Starting phenix.real_space_refine
on Mon Apr 28 19:06:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bof_44734/04_2025/9bof_44734_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bof_44734/04_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_44734/04_2025/9bof_44734.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bof_44734/04_2025/9bof_44734.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bof_44734/04_2025/9bof_44734_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bof_44734/04_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-5669/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: 8.83, per 1000 atoms: 1.09
  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: 2.18
  Conformation dependent library (CDL) restraints added in 2.1 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: 1.14
  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: 2.33

  Time building geometry restraints manager: 2.47 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:             1.150
  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:                     27.560
  Find NCS groups from input model:        0.140
  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:12.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.580
-------------------------------------------------------------------------------
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  : 0.833 
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: 1.0066
  time to fit residues: 259.3244
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  : 0.902 
-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.106306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.089551 restraints weight = 104410.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 7.30
r_work: 0.3313 rms_B_bonded: 6.83 restraints_weight: 2.0000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
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       1.00125 (    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  : 0.825 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8216 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7486 (OUTLIER) cc_final: 0.7197 (t)
REVERT: A  322 ASP cc_start: 0.8270 (t70) cc_final: 0.7924 (t0)
REVERT: A  425 MET cc_start: 0.9259 (mmm) cc_final: 0.9007 (tpt)
REVERT: A  472 GLU cc_start: 0.7286 (pm20) cc_final: 0.6796 (pm20)
REVERT: B  275 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8242 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7182 (t)
REVERT: B  472 GLU cc_start: 0.7180 (pm20) cc_final: 0.6759 (pm20)
REVERT: C    4 MET cc_start: 0.7706 (mtp) cc_final: 0.7413 (mtp)
REVERT: C   41 TYR cc_start: 0.8620 (m-80) cc_final: 0.8140 (m-80)
REVERT: C   84 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7816 (mm-30)
REVERT: C   94 MET cc_start: 0.8828 (ttt) cc_final: 0.7999 (ttp)
REVERT: E   86 ARG cc_start: 0.8003 (ptp90) cc_final: 0.7357 (ptp90)
REVERT: E  125 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7521 (pm20)
REVERT: G   86 ARG cc_start: 0.7758 (ptp90) cc_final: 0.7432 (ptp90)
REVERT: H   82 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8709 (mtm110)
REVERT: H   84 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7967 (mm-30)
  outliers start: 38
  outliers final: 9
  residues processed: 176
  average time/residue: 1.2120
  time to fit residues: 226.1683
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  : 0.904 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0030
   chunk 18 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 17 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.1992

-------------------------------------------------------------------------------
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**
A 486 ASN
A 494 GLN
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 486 ASN
B 494 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.104300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.088483 restraints weight = 91457.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 6.83
r_work: 0.3286 rms_B_bonded: 6.53 restraints_weight: 2.0000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3293
