Starting phenix.real_space_refine
on Tue Feb 11 15:32:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vwy_43605/02_2025/8vwy_43605.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vwy_43605/02_2025/8vwy_43605.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vwy_43605/02_2025/8vwy_43605.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vwy_43605/02_2025/8vwy_43605.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vwy_43605/02_2025/8vwy_43605.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vwy_43605/02_2025/8vwy_43605.cif"
  }
  resolution = 2.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     Ca      7      9.91       5
     S      52      5.16       5
     C    4047      2.51       5
     N    1016      2.21       5
     O    1171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6293
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1058
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "E"
      Number of atoms: 1034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1034
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 4, 'TRANS': 127}
    Chain: "H"
      Number of atoms: 1036
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 132, 1031
          Classifications: {'peptide': 132}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 127}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 132, 1031
          Classifications: {'peptide': 132}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 127}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1052
    Chain: "I"
      Number of atoms: 1034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1034
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 4, 'TRANS': 127}
    Chain: "B"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1058
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1058
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "E"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "I"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.34, per 1000 atoms: 0.85
  Number of scatterers: 6293
  At special positions: 0
  Unit cell: (99.256, 104.48, 78.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      7     19.99
     S      52     16.00
     O    1171      8.00
     N    1016      7.00
     C    4047      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  29 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 152 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  29 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 142 " - pdb=" SG  CYS B 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 146 " - pdb=" SG  CYS B 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 152 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   4 " - pdb=" SG  CYS C  29 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  54 " - pdb=" SG  CYS C  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 152 " - pdb=" SG  CYS C 163 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 981.7 milliseconds
  

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 17 sheets defined
      10.5% alpha, 39.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 22
    Processing helix  chain 'A' and resid 68 through 79
    Processing helix  chain 'A' and resid 138 through 149
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 68 through 79
    Processing helix  chain 'B' and resid 138 through 149
    Processing helix  chain 'C' and resid 18 through 22
    Processing helix  chain 'C' and resid 68 through 79
    Processing helix  chain 'C' and resid 138 through 149
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 3.513A  pdb=" N   THR A   6 " --> pdb=" O   THR A  30 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU A  34 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR A  62 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A  60 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 17
      removed outlier: 3.563A  pdb=" N   GLY A  14 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   PHE A 126 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER A  48 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 29 through 34
      removed outlier: 5.106A  pdb=" N   VAL E  30 " --> pdb=" O   GLY E  14 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   GLY E  14 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ILE E  52 " --> pdb=" O   ILE E 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 20 through 21
      removed outlier: 3.734A  pdb=" N   GLY E 116 " --> pdb=" O   GLY E  21 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39
      removed outlier: 3.599A  pdb=" N   LYS E  44 " --> pdb=" O   ASP E  39 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 38 through 39
      removed outlier: 3.599A  pdb=" N   LYS E  44 " --> pdb=" O   ASP E  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 34
