Starting phenix.real_space_refine
on Sun May 11 11:03:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bof_44734/05_2025/9bof_44734_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bof_44734/05_2025/9bof_44734.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bof_44734/05_2025/9bof_44734.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bof_44734/05_2025/9bof_44734.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bof_44734/05_2025/9bof_44734_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bof_44734/05_2025/9bof_44734_neut.cif"
  }
  resolution = 2.61
  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=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    5142      2.51       5
     N    1344      2.21       5
     O    1562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8076
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2164
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 285, 2130
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 253}
          Unresolved chain links: 1
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
      Conformer: "B"
        Number of residues, atoms: 285, 2130
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 253}
          Unresolved chain links: 1
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
          bond proxies already assigned to first conformer: 2163
      Conformer: "C"
        Number of residues, atoms: 284, 2102
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 252}
          Unresolved chain links: 1
          Chain breaks: 1
          Unresolved chain link angles: 13
          Unresolved chain link dihedrals: 24
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
          bond proxies already assigned to first conformer: 2163
    Chain: "B"
      Number of atoms: 2164
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 285, 2130
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 253}
          Unresolved chain links: 1
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
      Conformer: "B"
        Number of residues, atoms: 285, 2130
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 253}
          Unresolved chain links: 1
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
          bond proxies already assigned to first conformer: 2163
      Conformer: "C"
        Number of residues, atoms: 284, 2102
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 252}
          Unresolved chain links: 1
          Chain breaks: 1
          Unresolved chain link angles: 13
          Unresolved chain link dihedrals: 24
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
          bond proxies already assigned to first conformer: 2163
    Chain: "C"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 853
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103}
    Chain: "E"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1021
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 5, 'TRANS': 127}
    Chain: "G"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1021
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 5, 'TRANS': 127}
    Chain: "H"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 853
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AASP A 350 " occ=0.53
      ... (14 atoms not shown)
      pdb=" OD2BASP A 350 " occ=0.47
    residue:
      pdb=" N  AASP B 350 " occ=0.53
      ... (14 atoms not shown)
      pdb=" OD2BASP B 350 " occ=0.47
  Time building chain proxies: 8.57, per 1000 atoms: 1.06
  Number of scatterers: 8076
  At special positions: 0
  Unit cell: (78.02, 126.99, 62.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1562      8.00
     N    1344      7.00
     C    5142      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  95 " distance=2.05
    Simple disulfide: pdb=" SG  CYS G  21 " - pdb=" SG  CYS G  95 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  93 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.88
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1924

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 16 sheets defined
      7.2% alpha, 36.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 237 through 241
    Processing helix  chain 'A' and resid 438 through 449
    Processing helix  chain 'A' and resid 491 through 495
    Processing helix  chain 'B' and resid 237 through 241
    Processing helix  chain 'B' and resid 438 through 449
    Processing helix  chain 'B' and resid 491 through 495
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 86 through 90
    Processing helix  chain 'E' and resid 106 through 111
    Processing helix  chain 'G' and resid 27 through 31
    Processing helix  chain 'G' and resid 86 through 90
    Processing helix  chain 'G' and resid 106 through 111
    Processing sheet with id=AA1, first strand: chain 'A' and resid 250 through 255
      removed outlier: 7.640A  pdb=" N   ILE A 250 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LYS A 424 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   TYR A 431 " --> pdb=" O   MET A 425 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 250 through 255
      removed outlier: 7.640A  pdb=" N   ILE A 250 " --> pdb=" O   LYS A 424 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LYS A 424 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   LEU A 481 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE A 480 " --> pdb=" O   TYR A 476 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   GLY A 471 " --> pdb=" O   TYR A 461 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ALA A 456 " --> pdb=" O   TRP A 506 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   TRP A 506 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU A 458 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 345