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3293
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8328  Z= 0.160
  Angle     :  0.638   6.364  11398  Z= 0.323
  Chirality :  0.044   0.183   1242
  Planarity :  0.005   0.064   1500
  Dihedral  :  5.304  55.142   1164
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 25.39 %
    Favored  : 72.06 %
  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: -0.31 (0.26), residues: 1064
  helix:  2.15 (1.12), residues: 26
  sheet: -0.44 (0.25), residues: 384
  loop : -0.04 (0.26), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  35 
 HIS   0.004   0.001   HIS B 329 
 PHE   0.026   0.002   PHE A 312 
 TYR   0.014   0.001   TYR H  41 
 ARG   0.004   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02934 (  266)
  hydrogen bonds       : angle       5.74347 (  750)
  SS BOND              : bond        0.00397 (    4)
  SS BOND              : angle       0.77656 (    8)
  covalent geometry    : bond        0.00386 ( 8324)
  covalent geometry    : angle       0.63811 (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
  157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8023 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7264 (t)
REVERT: A  322 ASP cc_start: 0.8335 (t70) cc_final: 0.7968 (t0)
REVERT: A  388 ASP cc_start: 0.8216 (t0) cc_final: 0.7878 (t0)
REVERT: A  459 LEU cc_start: 0.6525 (mt) cc_final: 0.6160 (mt)
REVERT: A  472 GLU cc_start: 0.7608 (pm20) cc_final: 0.6986 (pm20)
REVERT: B  275 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8089 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7226 (t)
REVERT: B  424 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8862 (mtmp)
REVERT: B  472 GLU cc_start: 0.7551 (pm20) cc_final: 0.6939 (pm20)
REVERT: C    4 MET cc_start: 0.7671 (mtp) cc_final: 0.7427 (mmm)
REVERT: C   84 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7970 (mm-30)
REVERT: C   94 MET cc_start: 0.8862 (ttt) cc_final: 0.8149 (ttp)
REVERT: C   98 GLN cc_start: 0.6745 (pt0) cc_final: 0.6374 (pp30)
REVERT: H   27 GLN cc_start: 0.8349 (mp10) cc_final: 0.7940 (mp10)
REVERT: H   82 ARG cc_start: 0.8936 (mtm-85) cc_final: 0.8678 (mtm110)
REVERT: H   84 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8061 (mm-30)
REVERT: H   95 GLN cc_start: 0.9261 (pp30) cc_final: 0.8151 (pp30)
REVERT: H   98 GLN cc_start: 0.6777 (pt0) cc_final: 0.6444 (pp30)
  outliers start: 21
  outliers final: 7
  residues processed: 149
  average time/residue: 1.2250
  time to fit residues: 193.3721
Evaluate side-chains
  130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 VAL
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  100 ASP
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0670
   chunk 57 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    0.9522

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.105179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.088920 restraints weight = 92520.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 6.92
r_work: 0.3322 rms_B_bonded: 6.61 restraints_weight: 2.0000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8328  Z= 0.136
  Angle     :  0.606   5.873  11398  Z= 0.306
  Chirality :  0.044   0.175   1242
  Planarity :  0.005   0.063   1500
  Dihedral  :  5.164  57.916   1164
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 25.61 %
    Favored  : 71.62 %
  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:  0.05 (0.27), residues: 1064
  helix:  2.35 (1.14), residues: 26
  sheet: -0.22 (0.26), residues: 372
  loop :  0.21 (0.26), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G  46 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.024   0.001   PHE A 312 
 TYR   0.012   0.001   TYR B 441 
 ARG   0.006   0.001   ARG E  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02658 (  266)
  hydrogen bonds       : angle       5.58054 (  750)
  SS BOND              : bond        0.00369 (    4)
  SS BOND              : angle       0.97402 (    8)
  covalent geometry    : bond        0.00332 ( 8324)