      removed outlier: 6.379A  pdb=" N   TYR H  12 " --> pdb=" O   VAL H  31 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASN H  33 " --> pdb=" O   ALA H  10 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ALA H  10 " --> pdb=" O   ASN H  33 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ILE H  52 " --> pdb=" O   ILE H 134 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 38 through 39
      removed outlier: 3.557A  pdb=" N   LYS H  44 " --> pdb=" O   ASP H  39 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU H  73 " --> pdb=" O   ARG H  80 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 38 through 39
      removed outlier: 3.557A  pdb=" N   LYS H  44 " --> pdb=" O   ASP H  39 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 29 through 34
      removed outlier: 5.226A  pdb=" N   VAL I  30 " --> pdb=" O   GLY I  14 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   GLY I  14 " --> pdb=" O   VAL I  30 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA I  10 " --> pdb=" O   LEU I  34 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE I  52 " --> pdb=" O   ILE I 134 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 19 through 20
    Processing sheet with id=AB3, first strand: chain 'I' and resid 38 through 39
      removed outlier: 3.552A  pdb=" N   LYS I  44 " --> pdb=" O   ASP I  39 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU I  73 " --> pdb=" O   ARG I  80 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'I' and resid 38 through 39
      removed outlier: 3.552A  pdb=" N   LYS I  44 " --> pdb=" O   ASP I  39 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8
      removed outlier: 3.539A  pdb=" N   THR B   6 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU B  34 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR B  62 " --> pdb=" O   GLN B 103 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU B  60 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 13 through 17
      removed outlier: 3.660A  pdb=" N   GLY B  14 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   PHE B 126 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE B  43 " --> pdb=" O   TYR B  97 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 5 through 8
      removed outlier: 3.535A  pdb=" N   THR C   6 " --> pdb=" O   THR C  30 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU C  34 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR C  62 " --> pdb=" O   GLN C 103 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU C  60 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 13 through 17
      removed outlier: 3.645A  pdb=" N   GLY C  14 " --> pdb=" O   PHE C 129 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   PHE C 126 " --> pdb=" O   SER C  48 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    731 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: 1.79

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1966
        1.34 -     1.46: 1609
        1.46 -     1.58: 2795
        1.58 -     1.70: 0
        1.70 -     1.82: 68
  Bond restraints: 6438
  Sorted by residual:
  bond pdb=" C   PHE E 132 "
       pdb=" N   ILE E 133 "
    ideal  model  delta    sigma   weight residual
    1.329  1.304  0.025 1.46e-02 4.69e+03 2.83e+00
  bond pdb=" CB  VAL H  99 "
       pdb=" CG1 VAL H  99 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.62e+00
  bond pdb=" CB  VAL E  99 "
       pdb=" CG1 VAL E  99 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.58e+00
  bond pdb=" CB  VAL I  99 "
       pdb=" CG1 VAL I  99 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  bond pdb=" C   PHE I 132 "
       pdb=" N   ILE I 133 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.96e-02 2.60e+03 1.36e+00
  ... (remaining 6433 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 8262
        1.14 -     2.27: 405
        2.27 -     3.41: 58
        3.41 -     4.55: 20
        4.55 -     5.68: 2
  Bond angle restraints: 8747
  Sorted by residual:
  angle pdb=" C   ASN E  76 "
        pdb=" CA  ASN E  76 "
        pdb=" CB  ASN E  76 "
      ideal   model   delta    sigma   weight residual
     110.42  115.45   -5.03 1.99e+00 2.53e-01 6.39e+00
  angle pdb=" CA  TYR E  53 "
        pdb=" CB  TYR E  53 "
        pdb=" CG  TYR E  53 "
      ideal   model   delta    sigma   weight residual
     113.90  117.88   -3.98 1.80e+00 3.09e-01 4.89e+00
  angle pdb=" CA  TYR I  53 "
        pdb=" CB  TYR I  53 "
        pdb=" CG  TYR I  53 "
      ideal   model   delta    sigma   weight residual
     113.90  117.70   -3.80 1.80e+00 3.09e-01 4.47e+00
  angle pdb=" CA  TYR H  53 "
        pdb=" CB  TYR H  53 "
        pdb=" CG  TYR H  53 "
      ideal   model   delta    sigma   weight residual
