Starting phenix.real_space_refine
on Wed Sep 17 10:08:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bof_44734/09_2025/9bof_44734_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bof_44734/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bof_44734/09_2025/9bof_44734_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bof_44734/09_2025/9bof_44734_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bof_44734/09_2025/9bof_44734.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bof_44734/09_2025/9bof_44734.map"
  }
  resolution = 2.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG:plan': 2}
          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: {'ASP:plan': 1, 'ARG:plan': 2}
          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: {'ASP:plan': 1, 'ARG:plan': 2}
          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: {'ASP:plan': 1, 'ARG:plan': 2}
          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: {'ASP:plan': 1, 'ARG:plan': 2}
          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: {'ASP:plan': 1, 'ARG:plan': 2}
          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: 3.32, per 1000 atoms: 0.41
  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: 0.73
  Conformation dependent library (CDL) restraints added in 638.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 16 sheets defined
      7.2% alpha, 36.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  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: 1.43

  Time building geometry restraints manager: 0.96 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: 0.02
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:             1.440
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.580
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:6.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.270
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG H  24 
 TYR   0.014   0.002   TYR B 395 
 PHE   0.025   0.003   PHE A 231 
 TRP   0.010   0.002   TRP A 390 
 HIS   0.008   0.002   HIS A 310 

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

*********************** 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  : 0.312 
Fit side-chains
REVERT: H   41 TYR cc_start: 0.8322 (m-80) cc_final: 0.8031 (m-80)
  outliers start: 60
  outliers final: 18
  residues processed: 241
  average time/residue: 0.4926
  time to fit residues: 126.3664
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  : 0.307 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    0.0370
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.4856

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.107868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.091235 restraints weight = 98935.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 7.17
r_work: 0.3344 rms_B_bonded: 6.73 restraints_weight: 2.0000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8328  Z= 0.141
  Angle     :  0.664   8.395  11398  Z= 0.340
  Chirality :  0.045   0.194   1242
  Planarity :  0.006   0.064   1500
  Dihedral  :  6.192  53.255   1189
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 22.51 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.26), residues: 1064
  helix:  1.31 (1.09), residues: 26
  sheet: -0.62 (0.25), residues: 384
  loop : -0.39 (0.25), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  24 
 TYR   0.011   0.001   TYR A 441 
 PHE   0.031   0.002   PHE B 312 
 TRP   0.018   0.002   TRP A 506 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8324)
  covalent geometry    : angle       0.66349 (11390)
  SS BOND              : bond        0.00316 (    4)
  SS BOND              : angle       0.96771 (    8)
  hydrogen bonds       : bond        0.03018 (  266)
  hydrogen bonds       : angle       6.21271 (  750)

*********************** 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
  192 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8201 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7193 (t)
REVERT: A  472 GLU cc_start: 0.7146 (pm20) cc_final: 0.6745 (pm20)
REVERT: B  298 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7156 (t)
REVERT: B  472 GLU cc_start: 0.7084 (pm20) cc_final: 0.6782 (pm20)
REVERT: C    4 MET cc_start: 0.7620 (mtp) cc_final: 0.7400 (mtp)
REVERT: C   84 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7806 (mm-30)
REVERT: E   86 ARG cc_start: 0.7942 (ptp90) cc_final: 0.7302 (ptp90)
REVERT: E  125 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7454 (pm20)
REVERT: G   86 ARG cc_start: 0.7733 (ptp90) cc_final: 0.7228 (ptp90)
REVERT: H    4 MET cc_start: 0.7551 (mtp) cc_final: 0.7329 (mtp)
REVERT: H   82 ARG cc_start: 0.8912 (mtm-85) cc_final: 0.8707 (mtm110)
REVERT: H   84 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7940 (mm-30)
  outliers start: 40
  outliers final: 9
  residues processed: 179
  average time/residue: 0.5845
  time to fit residues: 110.7530
Evaluate side-chains
  134 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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   74 THR
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain G residue   80 LEU
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 2 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0670
   chunk 86 optimal weight:    0.0060
   chunk 89 optimal weight:    7.9990
   chunk 100 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.9138