      removed outlier: 6.475A  pdb=" N   ASP A 327 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE A 376 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   HIS A 329 " --> pdb=" O   SER A 374 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ARG A 291 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 250 through 255
      removed outlier: 7.640A  pdb=" N   ILE B 250 " --> pdb=" O   LYS B 424 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LYS B 424 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   TYR B 431 " --> pdb=" O   MET B 425 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 255
      removed outlier: 7.640A  pdb=" N   ILE B 250 " --> pdb=" O   LYS B 424 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LYS B 424 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   LEU B 481 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE B 480 " --> pdb=" O   TYR B 476 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   GLY B 471 " --> pdb=" O   TYR B 461 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ALA B 456 " --> pdb=" O   TRP B 506 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   TRP B 506 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU B 458 " --> pdb=" O   VAL B 504 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345
      removed outlier: 6.474A  pdb=" N   ASP B 327 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ILE B 376 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   HIS B 329 " --> pdb=" O   SER B 374 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ARG B 291 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.621A  pdb=" N   VAL C  38 " --> pdb=" O   TYR C  54 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   TYR C  54 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   TRP C  40 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 59
      removed outlier: 6.562A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLY E  49 " --> pdb=" O   PHE E  33 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   PHE E  33 " --> pdb=" O   GLY E  49 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER E 122 " --> pdb=" O   LYS E  97 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 59
      removed outlier: 6.562A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLY E  49 " --> pdb=" O   PHE E  33 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   PHE E  33 " --> pdb=" O   GLY E  49 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 2 through 6
    Processing sheet with id=AB4, first strand: chain 'G' and resid 57 through 59
      removed outlier: 6.562A  pdb=" N   TRP G  35 " --> pdb=" O   VAL G  47 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLY G  49 " --> pdb=" O   PHE G  33 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   PHE G  33 " --> pdb=" O   GLY G  49 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER G 122 " --> pdb=" O   LYS G  97 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 57 through 59
      removed outlier: 6.562A  pdb=" N   TRP G  35 " --> pdb=" O   VAL G  47 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   GLY G  49 " --> pdb=" O   PHE G  33 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   PHE G  33 " --> pdb=" O   GLY G  49 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 7
    Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 13
      removed outlier: 6.621A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  54 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   TYR H  54 " --> pdb=" O   VAL H  38 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   TRP H  40 " --> pdb=" O   LEU H  52 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.41

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1338
        1.31 -     1.44: 2338
        1.44 -     1.57: 4608
        1.57 -     1.69: 0
        1.69 -     1.82: 40
  Bond restraints: 8324
  Sorted by residual:
  bond pdb=" CA  GLU A 416 "
       pdb=" C   GLU A 416 "
    ideal  model  delta    sigma   weight residual
    1.520  1.425  0.096 1.22e-02 6.72e+03 6.17e+01
  bond pdb=" CA  PHE A 231 "
       pdb=" CB  PHE A 231 "
    ideal  model  delta    sigma   weight residual
    1.529  1.449  0.080 1.53e-02 4.27e+03 2.70e+01
  bond pdb=" CA  PHE B 231 "
       pdb=" CB  PHE B 231 "
    ideal  model  delta    sigma   weight residual
    1.529  1.450  0.079 1.53e-02 4.27e+03 2.64e+01
  bond pdb=" CA  PHE B 231 "
       pdb=" C   PHE B 231 "
    ideal  model  delta    sigma   weight residual
    1.523  1.462  0.061 1.30e-02 5.92e+03 2.23e+01
  bond pdb=" CA  PHE A 231 "
       pdb=" C   PHE A 231 "
    ideal  model  delta    sigma   weight residual
    1.523  1.462  0.061 1.30e-02 5.92e+03 2.21e+01
  ... (remaining 8319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 11200
        2.75 -     5.51: 168
        5.51 -     8.26: 18
        8.26 -    11.02: 3
       11.02 -    13.77: 1
  Bond angle restraints: 11390
  Sorted by residual:
  angle pdb=" N   PHE A 414 "
        pdb=" CA  PHE A 414 "
        pdb=" C   PHE A 414 "
      ideal   model   delta    sigma   weight residual
     110.80  124.57  -13.77 2.13e+00 2.20e-01 4.18e+01
  angle pdb=" C   PRO A 411 "
        pdb=" N   PRO A 412 "
        pdb=" CA  PRO A 412 "
      ideal   model   delta    sigma   weight residual
     119.84  125.33   -5.49 1.25e+00 6.40e-01 1.93e+01
  angle pdb=" CA  GLU C  86 "
        pdb=" CB  GLU C  86 "
        pdb=" CG  GLU C  86 "
      ideal   model   delta    sigma   weight residual
     114.10  122.72   -8.62 2.00e+00 2.50e-01 1.86e+01
  angle pdb=" CA  GLU H  86 "
        pdb=" CB  GLU H  86 "
        pdb=" CG  GLU H  86 "
      ideal   model   delta    sigma   weight residual
     114.10  122.69   -8.59 2.00e+00 2.50e-01 1.85e+01
  angle pdb=" C   GLY A 413 "
        pdb=" N   PHE A 414 "
        pdb=" CA  PHE A 414 "
      ideal   model   delta    sigma   weight residual
     121.54  129.36   -7.82 1.91e+00 2.74e-01 1.68e+01