     113.90  117.52   -3.62 1.80e+00 3.09e-01 4.04e+00
  angle pdb=" N   ASN E  76 "
        pdb=" CA  ASN E  76 "
        pdb=" C   ASN E  76 "
      ideal   model   delta    sigma   weight residual
     110.80  106.58    4.22 2.13e+00 2.20e-01 3.92e+00
  ... (remaining 8742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.43: 3435
       16.43 -    32.85: 245
       32.85 -    49.27: 64
       49.27 -    65.70: 8
       65.70 -    82.12: 3
  Dihedral angle restraints: 3755
    sinusoidal: 1345
      harmonic: 2410
  Sorted by residual:
  dihedral pdb=" CA  ASP H  29 "
           pdb=" C   ASP H  29 "
           pdb=" N   VAL H  30 "
           pdb=" CA  VAL H  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.07  -15.93     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  LYS C  99 "
           pdb=" C   LYS C  99 "
           pdb=" N   ASN C 100 "
           pdb=" CA  ASN C 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.42  -15.58     0      5.00e+00 4.00e-02 9.71e+00
  dihedral pdb=" CA  ASP I  29 "
           pdb=" C   ASP I  29 "
           pdb=" N   VAL I  30 "
           pdb=" CA  VAL I  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.60  -15.40     0      5.00e+00 4.00e-02 9.49e+00
  ... (remaining 3752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 516
       0.027 -    0.053: 280
       0.053 -    0.080: 95
       0.080 -    0.106: 44
       0.106 -    0.132: 29
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" CA  ILE I  49 "
            pdb=" N   ILE I  49 "
            pdb=" C   ILE I  49 "
            pdb=" CB  ILE I  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE H  49 "
            pdb=" N   ILE H  49 "
            pdb=" C   ILE H  49 "
            pdb=" CB  ILE H  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  PRO H  40 "
            pdb=" N   PRO H  40 "
            pdb=" C   PRO H  40 "
            pdb=" CB  PRO H  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 961 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I  32 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.34e+00
        pdb=" C   THR I  32 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   THR I  32 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ASN I  33 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  53 "   -0.012 2.00e-02 2.50e+03   8.15e-03 1.33e+00
        pdb=" CG  TYR H  53 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR H  53 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  53 "    0.012 2.00e-02 2.50e+03   7.97e-03 1.27e+00
        pdb=" CG  TYR E  53 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  53 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  53 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  53 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E  53 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 185
        2.69 -     3.24: 5793
        3.24 -     3.79: 10529
        3.79 -     4.35: 14023
        4.35 -     4.90: 23755
  Nonbonded interactions: 54285
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  62 "
            pdb=" OE1 GLN A 103 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OH  TYR C  62 "
            pdb=" OE1 GLN C 103 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OH  TYR B  62 "
            pdb=" OE1 GLN B 103 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" OD1 ASP H  39 "
            pdb=" OG1 THR H  41 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OD1 ASP I  39 "
            pdb=" OG1 THR I  41 "
     model   vdw
     2.215 3.040
  ... (remaining 54280 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 4 through 173)
  selection = (chain 'C' and resid 4 through 173)
}
ncs_group {
  reference = (chain 'E' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 124 through 137 or re \ 
sid 201))
  selection = (chain 'H' and (resid 6 through 68 or resid 70 through 137 or resid 201))
  selection = (chain 'I' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 124 through 137 or re \ 
sid 201))
}

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=0.39 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.280
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6438  Z= 0.426
  Angle     :  0.580   5.682   8747  Z= 0.323
  Chirality :  0.042   0.132    964
  Planarity :  0.003   0.021   1116
  Dihedral  : 12.577  82.124   2166
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 10.33 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.28), residues: 802
  helix: -0.16 (0.52), residues: 93
  sheet: -0.60 (0.29), residues: 304
  loop : -1.29 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  31 
 HIS   0.003   0.001   HIS I 102 
 PHE   0.007   0.002   PHE I  55 
 TYR   0.019   0.002   TYR H  53 