-------------------------------------------------------------------------------
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 432 ASN
A 494 GLN
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 GLN
E   2 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.106358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.090201 restraints weight = 86041.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 6.80
r_work: 0.3339 rms_B_bonded: 6.51 restraints_weight: 2.0000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3346
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8328  Z= 0.147
  Angle     :  0.627   6.581  11398  Z= 0.317
  Chirality :  0.044   0.176   1242
  Planarity :  0.005   0.065   1500
  Dihedral  :  5.204  55.130   1164
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 25.06 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.26), residues: 1064
  helix:  2.12 (1.13), residues: 26
  sheet: -0.43 (0.25), residues: 378
  loop :  0.03 (0.26), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  24 
 TYR   0.013   0.001   TYR H  41 
 PHE   0.026   0.002   PHE A 312 
 TRP   0.014   0.001   TRP E  35 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8324)
  covalent geometry    : angle       0.62707 (11390)
  SS BOND              : bond        0.00330 (    4)
  SS BOND              : angle       0.80136 (    8)
  hydrogen bonds       : bond        0.02760 (  266)
  hydrogen bonds       : angle       5.62785 (  750)

*********************** 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
  162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8022 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.7210 (t)
REVERT: A  472 GLU cc_start: 0.7459 (pm20) cc_final: 0.6919 (pm20)
REVERT: B  298 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7152 (t)
REVERT: B  472 GLU cc_start: 0.7409 (pm20) cc_final: 0.6925 (pm20)
REVERT: C    4 MET cc_start: 0.7669 (mtp) cc_final: 0.7356 (mtp)
REVERT: C   37 TYR cc_start: 0.7740 (m-80) cc_final: 0.7475 (m-80)
REVERT: C   84 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7960 (mm-30)
REVERT: C   98 GLN cc_start: 0.6770 (pt0) cc_final: 0.6478 (pp30)
REVERT: E   86 ARG cc_start: 0.7990 (ptp90) cc_final: 0.7780 (ptp90)
REVERT: G   86 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7534 (ptp90)
REVERT: G  107 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7136 (mtt-85)
REVERT: H   27 GLN cc_start: 0.8366 (mp10) cc_final: 0.7951 (mp10)
REVERT: H   44 LYS cc_start: 0.9043 (mttt) cc_final: 0.8035 (mttt)
REVERT: H   47 GLN cc_start: 0.7922 (mp10) cc_final: 0.7438 (mp10)
REVERT: H   82 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8650 (mtm110)
REVERT: H   84 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8104 (mm-30)
REVERT: H   95 GLN cc_start: 0.9156 (pp30) cc_final: 0.8142 (pp30)
  outliers start: 24
  outliers final: 5
  residues processed: 152
  average time/residue: 0.6418
  time to fit residues: 102.9195
Evaluate side-chains
  133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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   20 SER
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain G residue  107 ARG
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 45 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 41 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.101451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.085099 restraints weight = 100063.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 7.06
r_work: 0.3243 rms_B_bonded: 6.59 restraints_weight: 2.0000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   8328  Z= 0.196
  Angle     :  0.651   6.733  11398  Z= 0.328
  Chirality :  0.045   0.173   1242
  Planarity :  0.005   0.063   1500
  Dihedral  :  5.413  56.883   1164
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.39 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.27), residues: 1064
  helix:  1.96 (1.11), residues: 26
  sheet: -0.26 (0.26), residues: 372
  loop :  0.16 (0.26), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  71 
 TYR   0.015   0.001   TYR G  94 
 PHE   0.025   0.002   PHE A 312 
 TRP   0.010   0.001   TRP E 123 
 HIS   0.005   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 8324)
  covalent geometry    : angle       0.65128 (11390)
  SS BOND              : bond        0.00437 (    4)
  SS BOND              : angle       0.85682 (    8)
  hydrogen bonds       : bond        0.03062 (  266)
  hydrogen bonds       : angle       5.87103 (  750)