  covalent geometry    : angle       0.60575 (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
  157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8006 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7283 (t)
REVERT: A  322 ASP cc_start: 0.8364 (t70) cc_final: 0.8075 (t0)
REVERT: A  424 LYS cc_start: 0.9175 (mtmp) cc_final: 0.8877 (mtmm)
REVERT: A  459 LEU cc_start: 0.6609 (mt) cc_final: 0.6304 (mt)
REVERT: A  472 GLU cc_start: 0.7690 (pm20) cc_final: 0.6932 (pm20)
REVERT: B  275 ARG cc_start: 0.8281 (ttp80) cc_final: 0.8007 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7185 (t)
REVERT: B  472 GLU cc_start: 0.7566 (pm20) cc_final: 0.6930 (pm20)
REVERT: C    4 MET cc_start: 0.7770 (mtp) cc_final: 0.7451 (mmm)
REVERT: C   84 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8031 (mm-30)
REVERT: C   95 GLN cc_start: 0.9055 (pp30) cc_final: 0.8051 (pp30)
REVERT: C   98 GLN cc_start: 0.6905 (pt0) cc_final: 0.6509 (pp30)
REVERT: E    4 LEU cc_start: 0.8772 (mm) cc_final: 0.8497 (mm)
REVERT: E   42 LYS cc_start: 0.8281 (mppt) cc_final: 0.8037 (mppt)
REVERT: E   86 ARG cc_start: 0.7786 (ptp-110) cc_final: 0.7240 (ptp90)
REVERT: E  125 GLN cc_start: 0.8242 (pm20) cc_final: 0.7907 (mm-40)
REVERT: H   27 GLN cc_start: 0.8333 (mp10) cc_final: 0.7885 (mp10)
REVERT: H   82 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8698 (mtm110)
REVERT: H   84 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8386 (mp0)
REVERT: H   95 GLN cc_start: 0.9120 (pp30) cc_final: 0.8367 (pp30)
  outliers start: 23
  outliers final: 8
  residues processed: 149
  average time/residue: 1.2005
  time to fit residues: 189.8473
Evaluate side-chains
  139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  298 VAL
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 E residue  100 ASP
Chi-restraints excluded: chain H residue    2 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 61 optimal weight:    0.0000
   chunk 20 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0000
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.3588

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.108814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.092375 restraints weight = 112119.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 7.45
r_work: 0.3376 rms_B_bonded: 7.06 restraints_weight: 2.0000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3382
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    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 = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8328  Z= 0.107
  Angle     :  0.588   7.922  11398  Z= 0.292
  Chirality :  0.043   0.161   1242
  Planarity :  0.005   0.057   1500
  Dihedral  :  4.727  48.055   1164
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 25.94 %
    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:  0.36 (0.27), residues: 1064
  helix:  2.58 (1.16), residues: 26
  sheet: -0.02 (0.26), residues: 394
  loop :  0.46 (0.27), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP G  46 
 HIS   0.002   0.000   HIS A 329 
 PHE   0.022   0.001   PHE A 312 
 TYR   0.011   0.001   TYR B 441 
 ARG   0.004   0.001   ARG H  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02408 (  266)
  hydrogen bonds       : angle       5.19835 (  750)
  SS BOND              : bond        0.00559 (    4)
  SS BOND              : angle       1.27849 (    8)
  covalent geometry    : bond        0.00259 ( 8324)
  covalent geometry    : angle       0.58755 (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
  174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8199 (t70) cc_final: 0.7934 (t0)
REVERT: A  388 ASP cc_start: 0.8276 (t0) cc_final: 0.7925 (t0)
REVERT: A  459 LEU cc_start: 0.6356 (mt) cc_final: 0.6083 (mt)
REVERT: A  472 GLU cc_start: 0.7510 (pm20) cc_final: 0.6830 (pm20)
REVERT: B  275 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7932 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7206 (t)
REVERT: B  459 LEU cc_start: 0.6476 (mt) cc_final: 0.6219 (mt)
REVERT: B  472 GLU cc_start: 0.7459 (pm20) cc_final: 0.6810 (pm20)
REVERT: C    4 MET cc_start: 0.7815 (mtp) cc_final: 0.7427 (mmm)