 ARG   0.002   0.000   ARG E  17 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.7404 (m-30) cc_final: 0.6970 (t70)
REVERT: E   39 ASP cc_start: 0.8067 (t0) cc_final: 0.7698 (m-30)
REVERT: E   41 THR cc_start: 0.7057 (p) cc_final: 0.6671 (m)
REVERT: H   20 GLU cc_start: 0.8512 (tt0) cc_final: 0.7712 (pm20)
REVERT: H   39 ASP cc_start: 0.8037 (t0) cc_final: 0.7682 (m-30)
REVERT: H   41 THR cc_start: 0.7094 (p) cc_final: 0.6715 (m)
REVERT: I   20 GLU cc_start: 0.8458 (tt0) cc_final: 0.7662 (pm20)
REVERT: I   39 ASP cc_start: 0.8012 (t0) cc_final: 0.7667 (m-30)
REVERT: I   41 THR cc_start: 0.7280 (p) cc_final: 0.6867 (m)
REVERT: B   12 ILE cc_start: 0.8023 (mt) cc_final: 0.7748 (mp)
REVERT: B   65 ASP cc_start: 0.7189 (m-30) cc_final: 0.6840 (t70)
REVERT: B  138 SER cc_start: 0.6019 (p) cc_final: 0.5658 (t)
REVERT: C   65 ASP cc_start: 0.7272 (m-30) cc_final: 0.6952 (t70)
  outliers start: 39
  outliers final: 18
  residues processed: 176
  average time/residue: 0.7602
  time to fit residues: 143.9690
Evaluate side-chains
  143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain E residue   28 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  114 ASP
Chi-restraints excluded: chain E residue  130 SER
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   15 LEU
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0970
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** E  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  91 ASN
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.198370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.127209 restraints weight = 14161.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 3.28
r_work: 0.3457 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3455
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6438  Z= 0.216
  Angle     :  0.579   6.810   8747  Z= 0.307
  Chirality :  0.043   0.150    964
  Planarity :  0.003   0.044   1116
  Dihedral  :  7.023  56.498    905
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 16.90 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.29), residues: 802
  helix:  0.52 (0.54), residues: 93
  sheet: -0.69 (0.28), residues: 334
  loop : -1.22 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  31 
 HIS   0.004   0.001   HIS H  37 
 PHE   0.015   0.001   PHE C 101 
 TYR   0.016   0.001   TYR B  13 
 ARG   0.005   0.001   ARG B 106 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7184 (tppt)
REVERT: A   83 MET cc_start: 0.6491 (tpp) cc_final: 0.6288 (tmm)
REVERT: A   96 GLN cc_start: 0.8265 (tt0) cc_final: 0.8002 (tm-30)
REVERT: A   99 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7986 (tttp)
REVERT: E   39 ASP cc_start: 0.7921 (t0) cc_final: 0.7473 (m-30)
REVERT: E   41 THR cc_start: 0.6965 (p) cc_final: 0.6615 (m)
REVERT: H   39 ASP cc_start: 0.7916 (t0) cc_final: 0.7482 (m-30)
REVERT: H   41 THR cc_start: 0.7103 (p) cc_final: 0.6644 (m)
REVERT: I   39 ASP cc_start: 0.7966 (t0) cc_final: 0.7509 (m-30)
REVERT: I   41 THR cc_start: 0.7108 (p) cc_final: 0.6755 (m)
REVERT: B   12 ILE cc_start: 0.7954 (mt) cc_final: 0.7702 (mp)
REVERT: B   65 ASP cc_start: 0.7326 (m-30) cc_final: 0.6564 (t70)
REVERT: B   97 TYR cc_start: 0.8469 (m-80) cc_final: 0.8187 (m-80)
REVERT: B  138 SER cc_start: 0.4551 (p) cc_final: 0.4321 (t)
REVERT: C   65 ASP cc_start: 0.7117 (m-30) cc_final: 0.6420 (t70)
  outliers start: 26
  outliers final: 13
  residues processed: 167
  average time/residue: 0.7716
  time to fit residues: 138.4600
Evaluate side-chains
  155 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  127 PHE
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 47 optimal weight:    0.6980
   chunk 59 optimal weight:    8.9990
   chunk 72 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 124 ASN
** H  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 122 ASN
C  96 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.197682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.125745 restraints weight = 13604.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 3.33
r_work: 0.3454 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6438  Z= 0.226
  Angle     :  0.539   5.587   8747  Z= 0.287
  Chirality :  0.043   0.173    964
  Planarity :  0.003   0.032   1116
  Dihedral  :  6.220  57.274    893
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.75 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.29), residues: 802
  helix:  1.08 (0.54), residues: 90
  sheet: -0.64 (0.27), residues: 334
  loop : -1.33 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  31 
 HIS   0.004   0.001   HIS I 119 
 PHE   0.012   0.001   PHE C 101 
 TYR   0.018   0.001   TYR C  13 
 ARG   0.003   0.000   ARG E  80 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   39 ASP cc_start: 0.7939 (t0) cc_final: 0.7579 (m-30)
REVERT: E   41 THR cc_start: 0.6971 (p) cc_final: 0.6631 (m)