  ... (remaining 11385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4369
       17.97 -    35.95: 395
       35.95 -    53.92: 123
       53.92 -    71.89: 20
       71.89 -    89.86: 9
  Dihedral angle restraints: 4916
    sinusoidal: 1864
      harmonic: 3052
  Sorted by residual:
  dihedral pdb=" CA  SER B 398 "
           pdb=" C   SER B 398 "
           pdb=" N   ILE B 399 "
           pdb=" CA  ILE B 399 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.30  -26.70     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  SER A 398 "
           pdb=" C   SER A 398 "
           pdb=" N   ILE A 399 "
           pdb=" CA  ILE A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.30  -26.70     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  ASN E 116 "
           pdb=" C   ASN E 116 "
           pdb=" N   THR E 117 "
           pdb=" CA  THR E 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.78   26.22     0      5.00e+00 4.00e-02 2.75e+01
  ... (remaining 4913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 1221
       0.124 -    0.248: 20
       0.248 -    0.371: 0
       0.371 -    0.495: 0
       0.495 -    0.619: 1
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  PHE A 414 "
            pdb=" N   PHE A 414 "
            pdb=" C   PHE A 414 "
            pdb=" CB  PHE A 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.89    0.62 2.00e-01 2.50e+01 9.58e+00
  chirality pdb=" CA  PHE A 231 "
            pdb=" N   PHE A 231 "
            pdb=" C   PHE A 231 "
            pdb=" CB  PHE A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  PHE B 231 "
            pdb=" N   PHE B 231 "
            pdb=" C   PHE B 231 "
            pdb=" CB  PHE B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1239 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 509 "    0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   ARG A 509 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ARG A 509 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PHE A 510 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 509 "   -0.016 2.00e-02 2.50e+03   3.20e-02 1.03e+01
        pdb=" C   ARG B 509 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ARG B 509 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PHE B 510 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  51 "    0.031 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO G  52 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO G  52 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO G  52 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 65
        2.43 -     3.05: 5238
        3.05 -     3.67: 12379
        3.67 -     4.28: 19162
        4.28 -     4.90: 33372
  Nonbonded interactions: 70216
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 230 "
            pdb=" OE2 GLU B 448 "
     model   vdw
     1.813 3.040
  nonbonded pdb=" O   PRO A 230 "
            pdb=" OE2 GLU A 448 "
     model   vdw
     1.814 3.040
  nonbonded pdb=" OG1 THR A 271 "
            pdb=" OD1 ASP A 273 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OG1 THR B 271 "
            pdb=" OD1 ASP B 273 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OE1 GLU G   5 "
            pdb=" N   GLY G 126 "
     model   vdw
     2.164 3.120
  ... (remaining 70211 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
}

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=0.15 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.860
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.050
  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:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
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      :  0.010   0.096   8328  Z= 0.503
  Angle     :  0.868  13.771  11398  Z= 0.480
  Chirality :  0.054   0.619   1242
  Planarity :  0.005   0.046   1500
  Dihedral  : 15.876  89.865   2980
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.27 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 18.18 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -1.43 (0.25), residues: 1064
  helix: -0.70 (0.94), residues: 26
  sheet: -0.91 (0.26), residues: 340
  loop : -0.97 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 390 
 HIS   0.008   0.002   HIS A 310 
 PHE   0.025   0.003   PHE A 231 
 TYR   0.014   0.002   TYR B 395 
 ARG   0.008   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14237 (  266)
  hydrogen bonds       : angle       8.26695 (  750)
  SS BOND              : bond        0.01177 (    4)
  SS BOND              : angle       1.52557 (    8)
  covalent geometry    : bond        0.01042 ( 8324)
  covalent geometry    : angle       0.86686 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 207
  time to evaluate  : 0.899 
Fit side-chains
REVERT: H   41 TYR cc_start: 0.8322 (m-80) cc_final: 0.8031 (m-80)
  outliers start: 60
  outliers final: 18
  residues processed: 241
  average time/residue: 0.9910
  time to fit residues: 255.3510
Evaluate side-chains
  138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain C residue    5 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain E residue  104 ARG
Chi-restraints excluded: chain E residue  116 ASN
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue  104 ARG
Chi-restraints excluded: chain G residue  116 ASN
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain H residue    5 SER
Chi-restraints excluded: chain H residue    7 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 94 optimal weight:    8.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 439 GLN
A 444 HIS
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 ASN
B 439 GLN
B 444 HIS
C  36 ASN
C  58 ASN
E   2 GLN
G   2 GLN
H  36 ASN
H  58 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.106284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.089562 restraints weight = 104360.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 7.29