REVERT: C   98 GLN cc_start: 0.7123 (pt0) cc_final: 0.6887 (pp30)
REVERT: E    4 LEU cc_start: 0.8677 (mm) cc_final: 0.8469 (mm)
REVERT: E   42 LYS cc_start: 0.8311 (mppt) cc_final: 0.8070 (tmmt)
REVERT: E   86 ARG cc_start: 0.7614 (ptp-110) cc_final: 0.7127 (ptp90)
REVERT: E   98 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7771 (ttpp)
REVERT: G   12 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.8219 (t-90)
REVERT: G   86 ARG cc_start: 0.7932 (pmm-80) cc_final: 0.7512 (ptp90)
REVERT: H   27 GLN cc_start: 0.8304 (mp10) cc_final: 0.7860 (mp10)
REVERT: H   47 GLN cc_start: 0.7644 (mp10) cc_final: 0.7351 (mp10)
REVERT: H   95 GLN cc_start: 0.9073 (pp30) cc_final: 0.8402 (pp30)
REVERT: H   98 GLN cc_start: 0.7058 (pt0) cc_final: 0.6751 (pp30)
  outliers start: 24
  outliers final: 8
  residues processed: 163
  average time/residue: 1.1806
  time to fit residues: 204.0166
Evaluate side-chains
  139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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 C residue   26 SER
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  112 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    0.0170
   chunk 26 optimal weight:    0.2980
   chunk 33 optimal weight:    0.3980
   chunk 15 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0770
   chunk 46 optimal weight:    0.2980
   overall best weight:    0.2176

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.109396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.092919 restraints weight = 108967.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 7.50
r_work: 0.3402 rms_B_bonded: 7.06 restraints_weight: 2.0000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    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 = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3411
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8328  Z= 0.105
  Angle     :  0.590   8.494  11398  Z= 0.289
  Chirality :  0.043   0.178   1242
  Planarity :  0.005   0.057   1500
  Dihedral  :  4.256  21.319   1162
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 26.50 %
    Favored  : 71.73 %
  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:  0.27 (0.27), residues: 1064
  helix:  1.00 (0.98), residues: 38
  sheet: -0.04 (0.27), residues: 376
  loop :  0.41 (0.27), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G  46 
 HIS   0.002   0.000   HIS B 329 
 PHE   0.020   0.001   PHE A 312 
 TYR   0.008   0.001   TYR B 441 
 ARG   0.004   0.001   ARG C  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02364 (  266)
  hydrogen bonds       : angle       5.07846 (  750)
  SS BOND              : bond        0.00437 (    4)
  SS BOND              : angle       0.92059 (    8)
  covalent geometry    : bond        0.00253 ( 8324)
  covalent geometry    : angle       0.58967 (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
  159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8130 (t70) cc_final: 0.7876 (t0)
REVERT: A  424 LYS cc_start: 0.9063 (mtmp) cc_final: 0.8771 (mtmm)
REVERT: A  455 GLU cc_start: 0.6609 (tt0) cc_final: 0.6363 (tp30)
REVERT: A  459 LEU cc_start: 0.6320 (mt) cc_final: 0.6049 (mt)
REVERT: A  472 GLU cc_start: 0.7458 (pm20) cc_final: 0.6764 (pm20)
REVERT: B  275 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7750 (ttp-110)
REVERT: B  424 LYS cc_start: 0.9033 (mttp) cc_final: 0.8789 (mttp)
REVERT: B  459 LEU cc_start: 0.6430 (mt) cc_final: 0.6175 (mt)
REVERT: B  472 GLU cc_start: 0.7436 (pm20) cc_final: 0.6746 (pm20)
REVERT: C   26 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8666 (p)
REVERT: E   42 LYS cc_start: 0.8354 (mppt) cc_final: 0.8118 (tmmt)
REVERT: E   86 ARG cc_start: 0.7527 (ptp-110) cc_final: 0.7049 (ptp90)
REVERT: E   88 GLU cc_start: 0.9239 (mp0) cc_final: 0.8725 (pp20)
REVERT: E   92 GLN cc_start: 0.6597 (tt0) cc_final: 0.5854 (tm-30)
REVERT: E   98 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7668 (ttpp)
REVERT: G   12 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (t-90)
REVERT: G   55 HIS cc_start: 0.8791 (m-70) cc_final: 0.8536 (m170)