REVERT: H   39 ASP cc_start: 0.7880 (t0) cc_final: 0.7466 (m-30)
REVERT: H   41 THR cc_start: 0.7072 (p) cc_final: 0.6618 (m)
REVERT: I   39 ASP cc_start: 0.7977 (t0) cc_final: 0.7532 (m-30)
REVERT: I   41 THR cc_start: 0.7050 (p) cc_final: 0.6696 (m)
REVERT: B   12 ILE cc_start: 0.7966 (mt) cc_final: 0.7710 (mp)
REVERT: B   34 GLU cc_start: 0.7461 (tt0) cc_final: 0.7191 (tt0)
REVERT: B   65 ASP cc_start: 0.7344 (m-30) cc_final: 0.6671 (t70)
REVERT: B   97 TYR cc_start: 0.8458 (m-80) cc_final: 0.8225 (m-80)
REVERT: B   99 LYS cc_start: 0.8288 (ttmt) cc_final: 0.8033 (ttmt)
REVERT: B  138 SER cc_start: 0.4792 (p) cc_final: 0.4568 (t)
REVERT: C   34 GLU cc_start: 0.7563 (tt0) cc_final: 0.7348 (tt0)
REVERT: C   65 ASP cc_start: 0.7081 (m-30) cc_final: 0.6493 (t70)
REVERT: C  138 SER cc_start: 0.5147 (p) cc_final: 0.4840 (t)
  outliers start: 23
  outliers final: 12
  residues processed: 164
  average time/residue: 0.7452
  time to fit residues: 131.5080
Evaluate side-chains
  153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 80 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
A  96 GLN
A 133 ASN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.198802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.126674 restraints weight = 14761.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 3.48
r_work: 0.3467 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6438  Z= 0.196
  Angle     :  0.515   7.250   8747  Z= 0.272
  Chirality :  0.042   0.171    964
  Planarity :  0.003   0.025   1116
  Dihedral  :  5.644  58.476    890
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 22.22 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.28), residues: 802
  helix:  1.39 (0.53), residues: 90
  sheet: -0.54 (0.28), residues: 331
  loop : -1.31 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  31 
 HIS   0.004   0.001   HIS I 119 
 PHE   0.012   0.001   PHE C 101 
 TYR   0.020   0.001   TYR C  13 
 ARG   0.003   0.000   ARG E  80 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6415 (tpt) cc_final: 0.5797 (tpp)
REVERT: E   39 ASP cc_start: 0.7960 (t0) cc_final: 0.7613 (m-30)
REVERT: E   41 THR cc_start: 0.6965 (p) cc_final: 0.6659 (m)
REVERT: H   39 ASP cc_start: 0.7893 (t0) cc_final: 0.7478 (m-30)
REVERT: H   41 THR cc_start: 0.7022 (p) cc_final: 0.6566 (m)
REVERT: H   86 GLN cc_start: 0.8549 (tt0) cc_final: 0.8292 (tt0)
REVERT: I   39 ASP cc_start: 0.7968 (t0) cc_final: 0.7543 (m-30)
REVERT: I   41 THR cc_start: 0.7043 (p) cc_final: 0.6721 (m)
REVERT: B   12 ILE cc_start: 0.7966 (mt) cc_final: 0.7687 (mp)
REVERT: B   34 GLU cc_start: 0.7493 (tt0) cc_final: 0.7229 (tt0)
REVERT: B   65 ASP cc_start: 0.7339 (m-30) cc_final: 0.6636 (t70)
REVERT: B   97 TYR cc_start: 0.8456 (m-80) cc_final: 0.8195 (m-80)
REVERT: C    7 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6903 (tt)
REVERT: C   65 ASP cc_start: 0.7168 (m-30) cc_final: 0.6504 (t70)
REVERT: C  138 SER cc_start: 0.5065 (p) cc_final: 0.4801 (t)
  outliers start: 29
  outliers final: 16
  residues processed: 169
  average time/residue: 0.6994
  time to fit residues: 127.8467
Evaluate side-chains
  155 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue   99 LYS
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain E residue   68 SER
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 75 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
A  96 GLN
A 133 ASN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
C 133 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.195902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.123556 restraints weight = 13619.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.27
r_work: 0.3422 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6438  Z= 0.313
  Angle     :  0.549   5.514   8747  Z= 0.291
  Chirality :  0.043   0.166    964
  Planarity :  0.003   0.024   1116
  Dihedral  :  5.681  57.847    888
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 22.22 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.29), residues: 802
  helix:  1.67 (0.54), residues: 90
  sheet: -0.68 (0.27), residues: 340
  loop : -1.26 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  31 
 HIS   0.005   0.001   HIS I 119 
 PHE   0.011   0.001   PHE C 101 
 TYR   0.022   0.002   TYR C  13 
 ARG   0.002   0.000   ARG E  80 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6431 (tpt) cc_final: 0.5850 (tpp)
REVERT: A   96 GLN cc_start: 0.8272 (tt0) cc_final: 0.7702 (tm-30)
REVERT: E   39 ASP cc_start: 0.7945 (t0) cc_final: 0.7585 (m-30)
REVERT: E   41 THR cc_start: 0.6971 (p) cc_final: 0.6659 (m)
REVERT: H   39 ASP cc_start: 0.7880 (t0) cc_final: 0.7488 (m-30)
REVERT: H   41 THR cc_start: 0.7087 (p) cc_final: 0.6628 (m)
REVERT: H   96 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8389 (m)