r_work: 0.3315 rms_B_bonded: 6.78 restraints_weight: 2.0000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8328  Z= 0.155
  Angle     :  0.667   8.029  11398  Z= 0.342
  Chirality :  0.045   0.192   1242
  Planarity :  0.006   0.064   1500
  Dihedral  :  6.227  52.590   1189
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 23.17 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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 (0.26), residues: 1064
  helix:  1.38 (1.09), residues: 26
  sheet: -0.61 (0.25), residues: 386
  loop : -0.39 (0.26), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 506 
 HIS   0.004   0.001   HIS B 329 
 PHE   0.032   0.002   PHE A 312 
 TYR   0.012   0.001   TYR B 511 
 ARG   0.004   0.001   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03155 (  266)
  hydrogen bonds       : angle       6.20850 (  750)
  SS BOND              : bond        0.00395 (    4)
  SS BOND              : angle       1.00124 (    8)
  covalent geometry    : bond        0.00365 ( 8324)
  covalent geometry    : angle       0.66673 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8198 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7195 (t)
REVERT: A  322 ASP cc_start: 0.8268 (t70) cc_final: 0.7919 (t0)
REVERT: A  425 MET cc_start: 0.9255 (mmm) cc_final: 0.9001 (tpt)
REVERT: A  472 GLU cc_start: 0.7277 (pm20) cc_final: 0.6784 (pm20)
REVERT: B  275 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8228 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7421 (OUTLIER) cc_final: 0.7176 (t)
REVERT: B  472 GLU cc_start: 0.7172 (pm20) cc_final: 0.6748 (pm20)
REVERT: C    4 MET cc_start: 0.7714 (mtp) cc_final: 0.7421 (mtp)
REVERT: C   41 TYR cc_start: 0.8612 (m-80) cc_final: 0.8133 (m-80)
REVERT: C   84 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7811 (mm-30)
REVERT: C   94 MET cc_start: 0.8826 (ttt) cc_final: 0.7993 (ttp)
REVERT: E   86 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7347 (ptp90)
REVERT: E  125 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7512 (pm20)
REVERT: G   86 ARG cc_start: 0.7748 (ptp90) cc_final: 0.7420 (ptp90)
REVERT: H   82 ARG cc_start: 0.8907 (mtm-85) cc_final: 0.8704 (mtm110)
REVERT: H   84 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7958 (mm-30)
  outliers start: 38
  outliers final: 9
  residues processed: 176
  average time/residue: 1.1483
  time to fit residues: 214.4610
Evaluate side-chains
  136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain H residue    2 ILE
Chi-restraints excluded: chain H residue   26 SER
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   88 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0000
   chunk 18 optimal weight:    0.6980
   chunk 90 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0470
   chunk 17 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.5484

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 GLN
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 486 ASN
B 494 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.106925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.090537 restraints weight = 92648.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 7.07
r_work: 0.3350 rms_B_bonded: 6.71 restraints_weight: 2.0000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8328  Z= 0.126
  Angle     :  0.618   6.467  11398  Z= 0.312
  Chirality :  0.044   0.172   1242
  Planarity :  0.005   0.063   1500
  Dihedral  :  5.142  56.110   1164
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.50 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -0.28 (0.26), residues: 1064
  helix:  2.26 (1.14), residues: 26
  sheet: -0.43 (0.25), residues: 386
  loop : -0.02 (0.26), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E  35 
 HIS   0.003   0.001   HIS B 329 
 PHE   0.026   0.001   PHE A 312 
 TYR   0.013   0.001   TYR H  41 
 ARG   0.004   0.001   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02702 (  266)
  hydrogen bonds       : angle       5.51833 (  750)
  SS BOND              : bond        0.00419 (    4)
  SS BOND              : angle       0.80064 (    8)
  covalent geometry    : bond        0.00306 ( 8324)
  covalent geometry    : angle       0.61826 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8023 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7196 (t)
REVERT: A  322 ASP cc_start: 0.8214 (t70) cc_final: 0.7888 (t0)
REVERT: A  424 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8833 (mtmm)
REVERT: A  425 MET cc_start: 0.9218 (mmm) cc_final: 0.8985 (tpt)
REVERT: A  472 GLU cc_start: 0.7440 (pm20) cc_final: 0.6892 (pm20)
REVERT: B  275 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8065 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7137 (t)
REVERT: B  388 ASP cc_start: 0.8272 (t0) cc_final: 0.7932 (t0)
REVERT: B  424 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8899 (mtmm)
REVERT: B  459 LEU cc_start: 0.6422 (mt) cc_final: 0.6141 (mt)
REVERT: B  472 GLU cc_start: 0.7356 (pm20) cc_final: 0.6863 (pm20)
REVERT: C   41 TYR cc_start: 0.8701 (m-80) cc_final: 0.8188 (m-80)
REVERT: C   84 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7967 (mm-30)
REVERT: C   94 MET cc_start: 0.8800 (ttt) cc_final: 0.8129 (ttp)
REVERT: C   98 GLN cc_start: 0.6802 (pt0) cc_final: 0.6573 (pp30)
REVERT: E   42 LYS cc_start: 0.8275 (mppt) cc_final: 0.8010 (mppt)
REVERT: G   86 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7631 (ptp90)
REVERT: H    4 MET cc_start: 0.7761 (mmm) cc_final: 0.7548 (mtp)
REVERT: H   27 GLN cc_start: 0.8379 (mp10) cc_final: 0.7955 (mp10)
REVERT: H   44 LYS cc_start: 0.9074 (mttt) cc_final: 0.8090 (mttt)
REVERT: H   47 GLN cc_start: 0.7899 (mp10) cc_final: 0.7428 (mp10)
REVERT: H   82 ARG cc_start: 0.8920 (mtm-85) cc_final: 0.8675 (mtm110)
REVERT: H   84 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8065 (mm-30)