REVERT: G   86 ARG cc_start: 0.7861 (pmm-80) cc_final: 0.7454 (ptp90)
REVERT: H   27 GLN cc_start: 0.8274 (mp10) cc_final: 0.8045 (mp10)
REVERT: H   44 LYS cc_start: 0.8822 (mttt) cc_final: 0.7870 (mmtt)
REVERT: H   47 GLN cc_start: 0.7493 (mp10) cc_final: 0.7161 (mp10)
REVERT: H   95 GLN cc_start: 0.9009 (pp30) cc_final: 0.8413 (pp30)
REVERT: H   98 GLN cc_start: 0.7118 (pt0) cc_final: 0.6787 (pp30)
  outliers start: 14
  outliers final: 3
  residues processed: 153
  average time/residue: 1.2282
  time to fit residues: 199.7484
Evaluate side-chains
  129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
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  345 VAL
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain G residue   12 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 50 optimal weight:    0.2980
   chunk 10 optimal weight:    8.9990
   chunk 27 optimal weight:    0.1980
   chunk 71 optimal weight:    0.8980
   chunk 58 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.105933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.089440 restraints weight = 116277.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 7.55
r_work: 0.3346 rms_B_bonded: 7.06 restraints_weight: 2.0000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    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 = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8328  Z= 0.141
  Angle     :  0.616   7.063  11398  Z= 0.302
  Chirality :  0.045   0.164   1242
  Planarity :  0.005   0.056   1500
  Dihedral  :  4.389  18.950   1162
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 27.38 %
    Favored  : 70.84 %
  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:  0.46 (0.27), residues: 1064
  helix:  2.60 (1.17), residues: 26
  sheet: -0.02 (0.27), residues: 376
  loop :  0.56 (0.27), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.020   0.002   PHE A 312 
 TYR   0.019   0.001   TYR E  59 
 ARG   0.010   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02575 (  266)
  hydrogen bonds       : angle       5.23703 (  750)
  SS BOND              : bond        0.00559 (    4)
  SS BOND              : angle       0.78414 (    8)
  covalent geometry    : bond        0.00342 ( 8324)
  covalent geometry    : angle       0.61553 (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
  149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8323 (t70) cc_final: 0.8023 (t0)
REVERT: A  455 GLU cc_start: 0.6636 (tt0) cc_final: 0.6401 (tp30)
REVERT: A  459 LEU cc_start: 0.6729 (mt) cc_final: 0.6493 (mt)
REVERT: A  472 GLU cc_start: 0.7564 (pm20) cc_final: 0.6837 (pm20)
REVERT: B  275 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7741 (ttp-110)
REVERT: B  298 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7261 (t)
REVERT: B  459 LEU cc_start: 0.6701 (mt) cc_final: 0.6462 (mt)
REVERT: B  472 GLU cc_start: 0.7514 (pm20) cc_final: 0.6699 (pm20)
REVERT: B  511 TYR cc_start: 0.6910 (t80) cc_final: 0.6688 (t80)
REVERT: C    4 MET cc_start: 0.7942 (mmm) cc_final: 0.7730 (mtp)
REVERT: C   26 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8623 (p)
REVERT: C   95 GLN cc_start: 0.9225 (pp30) cc_final: 0.8563 (pp30)
REVERT: E   42 LYS cc_start: 0.8384 (mppt) cc_final: 0.8096 (tmmt)
REVERT: E   92 GLN cc_start: 0.6764 (tt0) cc_final: 0.5996 (tm-30)
REVERT: E   94 TYR cc_start: 0.7900 (m-80) cc_final: 0.7467 (m-80)
REVERT: G   12 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8299 (t-90)
REVERT: G   88 GLU cc_start: 0.9132 (pm20) cc_final: 0.8407 (pp20)
REVERT: H   27 GLN cc_start: 0.8343 (mp10) cc_final: 0.7903 (mp10)
REVERT: H   47 GLN cc_start: 0.7518 (mp10) cc_final: 0.7162 (mp10)
REVERT: H   95 GLN cc_start: 0.8914 (pp30) cc_final: 0.8222 (pp30)
REVERT: H   98 GLN cc_start: 0.7145 (pt0) cc_final: 0.6836 (pp30)
  outliers start: 14
  outliers final: 6
  residues processed: 145
  average time/residue: 1.1865
  time to fit residues: 183.0964
Evaluate side-chains
  135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
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   26 SER
Chi-restraints excluded: chain E residue   57 THR