REVERT: I   20 GLU cc_start: 0.8302 (tt0) cc_final: 0.7641 (pm20)
REVERT: I   39 ASP cc_start: 0.7917 (t0) cc_final: 0.7532 (m-30)
REVERT: I   41 THR cc_start: 0.7048 (p) cc_final: 0.6706 (m)
REVERT: B   12 ILE cc_start: 0.7986 (mt) cc_final: 0.7715 (mp)
REVERT: B   65 ASP cc_start: 0.7277 (m-30) cc_final: 0.6677 (t70)
REVERT: B   99 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8050 (tttp)
REVERT: B  136 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8351 (p)
REVERT: C    7 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6987 (tt)
REVERT: C   65 ASP cc_start: 0.7182 (m-30) cc_final: 0.6882 (t70)
REVERT: C   99 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7568 (tttp)
  outliers start: 33
  outliers final: 19
  residues processed: 150
  average time/residue: 0.7533
  time to fit residues: 122.1502
Evaluate side-chains
  147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue   26 PHE
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   68 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
A 133 ASN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 122 ASN
B 100 ASN
C  63 GLN
** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.197892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.135503 restraints weight = 7872.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 3.04
r_work: 0.3495 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6438  Z= 0.237
  Angle     :  0.540   8.100   8747  Z= 0.282
  Chirality :  0.043   0.167    964
  Planarity :  0.003   0.023   1116
  Dihedral  :  5.548  55.195    888
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 23.47 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.29), residues: 802
  helix:  1.82 (0.54), residues: 90
  sheet: -0.56 (0.28), residues: 331
  loop : -1.29 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  31 
 HIS   0.004   0.001   HIS I 119 
 PHE   0.010   0.001   PHE C  22 
 TYR   0.024   0.001   TYR C  13 
 ARG   0.002   0.000   ARG E  80 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6417 (tpt) cc_final: 0.5833 (tpp)
REVERT: A   96 GLN cc_start: 0.8315 (tt0) cc_final: 0.7727 (tm-30)
REVERT: E   39 ASP cc_start: 0.8051 (t0) cc_final: 0.7652 (m-30)
REVERT: E   41 THR cc_start: 0.6969 (p) cc_final: 0.6666 (m)
REVERT: H   39 ASP cc_start: 0.8005 (t0) cc_final: 0.7531 (m-30)
REVERT: H   41 THR cc_start: 0.7079 (p) cc_final: 0.6638 (m)
REVERT: H   96 SER cc_start: 0.8644 (p) cc_final: 0.8439 (m)
REVERT: H  128 THR cc_start: 0.7818 (p) cc_final: 0.7541 (p)
REVERT: I   39 ASP cc_start: 0.8030 (t0) cc_final: 0.7609 (m-30)
REVERT: I   41 THR cc_start: 0.7062 (p) cc_final: 0.6743 (m)
REVERT: B   12 ILE cc_start: 0.7962 (mt) cc_final: 0.7690 (mp)
REVERT: B   65 ASP cc_start: 0.7373 (m-30) cc_final: 0.6746 (t70)
REVERT: B   99 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8081 (tttp)
REVERT: C   99 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7301 (tttp)
  outliers start: 31
  outliers final: 21
  residues processed: 153
  average time/residue: 0.7268
  time to fit residues: 120.3630
Evaluate side-chains
  149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   68 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  114 ASP
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
A 133 ASN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 122 ASN
B 100 ASN
** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.196021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.125454 restraints weight = 9679.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.83
r_work: 0.3462 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6438  Z= 0.318
  Angle     :  0.571   7.490   8747  Z= 0.300
  Chirality :  0.044   0.162    964
  Planarity :  0.003   0.043   1116
  Dihedral  :  5.730  55.834    888
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 24.10 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.28), residues: 802
  helix:  1.83 (0.54), residues: 90
  sheet: -0.58 (0.28), residues: 331
  loop : -1.45 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  31 
 HIS   0.005   0.001   HIS I 119 
 PHE   0.012   0.001   PHE A  26 
 TYR   0.026   0.002   TYR C  13 
 ARG   0.002   0.000   ARG H  62 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6498 (tpt) cc_final: 0.5904 (tpp)
REVERT: A   96 GLN cc_start: 0.8263 (tt0) cc_final: 0.7682 (tm-30)
REVERT: A   99 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7614 (tttm)
REVERT: E   39 ASP cc_start: 0.7926 (t0) cc_final: 0.7544 (m-30)
REVERT: E   41 THR cc_start: 0.6944 (p) cc_final: 0.6640 (m)
REVERT: H   39 ASP cc_start: 0.7866 (t0) cc_final: 0.7464 (m-30)
REVERT: H   41 THR cc_start: 0.7082 (p) cc_final: 0.6640 (m)
REVERT: H   96 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8401 (m)