*********************** 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
  161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7978 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7323 (t)
REVERT: B  298 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7259 (t)
REVERT: B  424 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8805 (mtmp)
REVERT: C   37 TYR cc_start: 0.7896 (m-80) cc_final: 0.7696 (m-80)
REVERT: C   82 ARG cc_start: 0.8971 (mtm110) cc_final: 0.8754 (mtm110)
REVERT: C   84 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8030 (mm-30)
REVERT: C   94 MET cc_start: 0.9032 (ttt) cc_final: 0.8372 (ttp)
REVERT: C   98 GLN cc_start: 0.6868 (pt0) cc_final: 0.6601 (pp30)
REVERT: E   42 LYS cc_start: 0.8281 (mppt) cc_final: 0.8019 (mppt)
REVERT: G   86 ARG cc_start: 0.7740 (ptp90) cc_final: 0.7299 (ptp90)
REVERT: G  107 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7242 (mtt-85)
REVERT: H   27 GLN cc_start: 0.8309 (mp10) cc_final: 0.7833 (mp10)
REVERT: H   82 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8746 (mtm110)
REVERT: H   84 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8400 (mp0)
REVERT: H   95 GLN cc_start: 0.9234 (pp30) cc_final: 0.8021 (pp30)
REVERT: H   98 GLN cc_start: 0.6842 (pt0) cc_final: 0.6385 (pp30)
  outliers start: 33
  outliers final: 13
  residues processed: 148
  average time/residue: 0.5898
  time to fit residues: 92.2759
Evaluate side-chains
  137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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 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   12 HIS
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain G residue  107 ARG
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue    2 ILE
Chi-restraints excluded: chain H residue   20 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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**
** E   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.104602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.088352 restraints weight = 106168.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 7.15
r_work: 0.3315 rms_B_bonded: 6.71 restraints_weight: 2.0000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8328  Z= 0.127
  Angle     :  0.598   7.078  11398  Z= 0.298
  Chirality :  0.044   0.155   1242
  Planarity :  0.005   0.058   1500
  Dihedral  :  4.984  50.100   1164
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 25.28 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.27), residues: 1064
  helix:  2.26 (1.13), residues: 26
  sheet: -0.20 (0.27), residues: 372
  loop :  0.34 (0.26), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  86 
 TYR   0.012   0.001   TYR B 441 
 PHE   0.023   0.001   PHE A 312 
 TRP   0.011   0.001   TRP E  46 
 HIS   0.003   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8324)
  covalent geometry    : angle       0.59784 (11390)
  SS BOND              : bond        0.00379 (    4)
  SS BOND              : angle       0.68551 (    8)
  hydrogen bonds       : bond        0.02577 (  266)
  hydrogen bonds       : angle       5.53989 (  750)