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:    0.8980
   chunk 46 optimal weight:    0.0570
   chunk 53 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 27 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 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 = 0.3811 r_free = 0.3811 target = 0.108468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.092254 restraints weight = 104673.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 7.30
r_work: 0.3392 rms_B_bonded: 6.85 restraints_weight: 2.0000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8328  Z= 0.113
  Angle     :  0.612   9.021  11398  Z= 0.295
  Chirality :  0.044   0.148   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.278  23.467   1162
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 27.05 %
    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:  0.46 (0.27), residues: 1064
  helix:  2.55 (1.16), residues: 26
  sheet: -0.07 (0.27), residues: 376
  loop :  0.60 (0.27), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.019   0.001   PHE A 312 
 TYR   0.021   0.001   TYR G  59 
 ARG   0.012   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02350 (  266)
  hydrogen bonds       : angle       5.13690 (  750)
  SS BOND              : bond        0.00496 (    4)
  SS BOND              : angle       0.83083 (    8)
  covalent geometry    : bond        0.00274 ( 8324)
  covalent geometry    : angle       0.61158 (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
  151 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8223 (t70) cc_final: 0.7961 (t0)
REVERT: A  424 LYS cc_start: 0.9165 (mtmp) cc_final: 0.8795 (mtmp)
REVERT: A  455 GLU cc_start: 0.6607 (tt0) cc_final: 0.6345 (tp30)
REVERT: A  459 LEU cc_start: 0.6659 (mt) cc_final: 0.6421 (mt)
REVERT: A  472 GLU cc_start: 0.7494 (pm20) cc_final: 0.6820 (pm20)
REVERT: B  275 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7713 (ttp-110)
REVERT: B  459 LEU cc_start: 0.6680 (mt) cc_final: 0.6423 (mt)
REVERT: B  472 GLU cc_start: 0.7434 (pm20) cc_final: 0.6760 (pm20)
REVERT: B  511 TYR cc_start: 0.6912 (t80) cc_final: 0.6664 (t80)
REVERT: C   95 GLN cc_start: 0.9207 (pp30) cc_final: 0.8493 (pp30)
REVERT: E   42 LYS cc_start: 0.8388 (mppt) cc_final: 0.8146 (tmmt)
REVERT: E   92 GLN cc_start: 0.6617 (tt0) cc_final: 0.5858 (tm-30)
REVERT: E   98 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7811 (ttpp)
REVERT: G   12 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8346 (t-90)
REVERT: G   55 HIS cc_start: 0.8723 (m-70) cc_final: 0.8491 (m170)
REVERT: H   27 GLN cc_start: 0.8355 (mp10) cc_final: 0.8131 (mp10)
REVERT: H   44 LYS cc_start: 0.8784 (mttt) cc_final: 0.7770 (mmtt)
REVERT: H   47 GLN cc_start: 0.7445 (mp10) cc_final: 0.7122 (mp10)
REVERT: H   95 GLN cc_start: 0.8887 (pp30) cc_final: 0.8297 (pp30)
REVERT: H   98 GLN cc_start: 0.7178 (pt0) cc_final: 0.6964 (pp30)
REVERT: H  111 ILE cc_start: 0.7673 (pt) cc_final: 0.6983 (mt)
  outliers start: 15
  outliers final: 5
  residues processed: 144
  average time/residue: 1.1628
  time to fit residues: 177.9229
Evaluate side-chains
  135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 129
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
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  345 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain G residue   12 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0970
   chunk 26 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0050
   chunk 50 optimal weight:    5.9990
   chunk 52 optimal weight:    0.2980
   chunk 4 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.2792

-------------------------------------------------------------------------------
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 310 HIS
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.110295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.094070 restraints weight = 98491.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 7.23
r_work: 0.3427 rms_B_bonded: 7.00 restraints_weight: 2.0000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3433