REVERT: I   20 GLU cc_start: 0.8255 (tt0) cc_final: 0.7580 (pm20)
REVERT: I   39 ASP cc_start: 0.7920 (t0) cc_final: 0.7504 (m-30)
REVERT: I   41 THR cc_start: 0.7032 (p) cc_final: 0.6703 (m)
REVERT: I   44 LYS cc_start: 0.8305 (mttt) cc_final: 0.8037 (mtmt)
REVERT: B   12 ILE cc_start: 0.7961 (mt) cc_final: 0.7588 (mp)
REVERT: B   65 ASP cc_start: 0.7187 (m-30) cc_final: 0.6556 (t70)
  outliers start: 31
  outliers final: 24
  residues processed: 151
  average time/residue: 0.7304
  time to fit residues: 119.2974
Evaluate side-chains
  148 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue   99 LYS
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   68 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  114 ASP
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:    0.0970
   chunk 2 optimal weight:    6.9990
   chunk 75 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0000
   chunk 33 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 42 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.4582

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
A 133 ASN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 122 ASN
** I  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 122 ASN
B  63 GLN
B 100 ASN
C 100 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.201109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.130829 restraints weight = 11734.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.08
r_work: 0.3520 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6438  Z= 0.154
  Angle     :  0.522   8.334   8747  Z= 0.273
  Chirality :  0.042   0.165    964
  Planarity :  0.003   0.049   1116
  Dihedral  :  5.304  44.448    888
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 25.51 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.28), residues: 802
  helix:  1.98 (0.53), residues: 90
  sheet: -0.46 (0.28), residues: 331
  loop : -1.28 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  31 
 HIS   0.003   0.001   HIS I  37 
 PHE   0.009   0.001   PHE C 140 
 TYR   0.023   0.001   TYR C  13 
 ARG   0.001   0.000   ARG H  17 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 LYS cc_start: 0.7301 (ttpt) cc_final: 0.6329 (tptt)
REVERT: A   83 MET cc_start: 0.6399 (tpt) cc_final: 0.5867 (tpp)
REVERT: A   96 GLN cc_start: 0.8179 (tt0) cc_final: 0.7689 (tm-30)
REVERT: A   99 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7499 (tttm)
REVERT: E   39 ASP cc_start: 0.7932 (t0) cc_final: 0.7587 (m-30)
REVERT: E   41 THR cc_start: 0.6942 (p) cc_final: 0.6665 (m)
REVERT: H   39 ASP cc_start: 0.7909 (t0) cc_final: 0.7477 (m-30)
REVERT: H   41 THR cc_start: 0.6990 (p) cc_final: 0.6577 (m)
REVERT: I    9 ILE cc_start: 0.8381 (mt) cc_final: 0.8116 (mt)
REVERT: I   39 ASP cc_start: 0.7961 (t0) cc_final: 0.7583 (m-30)
REVERT: I   41 THR cc_start: 0.6970 (p) cc_final: 0.6677 (m)
REVERT: B   12 ILE cc_start: 0.7834 (mt) cc_final: 0.7503 (mp)
REVERT: B   96 GLN cc_start: 0.8249 (tt0) cc_final: 0.7333 (tm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 155
  average time/residue: 0.7497
  time to fit residues: 125.7089
Evaluate side-chains
  145 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue   99 LYS
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  135 TYR
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 80 optimal weight:   30.0000
   chunk 56 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 122 ASN
** I  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  90 GLN
I 122 ASN
I 124 ASN
B 100 ASN
C 100 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.199260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.127930 restraints weight = 11711.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 3.09
r_work: 0.3487 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6438  Z= 0.229
  Angle     :  0.557   9.659   8747  Z= 0.292
  Chirality :  0.044   0.210    964
  Planarity :  0.003   0.063   1116
  Dihedral  :  5.483  46.051    887
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 26.60 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.29), residues: 802
  helix:  1.86 (0.54), residues: 90
  sheet: -0.45 (0.28), residues: 331
  loop : -1.31 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  31 
 HIS   0.004   0.001   HIS I 119 
 PHE   0.008   0.001   PHE A  26 
 TYR   0.024   0.001   TYR C  13 
 ARG   0.001   0.000   ARG A 105 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6367 (tptt)
REVERT: A   83 MET cc_start: 0.6446 (tpt) cc_final: 0.5919 (tpp)
REVERT: A   96 GLN cc_start: 0.8194 (tt0) cc_final: 0.7678 (tm-30)
REVERT: A   99 LYS cc_start: 0.8013 (tttp) cc_final: 0.7547 (tttm)
REVERT: E   39 ASP cc_start: 0.7940 (t0) cc_final: 0.7532 (m-30)
REVERT: E   41 THR cc_start: 0.6946 (p) cc_final: 0.6656 (m)