REVERT: H   95 GLN cc_start: 0.9239 (pp30) cc_final: 0.8241 (pp30)
  outliers start: 22
  outliers final: 6
  residues processed: 158
  average time/residue: 1.1348
  time to fit residues: 190.6835
Evaluate side-chains
  136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  424 LYS
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain E residue   82 MET
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain H residue    2 ILE
Chi-restraints excluded: chain H residue   20 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.105546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.089039 restraints weight = 93587.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 6.97
r_work: 0.3338 rms_B_bonded: 6.62 restraints_weight: 2.0000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3346
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8328  Z= 0.135
  Angle     :  0.602   5.841  11398  Z= 0.304
  Chirality :  0.044   0.169   1242
  Planarity :  0.005   0.063   1500
  Dihedral  :  4.993  51.686   1164
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.72 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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:  0.02 (0.27), residues: 1064
  helix:  2.39 (1.14), residues: 26
  sheet: -0.19 (0.26), residues: 380
  loop :  0.16 (0.26), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 123 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.024   0.002   PHE A 312 
 TYR   0.011   0.001   TYR B 441 
 ARG   0.007   0.001   ARG E  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02601 (  266)
  hydrogen bonds       : angle       5.45157 (  750)
  SS BOND              : bond        0.00401 (    4)
  SS BOND              : angle       0.78170 (    8)
  covalent geometry    : bond        0.00327 ( 8324)
  covalent geometry    : angle       0.60156 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7902 (ttp-110)
REVERT: A  322 ASP cc_start: 0.8246 (t70) cc_final: 0.7918 (t0)
REVERT: A  459 LEU cc_start: 0.6497 (mt) cc_final: 0.6196 (mt)
REVERT: A  472 GLU cc_start: 0.7612 (pm20) cc_final: 0.6955 (pm20)
REVERT: B  275 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7978 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7196 (t)
REVERT: B  459 LEU cc_start: 0.6535 (mt) cc_final: 0.6279 (mt)
REVERT: B  472 GLU cc_start: 0.7546 (pm20) cc_final: 0.6925 (pm20)
REVERT: C   84 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8002 (mm-30)
REVERT: C   98 GLN cc_start: 0.6915 (pt0) cc_final: 0.6604 (pp30)
REVERT: E   86 ARG cc_start: 0.7761 (ptp-110) cc_final: 0.7223 (ptp90)
REVERT: E  125 GLN cc_start: 0.8185 (pm20) cc_final: 0.7870 (mm-40)
REVERT: G   86 ARG cc_start: 0.7945 (ptp90) cc_final: 0.7467 (ptp90)
REVERT: H   44 LYS cc_start: 0.9033 (mttt) cc_final: 0.8025 (mttt)
REVERT: H   47 GLN cc_start: 0.7777 (mp10) cc_final: 0.7335 (mp10)
REVERT: H   95 GLN cc_start: 0.9203 (pp30) cc_final: 0.8116 (pp30)
REVERT: H   98 GLN cc_start: 0.6882 (pt0) cc_final: 0.6547 (pp30)
  outliers start: 26
  outliers final: 9
  residues processed: 155
  average time/residue: 1.2236
  time to fit residues: 200.9198
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue    2 ILE
Chi-restraints excluded: chain H residue   20 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 73 optimal weight:    0.0030
   chunk 92 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0570
   chunk 45 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.5308

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   2 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.107843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.091339 restraints weight = 112105.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 7.54
r_work: 0.3368 rms_B_bonded: 7.04 restraints_weight: 2.0000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3376
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8328  Z= 0.113
  Angle     :  0.591   6.188  11398  Z= 0.293
  Chirality :  0.043   0.163   1242
  Planarity :  0.005   0.057   1500
  Dihedral  :  4.369  21.822   1162
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 27.05 %
    Favored  : 70.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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:  0.38 (0.27), residues: 1064
  helix:  2.64 (1.17), residues: 26
  sheet:  0.07 (0.27), residues: 392
  loop :  0.40 (0.27), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP G  46 
 HIS   0.002   0.001   HIS A 329 
 PHE   0.022   0.001   PHE A 312 
 TYR   0.012   0.001   TYR B 441 
 ARG   0.004   0.001   ARG E  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02451 (  266)
  hydrogen bonds       : angle       5.25819 (  750)
  SS BOND              : bond        0.00423 (    4)
  SS BOND              : angle       1.10067 (    8)
  covalent geometry    : bond        0.00272 ( 8324)
  covalent geometry    : angle       0.59058 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7855 (ttp-110)
REVERT: A  322 ASP cc_start: 0.8187 (t70) cc_final: 0.7904 (t0)
REVERT: A  459 LEU cc_start: 0.6459 (mt) cc_final: 0.6185 (mt)
REVERT: A  472 GLU cc_start: 0.7555 (pm20) cc_final: 0.6859 (pm20)
REVERT: B  275 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7933 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7167 (t)
REVERT: B  424 LYS cc_start: 0.9165 (mtmp) cc_final: 0.8857 (mtmm)
REVERT: B  459 LEU cc_start: 0.6471 (mt) cc_final: 0.6208 (mt)
REVERT: B  472 GLU cc_start: 0.7464 (pm20) cc_final: 0.6809 (pm20)
REVERT: E   42 LYS cc_start: 0.8260 (mppt) cc_final: 0.8033 (mppt)
REVERT: E   86 ARG cc_start: 0.7587 (ptp-110) cc_final: 0.7110 (ptp90)
REVERT: G   12 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8195 (t-90)
REVERT: G   56 ASP cc_start: 0.8331 (m-30) cc_final: 0.8120 (m-30)
REVERT: G   86 ARG cc_start: 0.7925 (ptp90) cc_final: 0.7531 (ptp90)