*********************** 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
  161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7954 (ttp-110)
REVERT: A  298 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7248 (t)
REVERT: A  472 GLU cc_start: 0.7530 (pm20) cc_final: 0.6897 (pm20)
REVERT: B  298 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7229 (t)
REVERT: B  472 GLU cc_start: 0.7483 (pm20) cc_final: 0.6869 (pm20)
REVERT: C   37 TYR cc_start: 0.7851 (m-80) cc_final: 0.7593 (m-80)
REVERT: C   84 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8101 (mm-30)
REVERT: C   95 GLN cc_start: 0.9182 (pp30) cc_final: 0.7992 (pp30)
REVERT: C   98 GLN cc_start: 0.6850 (pt0) cc_final: 0.6539 (pp30)
REVERT: E   86 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7613 (ptp90)
REVERT: G   42 LYS cc_start: 0.8031 (mppt) cc_final: 0.7766 (tmmt)
REVERT: G   86 ARG cc_start: 0.7848 (ptp90) cc_final: 0.7531 (ptp90)
REVERT: G  107 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7199 (mtt-85)
REVERT: G  125 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6987 (mm-40)
REVERT: H   95 GLN cc_start: 0.9212 (pp30) cc_final: 0.8024 (pp30)
REVERT: H   98 GLN cc_start: 0.6940 (pt0) cc_final: 0.6627 (pp30)
  outliers start: 23
  outliers final: 9
  residues processed: 151
  average time/residue: 0.5976
  time to fit residues: 95.6610
Evaluate side-chains
  143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  112 SER
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  107 ARG
Chi-restraints excluded: chain H residue   20 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 99 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**
** E   2 GLN ** 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 = 0.3767 r_free = 0.3767 target = 0.105803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.089655 restraints weight = 97989.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 7.00
r_work: 0.3334 rms_B_bonded: 6.64 restraints_weight: 2.0000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3343
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8328  Z= 0.119
  Angle     :  0.596   7.687  11398  Z= 0.296
  Chirality :  0.043   0.155   1242
  Planarity :  0.005   0.057   1500
  Dihedral  :  4.443  21.625   1162
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 25.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.27), residues: 1064
  helix:  2.42 (1.14), residues: 26
  sheet: -0.12 (0.27), residues: 372
  loop :  0.43 (0.26), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  82 
 TYR   0.011   0.001   TYR B 441 
 PHE   0.021   0.001   PHE B 312 
 TRP   0.015   0.001   TRP E  46 
 HIS   0.004   0.001   HIS A 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8324)
  covalent geometry    : angle       0.59559 (11390)
  SS BOND              : bond        0.00487 (    4)
  SS BOND              : angle       0.86096 (    8)
  hydrogen bonds       : bond        0.02440 (  266)
  hydrogen bonds       : angle       5.38898 (  750)

*********************** 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
  163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7948 (ttm-80)
REVERT: A  298 VAL cc_start: 0.7409 (OUTLIER) cc_final: 0.7205 (t)
REVERT: A  424 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8642 (mtmp)
REVERT: A  459 LEU cc_start: 0.6679 (mt) cc_final: 0.6434 (mt)
REVERT: A  472 GLU cc_start: 0.7498 (pm20) cc_final: 0.6800 (pm20)
REVERT: B  298 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.7175 (t)
REVERT: B  424 LYS cc_start: 0.9115 (mttp) cc_final: 0.8784 (mtmp)
REVERT: B  472 GLU cc_start: 0.7454 (pm20) cc_final: 0.6795 (pm20)
REVERT: C   37 TYR cc_start: 0.7875 (m-80) cc_final: 0.7640 (m-80)
REVERT: C   95 GLN cc_start: 0.9077 (pp30) cc_final: 0.8570 (pp30)
REVERT: C   98 GLN cc_start: 0.7012 (pt0) cc_final: 0.6724 (pp30)
REVERT: E   42 LYS cc_start: 0.8310 (mppt) cc_final: 0.8108 (mppt)
REVERT: E   86 ARG cc_start: 0.7609 (ptp90) cc_final: 0.7271 (ptp90)
REVERT: E   92 GLN cc_start: 0.6679 (tt0) cc_final: 0.5968 (tm-30)
REVERT: G    4 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8510 (tm)
REVERT: G   12 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8220 (t-90)
REVERT: G  107 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7202 (mtt-85)
REVERT: G  125 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7021 (mm-40)
REVERT: H   47 GLN cc_start: 0.7674 (mp10) cc_final: 0.7242 (mp10)
REVERT: H   95 GLN cc_start: 0.9241 (pp30) cc_final: 0.8096 (pp30)
REVERT: H   98 GLN cc_start: 0.6970 (pt0) cc_final: 0.6651 (pp30)
  outliers start: 20
  outliers final: 9
  residues processed: 155
  average time/residue: 0.6025
  time to fit residues: 98.6015
Evaluate side-chains
  144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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 B residue  448 GLU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  107 ARG
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue   38 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 69 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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**
G  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.106659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.090479 restraints weight = 99795.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 7.14
r_work: 0.3350 rms_B_bonded: 6.78 restraints_weight: 2.0000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3358
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3358
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4127