REVERT: H   39 ASP cc_start: 0.7897 (t0) cc_final: 0.7447 (m-30)
REVERT: H   41 THR cc_start: 0.7050 (p) cc_final: 0.6604 (m)
REVERT: I   39 ASP cc_start: 0.7967 (t0) cc_final: 0.7516 (m-30)
REVERT: I   41 THR cc_start: 0.7001 (p) cc_final: 0.6677 (m)
REVERT: B   12 ILE cc_start: 0.7860 (mt) cc_final: 0.7601 (mp)
REVERT: B   96 GLN cc_start: 0.8252 (tt0) cc_final: 0.7322 (tm-30)
REVERT: B   99 LYS cc_start: 0.8271 (tttp) cc_final: 0.7791 (tttm)
REVERT: C   99 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7495 (tttp)
  outliers start: 23
  outliers final: 18
  residues processed: 147
  average time/residue: 0.7512
  time to fit residues: 118.8668
Evaluate side-chains
  143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   68 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0670
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 43 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7122

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 122 ASN
** I  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  90 GLN
I 122 ASN
B 100 ASN
C 100 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.200661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.129910 restraints weight = 13538.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 3.23
r_work: 0.3501 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6438  Z= 0.183
  Angle     :  0.540   6.802   8747  Z= 0.283
  Chirality :  0.043   0.160    964
  Planarity :  0.003   0.048   1116
  Dihedral  :  5.367  41.375    887
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 27.39 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.29), residues: 802
  helix:  2.03 (0.54), residues: 90
  sheet: -0.42 (0.27), residues: 337
  loop : -1.28 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A  31 
 HIS   0.003   0.001   HIS I 119 
 PHE   0.014   0.001   PHE B 140 
 TYR   0.025   0.001   TYR B  13 
 ARG   0.001   0.000   ARG E  62 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6259 (tptt)
REVERT: A   83 MET cc_start: 0.6440 (tpt) cc_final: 0.5887 (tpp)
REVERT: A   96 GLN cc_start: 0.8173 (tt0) cc_final: 0.7727 (tm-30)
REVERT: A   99 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7449 (tttm)
REVERT: E   39 ASP cc_start: 0.7941 (t0) cc_final: 0.7581 (m-30)
REVERT: E   41 THR cc_start: 0.6925 (p) cc_final: 0.6647 (m)
REVERT: H   39 ASP cc_start: 0.7925 (t0) cc_final: 0.7485 (m-30)
REVERT: H   41 THR cc_start: 0.7012 (p) cc_final: 0.6596 (m)
REVERT: I    9 ILE cc_start: 0.8377 (mt) cc_final: 0.8107 (mt)
REVERT: I   39 ASP cc_start: 0.7978 (t0) cc_final: 0.7532 (m-30)
REVERT: I   41 THR cc_start: 0.6945 (p) cc_final: 0.6642 (m)
REVERT: B   12 ILE cc_start: 0.7824 (mt) cc_final: 0.7555 (mp)
REVERT: B   96 GLN cc_start: 0.8279 (tt0) cc_final: 0.7392 (tm-30)
REVERT: B   99 LYS cc_start: 0.8243 (tttp) cc_final: 0.7778 (tttp)
REVERT: C   99 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7523 (tttp)
REVERT: C  136 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8383 (p)
  outliers start: 19
  outliers final: 14
  residues processed: 141
  average time/residue: 0.7841
  time to fit residues: 118.8399
Evaluate side-chains
  143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASP
Chi-restraints excluded: chain A residue   99 LYS
Chi-restraints excluded: chain E residue   67 THR
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   68 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  130 SER
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    7 LEU
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue  136 SER
Chi-restraints excluded: chain C residue  165 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
** E  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 122 ASN
** I  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  90 GLN
I 122 ASN
B 100 ASN
C 100 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.198912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.126310 restraints weight = 14495.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 3.37
r_work: 0.3458 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6438  Z= 0.246
  Angle     :  0.571  10.208   8747  Z= 0.296
  Chirality :  0.044   0.155    964
  Planarity :  0.003   0.055   1116
  Dihedral  :  5.536  44.750    887
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 26.76 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.28), residues: 802
  helix:  1.71 (0.55), residues: 93
  sheet: -0.48 (0.27), residues: 337
  loop : -1.26 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP B  31 
 HIS   0.004   0.001   HIS I 119 
 PHE   0.014   0.001   PHE C  22 
 TYR   0.025   0.002   TYR B  13 
 ARG   0.001   0.000   ARG A 105 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5710.18 seconds
wall clock time: 101 minutes 16.57 seconds (6076.57 seconds total)