REVERT: H   27 GLN cc_start: 0.8195 (mp10) cc_final: 0.7988 (mp10)
REVERT: H   44 LYS cc_start: 0.8988 (mttt) cc_final: 0.8010 (mttt)
REVERT: H   47 GLN cc_start: 0.7625 (mp10) cc_final: 0.7185 (mp10)
REVERT: H   95 GLN cc_start: 0.9190 (pp30) cc_final: 0.8197 (pp30)
REVERT: H   98 GLN cc_start: 0.7025 (pt0) cc_final: 0.6668 (pp30)
  outliers start: 24
  outliers final: 7
  residues processed: 158
  average time/residue: 1.1237
  time to fit residues: 188.6193
Evaluate side-chains
  142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue    2 ILE
Chi-restraints excluded: chain H residue   20 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0070
   chunk 15 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.1604

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.105235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.088810 restraints weight = 108270.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 7.38
r_work: 0.3319 rms_B_bonded: 6.87 restraints_weight: 2.0000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8328  Z= 0.147
  Angle     :  0.621   6.488  11398  Z= 0.307
  Chirality :  0.045   0.167   1242
  Planarity :  0.005   0.058   1500
  Dihedral  :  4.516  21.715   1162
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 26.94 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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:  0.36 (0.27), residues: 1064
  helix:  2.53 (1.15), residues: 26
  sheet: -0.05 (0.27), residues: 374
  loop :  0.46 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.021   0.002   PHE A 312 
 TYR   0.011   0.001   TYR E  94 
 ARG   0.009   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02666 (  266)
  hydrogen bonds       : angle       5.42584 (  750)
  SS BOND              : bond        0.00586 (    4)
  SS BOND              : angle       1.46503 (    8)
  covalent geometry    : bond        0.00358 ( 8324)
  covalent geometry    : angle       0.61960 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7870 (ttp-110)
REVERT: A  322 ASP cc_start: 0.8284 (t70) cc_final: 0.7991 (t0)
REVERT: A  472 GLU cc_start: 0.7610 (pm20) cc_final: 0.6830 (pm20)
REVERT: B  275 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7878 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7227 (t)
REVERT: B  472 GLU cc_start: 0.7605 (pm20) cc_final: 0.6858 (pm20)
REVERT: C   27 GLN cc_start: 0.8323 (mp10) cc_final: 0.8012 (mp10)
REVERT: G   12 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8253 (t-90)
REVERT: G   86 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7657 (ptp90)
REVERT: G  125 GLN cc_start: 0.8101 (pm20) cc_final: 0.6764 (mm-40)
REVERT: H   27 GLN cc_start: 0.8206 (mp10) cc_final: 0.7979 (mp10)
REVERT: H   44 LYS cc_start: 0.8978 (mttt) cc_final: 0.7997 (mttt)
REVERT: H   47 GLN cc_start: 0.7631 (mp10) cc_final: 0.7162 (mp10)
REVERT: H   95 GLN cc_start: 0.8968 (pp30) cc_final: 0.8311 (pp30)
REVERT: H   98 GLN cc_start: 0.7057 (pt0) cc_final: 0.6758 (pp30)
  outliers start: 16
  outliers final: 5
  residues processed: 148
  average time/residue: 1.1795
  time to fit residues: 185.0382
Evaluate side-chains
  138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  112 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 27 optimal weight:    0.2980
   chunk 71 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.105773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.089190 restraints weight = 114855.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 7.46
r_work: 0.3305 rms_B_bonded: 6.92 restraints_weight: 2.0000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8328  Z= 0.147
  Angle     :  0.623   6.785  11398  Z= 0.308
  Chirality :  0.044   0.164   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.458  20.968   1162
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 27.38 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.27), residues: 1064
  helix:  2.45 (1.15), residues: 26
  sheet: -0.09 (0.27), residues: 374
  loop :  0.50 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP G  46 
 HIS   0.004   0.001   HIS B 329 
 PHE   0.021   0.001   PHE A 312 
 TYR   0.011   0.001   TYR E  94 
 ARG   0.010   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02592 (  266)
  hydrogen bonds       : angle       5.40591 (  750)
  SS BOND              : bond        0.00348 (    4)
  SS BOND              : angle       0.93127 (    8)
  covalent geometry    : bond        0.00356 ( 8324)
  covalent geometry    : angle       0.62309 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7876 (ttp-110)
REVERT: A  322 ASP cc_start: 0.8300 (t70) cc_final: 0.8022 (t0)
REVERT: A  472 GLU cc_start: 0.7602 (pm20) cc_final: 0.6771 (pm20)
REVERT: B  275 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7866 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7261 (t)
REVERT: B  424 LYS cc_start: 0.9153 (mtmp) cc_final: 0.8802 (mtmp)
REVERT: B  472 GLU cc_start: 0.7559 (pm20) cc_final: 0.6804 (pm20)
REVERT: C   27 GLN cc_start: 0.8262 (mp10) cc_final: 0.7950 (mp10)
REVERT: G   12 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.8259 (t-90)
REVERT: G   42 LYS cc_start: 0.7329 (tmmt) cc_final: 0.7124 (tmmt)
REVERT: G   86 ARG cc_start: 0.7954 (ptp90) cc_final: 0.7637 (ptp90)
REVERT: G  125 GLN cc_start: 0.7944 (pm20) cc_final: 0.7329 (mm-40)
REVERT: H   27 GLN cc_start: 0.8187 (mp10) cc_final: 0.7717 (mp10)
REVERT: H   95 GLN cc_start: 0.8978 (pp30) cc_final: 0.7866 (pp30)
REVERT: H   98 GLN cc_start: 0.7101 (pt0) cc_final: 0.6780 (pp30)
  outliers start: 16
  outliers final: 8
  residues processed: 149
  average time/residue: 1.2067
  time to fit residues: 190.9753
Evaluate side-chains
  143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  112 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 41 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.105387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.089285 restraints weight = 103576.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 7.13