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= 0.119
  Angle     :  0.603   8.040  11398  Z= 0.297
  Chirality :  0.043   0.154   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.391  22.269   1162
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 25.28 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.27), residues: 1064
  helix:  2.45 (1.14), residues: 26
  sheet: -0.15 (0.27), residues: 374
  loop :  0.54 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  82 
 TYR   0.013   0.001   TYR G  59 
 PHE   0.021   0.001   PHE A 312 
 TRP   0.017   0.001   TRP G  46 
 HIS   0.004   0.001   HIS A 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8324)
  covalent geometry    : angle       0.60225 (11390)
  SS BOND              : bond        0.00448 (    4)
  SS BOND              : angle       1.14734 (    8)
  hydrogen bonds       : bond        0.02459 (  266)
  hydrogen bonds       : angle       5.33560 (  750)

*********************** 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
  170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7864 (ttm-80)
REVERT: A  298 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7253 (t)
REVERT: A  322 ASP cc_start: 0.8501 (t70) cc_final: 0.7997 (t0)
REVERT: A  424 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8620 (mtmp)
REVERT: A  459 LEU cc_start: 0.6684 (mt) cc_final: 0.6423 (mt)
REVERT: A  472 GLU cc_start: 0.7435 (pm20) cc_final: 0.6731 (pm20)
REVERT: A  511 TYR cc_start: 0.6491 (t80) cc_final: 0.6270 (t80)
REVERT: B  298 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.7189 (t)
REVERT: B  424 LYS cc_start: 0.9123 (mttp) cc_final: 0.8775 (mtmp)
REVERT: B  459 LEU cc_start: 0.6681 (mt) cc_final: 0.6421 (mt)
REVERT: B  472 GLU cc_start: 0.7431 (pm20) cc_final: 0.6750 (pm20)
REVERT: C    4 MET cc_start: 0.7351 (mtp) cc_final: 0.7129 (mtp)
REVERT: C   37 TYR cc_start: 0.7833 (m-80) cc_final: 0.7610 (m-80)
REVERT: C   95 GLN cc_start: 0.8876 (pp30) cc_final: 0.8253 (pp30)
REVERT: E   42 LYS cc_start: 0.8282 (mppt) cc_final: 0.8032 (mppt)
REVERT: E   86 ARG cc_start: 0.7586 (ptp90) cc_final: 0.7215 (ptp90)
REVERT: E   92 GLN cc_start: 0.6704 (tt0) cc_final: 0.6002 (tm-30)
REVERT: G   12 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8262 (t-90)
REVERT: G   86 ARG cc_start: 0.7842 (ptp90) cc_final: 0.7464 (ptp90)
REVERT: G  107 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7198 (mtt-85)
REVERT: G  125 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7140 (mm-40)
REVERT: H   26 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8754 (p)
REVERT: H   47 GLN cc_start: 0.7547 (mp10) cc_final: 0.7155 (mp10)
REVERT: H   95 GLN cc_start: 0.9231 (pp30) cc_final: 0.8175 (pp30)
REVERT: H   98 GLN cc_start: 0.6990 (pt0) cc_final: 0.6681 (pp30)
REVERT: H  111 ILE cc_start: 0.7756 (pt) cc_final: 0.7153 (mt)
  outliers start: 23
  outliers final: 11
  residues processed: 163
  average time/residue: 0.5451
  time to fit residues: 94.1232
Evaluate side-chains
  144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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 B residue  448 GLU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  107 ARG
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue   26 SER
Chi-restraints excluded: chain H residue   38 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 10 optimal weight:    7.9990
   chunk 95 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.106117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.089866 restraints weight = 105578.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 7.25
r_work: 0.3338 rms_B_bonded: 6.89 restraints_weight: 2.0000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8328  Z= 0.135
  Angle     :  0.637   8.039  11398  Z= 0.313
  Chirality :  0.044   0.151   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.438  23.153   1162
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 25.94 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.27), residues: 1064
  helix:  2.34 (1.14), residues: 26
  sheet: -0.16 (0.27), residues: 374
  loop :  0.62 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  82 
 TYR   0.023   0.001   TYR E  59 
 PHE   0.021   0.001   PHE A 312 
 TRP   0.017   0.001   TRP E  46 
 HIS   0.005   0.001   HIS A 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8324)
  covalent geometry    : angle       0.63619 (11390)
  SS BOND              : bond        0.00411 (    4)
  SS BOND              : angle       1.02853 (    8)
  hydrogen bonds       : bond        0.02514 (  266)
  hydrogen bonds       : angle       5.31695 (  750)