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3433
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.4581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8328  Z= 0.105
  Angle     :  0.618  11.601  11398  Z= 0.295
  Chirality :  0.043   0.149   1242
  Planarity :  0.005   0.054   1500
  Dihedral  :  4.164  22.022   1162
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 27.38 %
    Favored  : 70.95 %
  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:  0.54 (0.27), residues: 1064
  helix:  2.51 (1.15), residues: 26
  sheet:  0.06 (0.27), residues: 374
  loop :  0.60 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.019   0.001   PHE A 312 
 TYR   0.021   0.001   TYR G  59 
 ARG   0.012   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02268 (  266)
  hydrogen bonds       : angle       4.98282 (  750)
  SS BOND              : bond        0.00467 (    4)
  SS BOND              : angle       0.82476 (    8)
  covalent geometry    : bond        0.00250 ( 8324)
  covalent geometry    : angle       0.61813 (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
  159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8130 (t70) cc_final: 0.7882 (t0)
REVERT: A  455 GLU cc_start: 0.6610 (tt0) cc_final: 0.6212 (tp30)
REVERT: A  459 LEU cc_start: 0.6454 (mt) cc_final: 0.6203 (mt)
REVERT: A  472 GLU cc_start: 0.7389 (pm20) cc_final: 0.6719 (pm20)
REVERT: B  275 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7705 (ttp-110)
REVERT: B  459 LEU cc_start: 0.6575 (mt) cc_final: 0.6348 (mt)
REVERT: B  472 GLU cc_start: 0.7351 (pm20) cc_final: 0.6667 (pm20)
REVERT: C   26 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8629 (p)
REVERT: C   47 GLN cc_start: 0.7435 (mp10) cc_final: 0.7181 (mp10)
REVERT: C   95 GLN cc_start: 0.9202 (pp30) cc_final: 0.8184 (pp30)
REVERT: C   98 GLN cc_start: 0.7101 (pp30) cc_final: 0.6857 (pp30)
REVERT: C  111 ILE cc_start: 0.7776 (pt) cc_final: 0.7209 (mt)
REVERT: E   42 LYS cc_start: 0.8416 (mppt) cc_final: 0.8136 (tmmt)
REVERT: E   55 HIS cc_start: 0.8641 (m-70) cc_final: 0.8407 (m170)
REVERT: E   88 GLU cc_start: 0.9069 (pm20) cc_final: 0.8466 (pp20)
REVERT: E   92 GLN cc_start: 0.6587 (tt0) cc_final: 0.5859 (tm-30)
REVERT: E   98 LYS cc_start: 0.8050 (ttpp) cc_final: 0.7723 (ttpp)
REVERT: G   55 HIS cc_start: 0.8700 (m-70) cc_final: 0.8429 (m170)
REVERT: G   92 GLN cc_start: 0.6523 (tt0) cc_final: 0.5904 (tm-30)
REVERT: H   27 GLN cc_start: 0.8317 (mp10) cc_final: 0.8088 (mp10)
REVERT: H   44 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.7795 (mmtt)
REVERT: H   47 GLN cc_start: 0.7352 (mp10) cc_final: 0.7041 (mp10)
REVERT: H   95 GLN cc_start: 0.8804 (pp30) cc_final: 0.8189 (pp30)
REVERT: H  111 ILE cc_start: 0.7669 (pt) cc_final: 0.7021 (mt)
  outliers start: 13
  outliers final: 6
  residues processed: 155
  average time/residue: 1.1089
  time to fit residues: 183.2226
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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  345 VAL
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain E residue   58 TYR
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain H residue   44 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0470
   chunk 52 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 86 optimal weight:    0.4980
   chunk 75 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0060
   chunk 27 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.4294

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.110348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.093896 restraints weight = 101288.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 7.28
r_work: 0.3423 rms_B_bonded: 6.96 restraints_weight: 2.0000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.4663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8328  Z= 0.111
  Angle     :  0.653  12.474  11398  Z= 0.306
  Chirality :  0.044   0.153   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.226  26.386   1162
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 27.61 %
    Favored  : 71.40 %
  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:  2.45 (1.14), residues: 26