r_work: 0.3329 rms_B_bonded: 6.76 restraints_weight: 2.0000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3335
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8328  Z= 0.137
  Angle     :  0.617   7.000  11398  Z= 0.304
  Chirality :  0.044   0.160   1242
  Planarity :  0.005   0.056   1500
  Dihedral  :  4.445  19.723   1162
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 27.38 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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:  0.39 (0.27), residues: 1064
  helix:  2.43 (1.14), residues: 26
  sheet: -0.13 (0.26), residues: 374
  loop :  0.56 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.020   0.001   PHE B 312 
 TYR   0.018   0.001   TYR G  59 
 ARG   0.012   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02566 (  266)
  hydrogen bonds       : angle       5.36202 (  750)
  SS BOND              : bond        0.00400 (    4)
  SS BOND              : angle       0.86094 (    8)
  covalent geometry    : bond        0.00338 ( 8324)
  covalent geometry    : angle       0.61656 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7854 (ttp-110)
REVERT: A  322 ASP cc_start: 0.8274 (t70) cc_final: 0.8014 (t0)
REVERT: A  424 LYS cc_start: 0.9119 (mttp) cc_final: 0.8829 (mttp)
REVERT: A  459 LEU cc_start: 0.6749 (mt) cc_final: 0.6491 (mt)
REVERT: A  472 GLU cc_start: 0.7584 (pm20) cc_final: 0.6793 (pm20)
REVERT: A  511 TYR cc_start: 0.6510 (t80) cc_final: 0.6255 (t80)
REVERT: B  275 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7863 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7488 (OUTLIER) cc_final: 0.7258 (t)
REVERT: B  472 GLU cc_start: 0.7572 (pm20) cc_final: 0.6768 (pm20)
REVERT: C   27 GLN cc_start: 0.8212 (mp10) cc_final: 0.7865 (mp10)
REVERT: E   42 LYS cc_start: 0.8003 (tptp) cc_final: 0.7601 (tmmt)
REVERT: E   86 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7277 (ptp90)
REVERT: G   12 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8265 (t-90)
REVERT: G   55 HIS cc_start: 0.8715 (m-70) cc_final: 0.8500 (m170)
REVERT: G   86 ARG cc_start: 0.7943 (ptp90) cc_final: 0.7586 (ptp90)
REVERT: G   92 GLN cc_start: 0.6665 (tt0) cc_final: 0.6016 (tm-30)
REVERT: G  125 GLN cc_start: 0.8094 (pm20) cc_final: 0.7533 (mm-40)
REVERT: H   27 GLN cc_start: 0.8202 (mp10) cc_final: 0.7740 (mp10)
REVERT: H   95 GLN cc_start: 0.8955 (pp30) cc_final: 0.8455 (pp30)
REVERT: H   98 GLN cc_start: 0.7136 (pt0) cc_final: 0.6885 (pp30)
  outliers start: 16
  outliers final: 10
  residues processed: 150
  average time/residue: 1.1200
  time to fit residues: 178.9026
Evaluate side-chains
  144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue    2 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0270
   chunk 26 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 30 optimal weight:    0.1980
   chunk 86 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0970
   chunk 40 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.4640

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.108104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.091934 restraints weight = 96832.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 7.15
r_work: 0.3380 rms_B_bonded: 6.77 restraints_weight: 2.0000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8328  Z= 0.115
  Angle     :  0.615   7.223  11398  Z= 0.303
  Chirality :  0.045   0.382   1242
  Planarity :  0.005   0.054   1500
  Dihedral  :  4.233  17.687   1162
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 27.94 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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:  0.52 (0.28), residues: 1064
  helix:  2.54 (1.15), residues: 26
  sheet: -0.03 (0.27), residues: 374
  loop :  0.64 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E  46 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.019   0.001   PHE A 312 
 TYR   0.017   0.001   TYR G  59 
 ARG   0.012   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02468 (  266)
  hydrogen bonds       : angle       5.15352 (  750)
  SS BOND              : bond        0.00406 (    4)
  SS BOND              : angle       0.84573 (    8)
  covalent geometry    : bond        0.00276 ( 8324)
  covalent geometry    : angle       0.61460 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7884 (ttm-80)
REVERT: A  322 ASP cc_start: 0.8115 (t70) cc_final: 0.7879 (t0)
REVERT: A  424 LYS cc_start: 0.9114 (mttp) cc_final: 0.8789 (mtmp)
REVERT: A  459 LEU cc_start: 0.6616 (mt) cc_final: 0.6346 (mt)
REVERT: A  472 GLU cc_start: 0.7470 (pm20) cc_final: 0.6763 (pm20)
REVERT: A  511 TYR cc_start: 0.6540 (t80) cc_final: 0.6281 (t80)
REVERT: B  275 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7790 (ttp-110)
REVERT: B  424 LYS cc_start: 0.9119 (mttp) cc_final: 0.8795 (mtmp)
REVERT: B  459 LEU cc_start: 0.6650 (mt) cc_final: 0.6408 (mt)
REVERT: B  472 GLU cc_start: 0.7478 (pm20) cc_final: 0.6761 (pm20)
REVERT: C   27 GLN cc_start: 0.8200 (mp10) cc_final: 0.7815 (mp10)
REVERT: E   42 LYS cc_start: 0.7883 (tptp) cc_final: 0.7306 (tmmt)
REVERT: E   55 HIS cc_start: 0.8716 (m-70) cc_final: 0.8447 (m170)
REVERT: E   86 ARG cc_start: 0.7719 (ptp90) cc_final: 0.7214 (ptp90)
REVERT: E   92 GLN cc_start: 0.6728 (tt0) cc_final: 0.6009 (tm-30)
REVERT: G   12 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.8325 (t-90)
REVERT: G   55 HIS cc_start: 0.8705 (m-70) cc_final: 0.8433 (m170)
REVERT: G   92 GLN cc_start: 0.6642 (tt0) cc_final: 0.6033 (tm-30)
REVERT: G  125 GLN cc_start: 0.8013 (pm20) cc_final: 0.7580 (mm-40)
REVERT: H   27 GLN cc_start: 0.8201 (mp10) cc_final: 0.7983 (mp10)
REVERT: H   47 GLN cc_start: 0.7543 (mp10) cc_final: 0.7203 (mp10)
REVERT: H   95 GLN cc_start: 0.8868 (pp30) cc_final: 0.8531 (pp30)
