: 0.9008 (mt) cc_final: 0.8692 (tp)
REVERT: A  111 LEU cc_start: 0.8700 (tp) cc_final: 0.8487 (tp)
REVERT: A  227 GLN cc_start: 0.8907 (tp40) cc_final: 0.8685 (tp40)
REVERT: A  331 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8807 (ttp80)
REVERT: A  365 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7624 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1346
  time to fit residues: 14.4895
Evaluate side-chains
  46 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    0.2980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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: 0.8140
moved from start:          0.5079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4370  Z= 0.154
  Angle     :  0.518   5.179   5940  Z= 0.267
  Chirality :  0.038   0.126    742
  Planarity :  0.004   0.034    706
  Dihedral  :  4.212  22.934    572
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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: -0.46 (0.39), residues: 530
  helix:  0.85 (0.31), residues: 340
  sheet: -1.82 (0.75), residues: 46
  loop : -2.54 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.016   0.001   PHE B 114 
 TYR   0.004   0.001   TYR B 284 
 ARG   0.008   0.001   ARG B 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8763 (t) cc_final: 0.8259 (p)
REVERT: B  111 LEU cc_start: 0.8757 (tp) cc_final: 0.8505 (tp)
REVERT: B  309 THR cc_start: 0.7941 (p) cc_final: 0.7717 (p)
REVERT: B  365 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: A   75 CYS cc_start: 0.8765 (t) cc_final: 0.8259 (p)
REVERT: A  109 ILE cc_start: 0.9022 (mt) cc_final: 0.8682 (tp)
REVERT: A  111 LEU cc_start: 0.8674 (tp) cc_final: 0.8458 (tp)
REVERT: A  365 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7940 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1308
  time to fit residues: 13.7250
Evaluate side-chains
  55 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 38 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    2.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4370  Z= 0.185
  Angle     :  0.569   7.997   5940  Z= 0.287
  Chirality :  0.039   0.116    742
  Planarity :  0.004   0.032    706
  Dihedral  :  4.040  18.580    572
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -0.35 (0.39), residues: 530
  helix:  0.84 (0.30), residues: 338
  sheet: -1.87 (0.77), residues: 48
  loop : -2.12 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 122 
 HIS   0.003   0.001   HIS B 220 
 PHE   0.014   0.002   PHE A 114 
 TYR   0.012   0.001   TYR B  69 
 ARG   0.009   0.001   ARG B 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8766 (t) cc_final: 0.8258 (p)
REVERT: B  146 LEU cc_start: 0.9266 (tp) cc_final: 0.9035 (tp)
REVERT: B  365 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: A   75 CYS cc_start: 0.8775 (t) cc_final: 0.8271 (p)
REVERT: A  109 ILE cc_start: 0.9046 (mt) cc_final: 0.8757 (tp)
REVERT: A  365 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7826 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1338
  time to fit residues: 14.0441
Evaluate side-chains
  50 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 29 optimal weight:    0.4980
   chunk 21 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.5023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4370  Z= 0.257
  Angle     :  0.640   7.328   5940  Z= 0.316
  Chirality :  0.040   0.116    742
  Planarity :  0.004   0.034    706
  Dihedral  :  4.319  24.332    572
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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: -0.47 (0.39), residues: 530
  helix:  0.70 (0.30), residues: 348
  sheet: -1.77 (0.77), residues: 48
  loop : -2.31 (0.54), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 122 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.017   0.002   PHE B 342 
 TYR   0.012   0.001   TYR B 239 
 ARG   0.008   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8851 (t) cc_final: 0.8310 (p)
REVERT: B  146 LEU cc_start: 0.9307 (tp) cc_final: 0.9047 (tp)
REVERT: B  309 THR cc_start: 0.8449 (p) cc_final: 0.8227 (p)
REVERT: A   75 CYS cc_start: 0.8857 (t) cc_final: 0.8287 (p)
REVERT: A  109 ILE cc_start: 0.9106 (mt) cc_final: 0.8822 (tp)
REVERT: A  146 LEU cc_start: 0.9341 (tp) cc_final: 0.9100 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1386
  time to fit residues: 13.3032
Evaluate side-chains
  45 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:   40.0000
   chunk 43 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 227 GLN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.5519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4370  Z= 0.151
  Angle     :  0.580   8.444   5940  Z= 0.287
  Chirality :  0.038   0.122    742
  Planarity :  0.004   0.040    706
  Dihedral  :  4.069  18.871    572
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.25 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.39), residues: 530
  helix:  0.88 (0.30), residues: 340
  sheet: -1.04 (0.84), residues: 44
  loop : -2.06 (0.52), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 122 
 HIS   0.004   0.001   HIS B 345 
 PHE   0.015   0.001   PHE B 342 
 TYR   0.010   0.001   TYR A  69 
 ARG   0.010   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8830 (t) cc_final: 0.8345 (p)
REVERT: B  365 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: A   75 CYS cc_start: 0.8818 (t) cc_final: 0.8331 (p)
REVERT: A  109 ILE cc_start: 0.9151 (mt) cc_final: 0.8922 (tp)
REVERT: A  310 MET cc_start: 0.6607 (mmt) cc_final: 0.6315 (mmm)
REVERT: A  365 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8052 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 80
  average time/residue: 0.1309
  time to fit residues: 13.9969
Evaluate side-chains
  49 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0270
   chunk 42 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.3644

-------------------------------------------------------------------------------
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: 0.8110
moved from start:          0.5672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4370  Z= 0.166
  Angle     :  0.570   8.311   5940  Z= 0.284
  Chirality :  0.039   0.123    742
  Planarity :  0.004   0.036    706
  Dihedral  :  3.858  16.603    572
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -0.06 (0.39), residues: 530
  helix:  0.92 (0.30), residues: 342
  sheet: -1.53 (0.83), residues: 48
  loop : -1.78 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 152 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.012   0.001   PHE B 342 
 TYR   0.012   0.001   TYR B  69 
 ARG   0.009   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8819 (t) cc_final: 0.8312 (p)
REVERT: B  146 LEU cc_start: 0.9298 (tp) cc_final: 0.9085 (tp)
REVERT: B  365 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: A   75 CYS cc_start: 0.8814 (t) cc_final: 0.8315 (p)
REVERT: A  109 ILE cc_start: 0.9174 (mt) cc_final: 0.8947 (tp)
REVERT: A  111 LEU cc_start: 0.8589 (tp) cc_final: 0.8294 (tp)
REVERT: A  365 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7929 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1320
  time to fit residues: 14.5028
Evaluate side-chains
  57 residues out of total 482 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    0.2980
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 2 optimal weight:   20.0000
   chunk 30 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    2.4586

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.089756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.073784 restraints weight = 12544.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.075661 restraints weight = 7605.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.076894 restraints weight = 5402.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.5504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4370  Z= 0.195
  Angle     :  0.595   8.069   5940  Z= 0.295
  Chirality :  0.039   0.122    742
  Planarity :  0.004   0.039    706
  Dihedral  :  3.966  20.001    572
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -0.21 (0.40), residues: 530
  helix:  0.73 (0.30), residues: 352
  sheet: -1.44 (0.85), residues: 48
  loop : -1.88 (0.56), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.014   0.001   PHE B 342 
 TYR   0.004   0.001   TYR A  67 
 ARG   0.009   0.001   ARG B 331 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1072.71 seconds
wall clock time: 20 minutes 13.04 seconds (1213.04 seconds total)