  sheet:  0.07 (0.27), residues: 374
  loop :  0.64 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 286 
 PHE   0.019   0.001   PHE A 312 
 TYR   0.020   0.001   TYR G  59 
 ARG   0.013   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02319 (  266)
  hydrogen bonds       : angle       5.01084 (  750)
  SS BOND              : bond        0.00420 (    4)
  SS BOND              : angle       0.99544 (    8)
  covalent geometry    : bond        0.00272 ( 8324)
  covalent geometry    : angle       0.65245 (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
  146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.8186 (t70) cc_final: 0.7942 (t0)
REVERT: A  455 GLU cc_start: 0.6660 (tt0) cc_final: 0.6250 (tp30)
REVERT: A  459 LEU cc_start: 0.6494 (mt) cc_final: 0.6240 (mt)
REVERT: A  472 GLU cc_start: 0.7413 (pm20) cc_final: 0.6720 (pm20)
REVERT: B  275 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7736 (ttp-110)
REVERT: B  459 LEU cc_start: 0.6632 (mt) cc_final: 0.6399 (mt)
REVERT: B  472 GLU cc_start: 0.7405 (pm20) cc_final: 0.6683 (pm20)
REVERT: C   47 GLN cc_start: 0.7400 (mp10) cc_final: 0.7154 (mp10)
REVERT: C   98 GLN cc_start: 0.7125 (pp30) cc_final: 0.6782 (pp30)
REVERT: C  111 ILE cc_start: 0.7768 (pt) cc_final: 0.7218 (mt)
REVERT: E   42 LYS cc_start: 0.8367 (mppt) cc_final: 0.8056 (tmmt)
REVERT: E   55 HIS cc_start: 0.8654 (m-70) cc_final: 0.8405 (m170)
REVERT: E   88 GLU cc_start: 0.9054 (pm20) cc_final: 0.8410 (pp20)
REVERT: E   92 GLN cc_start: 0.6605 (tt0) cc_final: 0.5868 (tm-30)
REVERT: E   98 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7765 (ttpp)
REVERT: G   55 HIS cc_start: 0.8659 (m-70) cc_final: 0.8374 (m170)
REVERT: G   88 GLU cc_start: 0.9022 (pm20) cc_final: 0.8348 (pp20)
REVERT: G   92 GLN cc_start: 0.6549 (tt0) cc_final: 0.5900 (tm-30)
REVERT: H   27 GLN cc_start: 0.8322 (mp10) cc_final: 0.8099 (mp10)
REVERT: H   39 ASP cc_start: 0.8994 (m-30) cc_final: 0.8794 (m-30)
REVERT: H   44 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.7826 (mmtt)
REVERT: H   47 GLN cc_start: 0.7293 (mp10) cc_final: 0.7020 (mp10)
REVERT: H   95 GLN cc_start: 0.8628 (pp30) cc_final: 0.7915 (pp30)
REVERT: H  111 ILE cc_start: 0.7683 (pt) cc_final: 0.7026 (mt)
  outliers start: 7
  outliers final: 5
  residues processed: 144
  average time/residue: 1.1610
  time to fit residues: 177.7668
Evaluate side-chains
  139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  345 VAL
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain H residue   44 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 101 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 102 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
A 355 HIS
A 404 HIS
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.104676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.088534 restraints weight = 100460.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 7.06
r_work: 0.3330 rms_B_bonded: 6.67 restraints_weight: 2.0000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091   8328  Z= 0.185
  Angle     :  0.705  13.004  11398  Z= 0.335
  Chirality :  0.046   0.155   1242
  Planarity :  0.006   0.055   1500
  Dihedral  :  4.631  30.437   1162
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 27.38 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.45 (0.28), residues: 1064
  helix:  2.06 (1.11), residues: 26
  sheet: -0.11 (0.27), residues: 376
  loop :  0.65 (0.27), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP G  46 
 HIS   0.007   0.001   HIS B 329 
 PHE   0.023   0.002   PHE H 103 
 TYR   0.019   0.002   TYR E  59 
 ARG   0.013   0.001   ARG H  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02803 (  266)
  hydrogen bonds       : angle       5.49185 (  750)
  SS BOND              : bond        0.00444 (    4)
  SS BOND              : angle       0.77040 (    8)
  covalent geometry    : bond        0.00451 ( 8324)
  covalent geometry    : angle       0.70485 (11390)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6857.83 seconds
wall clock time: 117 minutes 37.55 seconds (7057.55 seconds total)