*********************** 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
  145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7869 (ttm-80)
REVERT: A  298 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7252 (t)
REVERT: A  322 ASP cc_start: 0.8514 (t70) cc_final: 0.8008 (t0)
REVERT: A  459 LEU cc_start: 0.6719 (mt) cc_final: 0.6478 (mt)
REVERT: A  472 GLU cc_start: 0.7438 (pm20) cc_final: 0.6727 (pm20)
REVERT: A  511 TYR cc_start: 0.6550 (t80) cc_final: 0.6314 (t80)
REVERT: B  298 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7233 (t)
REVERT: B  472 GLU cc_start: 0.7408 (pm20) cc_final: 0.6710 (pm20)
REVERT: C   37 TYR cc_start: 0.7869 (m-80) cc_final: 0.7567 (m-80)
REVERT: C   95 GLN cc_start: 0.8902 (pp30) cc_final: 0.8338 (pp30)
REVERT: E   92 GLN cc_start: 0.6718 (tt0) cc_final: 0.5975 (tm-30)
REVERT: G   12 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8319 (t-90)
REVERT: G   42 LYS cc_start: 0.7894 (tptp) cc_final: 0.7497 (tmmt)
REVERT: G   86 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7518 (ptp90)
REVERT: G  107 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7208 (mtt-85)
REVERT: H   98 GLN cc_start: 0.7090 (pt0) cc_final: 0.6803 (pp30)
REVERT: H  111 ILE cc_start: 0.7790 (pt) cc_final: 0.7203 (mt)
  outliers start: 17
  outliers final: 9
  residues processed: 140
  average time/residue: 0.5949
  time to fit residues: 88.0708
Evaluate side-chains
  137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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 B residue  448 GLU
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  107 ARG
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue   38 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0070
   chunk 81 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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**
** G  51 ASN ** 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 = 0.3786 r_free = 0.3786 target = 0.106927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.090688 restraints weight = 99798.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 7.18
r_work: 0.3347 rms_B_bonded: 6.86 restraints_weight: 2.0000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8328  Z= 0.123
  Angle     :  0.629   8.775  11398  Z= 0.307
  Chirality :  0.044   0.150   1242
  Planarity :  0.005   0.054   1500
  Dihedral  :  4.393  21.802   1162
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 25.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.28), residues: 1064
  helix:  2.27 (1.12), residues: 26
  sheet: -0.21 (0.27), residues: 374
  loop :  0.66 (0.27), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  82 
 TYR   0.022   0.001   TYR E  59 
 PHE   0.020   0.001   PHE A 312 
 TRP   0.020   0.001   TRP E  46 
 HIS   0.005   0.001   HIS A 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8324)
  covalent geometry    : angle       0.62864 (11390)
  SS BOND              : bond        0.00467 (    4)
  SS BOND              : angle       1.04777 (    8)
  hydrogen bonds       : bond        0.02446 (  266)
  hydrogen bonds       : angle       5.26608 (  750)