REVERT: H   98 GLN cc_start: 0.7090 (pt0) cc_final: 0.6851 (pp30)
  outliers start: 11
  outliers final: 8
  residues processed: 147
  average time/residue: 1.1552
  time to fit residues: 181.2045
Evaluate side-chains
  143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue   82 MET
Chi-restraints excluded: chain G residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:    0.0470
   chunk 85 optimal weight:    0.4980
   chunk 101 optimal weight:    1.9990
   chunk 52 optimal weight:    0.2980
   chunk 91 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 75 optimal weight:    9.9990
   chunk 20 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0060
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0980
   overall best weight:    0.1894

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.109806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.093694 restraints weight = 99242.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 7.17
r_work: 0.3413 rms_B_bonded: 6.87 restraints_weight: 2.0000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8328  Z= 0.107
  Angle     :  0.612   7.162  11398  Z= 0.299
  Chirality :  0.045   0.415   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.167  16.087   1162
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 27.83 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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:  0.57 (0.28), residues: 1064
  helix:  2.52 (1.13), residues: 26
  sheet: -0.03 (0.27), residues: 376
  loop :  0.71 (0.27), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.019   0.001   PHE A 312 
 TYR   0.023   0.001   TYR E  59 
 ARG   0.014   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02308 (  266)
  hydrogen bonds       : angle       4.98966 (  750)
  SS BOND              : bond        0.00315 (    4)
  SS BOND              : angle       0.56332 (    8)
  covalent geometry    : bond        0.00258 ( 8324)
  covalent geometry    : angle       0.61218 (11390)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7821 (ttm-80)
REVERT: A  322 ASP cc_start: 0.8061 (t70) cc_final: 0.7842 (t0)
REVERT: A  424 LYS cc_start: 0.9086 (mttp) cc_final: 0.8805 (mttp)
REVERT: A  459 LEU cc_start: 0.6542 (mt) cc_final: 0.6282 (mt)
REVERT: A  472 GLU cc_start: 0.7412 (pm20) cc_final: 0.6726 (pm20)
REVERT: A  511 TYR cc_start: 0.6520 (t80) cc_final: 0.6191 (t80)
REVERT: B  275 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7749 (ttp-110)
REVERT: B  424 LYS cc_start: 0.9114 (mttp) cc_final: 0.8833 (mttp)
REVERT: B  459 LEU cc_start: 0.6558 (mt) cc_final: 0.6331 (mt)
REVERT: B  472 GLU cc_start: 0.7380 (pm20) cc_final: 0.6712 (pm20)
REVERT: B  511 TYR cc_start: 0.6324 (t80) cc_final: 0.6089 (t80)
REVERT: C   27 GLN cc_start: 0.8184 (mp10) cc_final: 0.7839 (mp10)
REVERT: C   47 GLN cc_start: 0.7494 (mp10) cc_final: 0.7239 (mp10)
REVERT: C   98 GLN cc_start: 0.7323 (pp30) cc_final: 0.6886 (pp30)
REVERT: C  111 ILE cc_start: 0.7801 (pt) cc_final: 0.7201 (mt)
REVERT: E   42 LYS cc_start: 0.7765 (tptp) cc_final: 0.7204 (tmmt)
REVERT: E   55 HIS cc_start: 0.8725 (m-70) cc_final: 0.8438 (m170)
REVERT: E   86 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7170 (ptp90)
REVERT: E   88 GLU cc_start: 0.9202 (mp0) cc_final: 0.8679 (pp20)
REVERT: E   92 GLN cc_start: 0.6584 (tt0) cc_final: 0.5918 (tm-30)
REVERT: G   12 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8332 (t-90)
REVERT: G   55 HIS cc_start: 0.8697 (m-70) cc_final: 0.8447 (m170)
REVERT: G   92 GLN cc_start: 0.6639 (tt0) cc_final: 0.6029 (tm-30)
REVERT: G  125 GLN cc_start: 0.7946 (pm20) cc_final: 0.7582 (mm-40)
REVERT: H   27 GLN cc_start: 0.8230 (mp10) cc_final: 0.8004 (mp10)
REVERT: H   44 LYS cc_start: 0.8752 (mttt) cc_final: 0.7748 (mmtt)
REVERT: H   47 GLN cc_start: 0.7422 (mp10) cc_final: 0.7095 (mp10)
REVERT: H   95 GLN cc_start: 0.8863 (pp30) cc_final: 0.8317 (pp30)
REVERT: H   98 GLN cc_start: 0.7159 (pt0) cc_final: 0.6946 (pp30)
REVERT: H  111 ILE cc_start: 0.7787 (pt) cc_final: 0.7090 (mt)
  outliers start: 13
  outliers final: 7
  residues processed: 151
  average time/residue: 1.0770
  time to fit residues: 173.5089
Evaluate side-chains
  139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 101 optimal weight:   10.0000
   chunk 27 optimal weight:    0.1980
   chunk 99 optimal weight:    0.7980
   chunk 102 optimal weight:    1.9990
   chunk 81 optimal weight:    0.3980
   chunk 11 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.106796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.090639 restraints weight = 100427.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 7.19
r_work: 0.3357 rms_B_bonded: 6.82 restraints_weight: 2.0000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.4499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   8328  Z= 0.140
  Angle     :  0.645  12.489  11398  Z= 0.313
  Chirality :  0.045   0.393   1242
  Planarity :  0.005   0.054   1500
  Dihedral  :  4.285  15.638   1162
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 28.71 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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:  0.60 (0.28), residues: 1064
  helix:  2.40 (1.11), residues: 26
  sheet:  0.01 (0.27), residues: 364
  loop :  0.71 (0.27), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP G  46 
 HIS   0.005   0.001   HIS A 286 
 PHE   0.020   0.001   PHE A 312 
 TYR   0.021   0.001   TYR E  59 
 ARG   0.013   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02497 (  266)
  hydrogen bonds       : angle       5.13415 (  750)
  SS BOND              : bond        0.00356 (    4)
  SS BOND              : angle       0.60995 (    8)
  covalent geometry    : bond        0.00346 ( 8324)
  covalent geometry    : angle       0.64514 (11390)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6605.75 seconds
wall clock time: 114 minutes 18.93 seconds (6858.93 seconds total)