*********************** 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
  155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7868 (ttm-80)
REVERT: A  322 ASP cc_start: 0.8479 (t70) cc_final: 0.7990 (t0)
REVERT: A  455 GLU cc_start: 0.6670 (tt0) cc_final: 0.6464 (tp30)
REVERT: A  459 LEU cc_start: 0.6703 (mt) cc_final: 0.6482 (mt)
REVERT: A  472 GLU cc_start: 0.7390 (pm20) cc_final: 0.6722 (pm20)
REVERT: A  511 TYR cc_start: 0.6503 (t80) cc_final: 0.6195 (t80)
REVERT: B  459 LEU cc_start: 0.6737 (mt) cc_final: 0.6492 (mt)
REVERT: B  472 GLU cc_start: 0.7385 (pm20) cc_final: 0.6720 (pm20)
REVERT: B  511 TYR cc_start: 0.6423 (t80) cc_final: 0.6131 (t80)
REVERT: C   37 TYR cc_start: 0.7911 (m-80) cc_final: 0.7658 (m-80)
REVERT: C   95 GLN cc_start: 0.8940 (pp30) cc_final: 0.8411 (pp30)
REVERT: C   98 GLN cc_start: 0.6818 (pp30) cc_final: 0.6519 (pp30)
REVERT: E   55 HIS cc_start: 0.8712 (m-70) cc_final: 0.8439 (m170)
REVERT: E   72 ASP cc_start: 0.7061 (t0) cc_final: 0.6621 (t0)
REVERT: E   86 ARG cc_start: 0.7653 (ptp90) cc_final: 0.7113 (ptp90)
REVERT: E   92 GLN cc_start: 0.6696 (tt0) cc_final: 0.5979 (tm-30)
REVERT: G    4 LEU cc_start: 0.8883 (tm) cc_final: 0.8404 (mt)
REVERT: G    5 GLU cc_start: 0.6756 (pm20) cc_final: 0.6438 (pt0)
REVERT: G   12 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8355 (t-90)
REVERT: G   42 LYS cc_start: 0.7704 (tptp) cc_final: 0.7118 (tmmt)
REVERT: G   55 HIS cc_start: 0.8703 (m-70) cc_final: 0.8483 (m170)
REVERT: G   86 ARG cc_start: 0.7829 (ptp90) cc_final: 0.7456 (ptp90)
REVERT: G  107 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7219 (mtt-85)
REVERT: G  125 GLN cc_start: 0.7720 (pm20) cc_final: 0.6494 (mm-40)
REVERT: H   95 GLN cc_start: 0.9250 (pp30) cc_final: 0.8157 (pp30)
REVERT: H   98 GLN cc_start: 0.7115 (pt0) cc_final: 0.6829 (pp30)
REVERT: H  111 ILE cc_start: 0.7792 (pt) cc_final: 0.7188 (mt)
  outliers start: 18
  outliers final: 10
  residues processed: 151
  average time/residue: 0.5790
  time to fit residues: 92.7599
Evaluate side-chains
  145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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 B residue  448 GLU
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  107 ARG
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue   38 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0670
   chunk 45 optimal weight:    0.0170
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0030
   chunk 76 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.3368

-------------------------------------------------------------------------------
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**
** G  51 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.108330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.092071 restraints weight = 108385.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 7.43
r_work: 0.3377 rms_B_bonded: 6.99 restraints_weight: 2.0000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.4600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8328  Z= 0.116
  Angle     :  0.635   9.116  11398  Z= 0.310
  Chirality :  0.043   0.148   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.315  20.764   1162
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 26.27 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.28), residues: 1064
  helix:  2.26 (1.12), residues: 26
  sheet: -0.17 (0.27), residues: 376
  loop :  0.67 (0.27), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  82 
 TYR   0.019   0.001   TYR E  59 
 PHE   0.020   0.001   PHE A 312 
 TRP   0.020   0.001   TRP E  46 
 HIS   0.005   0.001   HIS A 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8324)
  covalent geometry    : angle       0.63433 (11390)
  SS BOND              : bond        0.00447 (    4)
  SS BOND              : angle       1.17594 (    8)
  hydrogen bonds       : bond        0.02386 (  266)
  hydrogen bonds       : angle       5.16340 (  750)

********************** 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
  148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7832 (ttm-80)
REVERT: A  455 GLU cc_start: 0.6596 (tt0) cc_final: 0.6354 (tp30)
REVERT: A  459 LEU cc_start: 0.6601 (mt) cc_final: 0.6384 (mt)
REVERT: A  472 GLU cc_start: 0.7413 (pm20) cc_final: 0.6718 (pm20)
REVERT: A  511 TYR cc_start: 0.6494 (t80) cc_final: 0.6252 (t80)
REVERT: B  459 LEU cc_start: 0.6716 (mt) cc_final: 0.6487 (mt)
REVERT: B  472 GLU cc_start: 0.7369 (pm20) cc_final: 0.6716 (pm20)
REVERT: B  511 TYR cc_start: 0.6392 (t80) cc_final: 0.6176 (t80)
REVERT: C   37 TYR cc_start: 0.7875 (m-80) cc_final: 0.7654 (m-80)
REVERT: C   98 GLN cc_start: 0.6854 (pp30) cc_final: 0.6479 (pp30)
REVERT: E   42 LYS cc_start: 0.7706 (tptp) cc_final: 0.7461 (tmmt)
REVERT: E   55 HIS cc_start: 0.8670 (m-70) cc_final: 0.8388 (m170)
REVERT: E   72 ASP cc_start: 0.7042 (t0) cc_final: 0.6586 (t0)
REVERT: E   92 GLN cc_start: 0.6586 (tt0) cc_final: 0.5851 (tm-30)
REVERT: E   98 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7778 (ttpp)
REVERT: G    4 LEU cc_start: 0.8886 (tm) cc_final: 0.8404 (mt)
REVERT: G    5 GLU cc_start: 0.6774 (pm20) cc_final: 0.6408 (pt0)
REVERT: G   12 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8382 (t-90)
REVERT: G   42 LYS cc_start: 0.7658 (tptp) cc_final: 0.7030 (tmmt)
REVERT: G   55 HIS cc_start: 0.8753 (m-70) cc_final: 0.8484 (m170)
REVERT: G   86 ARG cc_start: 0.7861 (ptp90) cc_final: 0.7428 (ptp90)
REVERT: G  107 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7215 (mtt-85)
REVERT: G  125 GLN cc_start: 0.7639 (pm20) cc_final: 0.6372 (mm-40)
REVERT: H   37 TYR cc_start: 0.8069 (m-80) cc_final: 0.7558 (m-80)
REVERT: H   47 GLN cc_start: 0.7337 (mp10) cc_final: 0.6951 (mp10)
REVERT: H   98 GLN cc_start: 0.7109 (pt0) cc_final: 0.6888 (pp30)
REVERT: H  111 ILE cc_start: 0.7797 (pt) cc_final: 0.7199 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 144
  average time/residue: 0.6036
  time to fit residues: 92.0286
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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 B residue  448 GLU
Chi-restraints excluded: chain E residue   82 MET
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain G residue   12 HIS
Chi-restraints excluded: chain G residue  107 ARG
Chi-restraints excluded: chain G residue  112 SER
Chi-restraints excluded: chain H residue   38 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0050
   chunk 41 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.6594

-------------------------------------------------------------------------------
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**
** G  51 ASN ** 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 = 0.3801 r_free = 0.3801 target = 0.107926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.091715 restraints weight = 102731.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 7.23
r_work: 0.3372 rms_B_bonded: 6.96 restraints_weight: 2.0000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3375
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.4621

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= 0.122
  Angle     :  0.632   8.142  11398  Z= 0.307
  Chirality :  0.043   0.147   1242
  Planarity :  0.005   0.055   1500
  Dihedral  :  4.309  19.382   1162
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 26.05 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.28), residues: 1064
  helix:  2.20 (1.11), residues: 26
  sheet: -0.14 (0.27), residues: 376
  loop :  0.71 (0.27), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H  82 
 TYR   0.020   0.001   TYR E  59 
 PHE   0.020   0.001   PHE A 312 
 TRP   0.022   0.001   TRP G  46 
 HIS   0.005   0.001   HIS A 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8324)
  covalent geometry    : angle       0.63166 (11390)
  SS BOND              : bond        0.00454 (    4)
  SS BOND              : angle       0.79902 (    8)
  hydrogen bonds       : bond        0.02417 (  266)
  hydrogen bonds       : angle       5.11885 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3345.42 seconds
wall clock time: 57 minutes 47.79 seconds (3467.79 seconds total)