Starting phenix.real_space_refine
on Thu Feb 13 09:30:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dz5_27789/02_2025/8dz5_27789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dz5_27789/02_2025/8dz5_27789.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dz5_27789/02_2025/8dz5_27789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dz5_27789/02_2025/8dz5_27789.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dz5_27789/02_2025/8dz5_27789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dz5_27789/02_2025/8dz5_27789.cif"
  }
  resolution = 3.84
  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=  -0.002 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    5655      2.51       5
     N    1530      2.21       5
     O    1730      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 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: 8950
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "I"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 280
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 10, 'TRANS': 29}
    Chain: "H"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "B"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "D"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "E"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "F"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "M"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 915
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
    Chain: "N"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
  Time building chain proxies: 5.64, per 1000 atoms: 0.63
  Number of scatterers: 8950
  At special positions: 0
  Unit cell: (72.45, 112.7, 115, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    1730      8.00
     N    1530      7.00
     C    5655      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 31 sheets defined
      8.5% alpha, 41.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.520A  pdb=" N   GLN H  64 " --> pdb=" O   ASP H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.699A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.701A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 61 through 64
    Processing helix  chain 'A' and resid 73 through 75
      No H-bonds generated for 'chain 'A' and resid 73 through 75'
    Processing helix  chain 'A' and resid 83 through 87
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.594A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 61 through 64
      removed outlier: 3.601A  pdb=" N   GLN C  64 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 61 through 64'
    Processing helix  chain 'C' and resid 83 through 87
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.565A  pdb=" N   PHE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 61 through 64
      removed outlier: 3.532A  pdb=" N   GLN E  64 " --> pdb=" O   ASP E  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 61 through 64'
    Processing helix  chain 'E' and resid 83 through 87
    Processing helix  chain 'F' and resid 79 through 83
      removed outlier: 3.773A  pdb=" N   PHE F  83 " --> pdb=" O   PRO F  80 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 28 through 32
    Processing helix  chain 'M' and resid 61 through 64
      removed outlier: 3.556A  pdb=" N   GLN M  64 " --> pdb=" O   ASP M  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 61 through 64'
    Processing helix  chain 'M' and resid 83 through 87
    Processing helix  chain 'N' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.547A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.389A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 109 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA H  93 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   MET H  34 " --> pdb=" O   ILE H  50 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ILE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.389A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 109 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   CYS H  92 " --> pdb=" O   TRP H 102 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   TRP H 102 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LYS H  94 " --> pdb=" O   ASP H 100C" (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.703A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA6, first strand: chain 'L' and resid 33 through 35
      removed outlier: 4.151A  pdb=" N   GLN L  89 " --> pdb=" O   ALA L  34 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.916A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.275A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   MET A  34 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ILE A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.275A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   CYS A  92 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   TRP A 102 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LYS A  94 " --> pdb=" O   ASP A 100C" (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.805A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 53 through 54
      removed outlier: 6.554A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLN B  89 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.732A  pdb=" N   SER C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU C  80 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER C  70 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.788A  pdb=" N   ALA C  93 " --> pdb=" O   HIS C  35 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   MET C  34 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   ILE C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.785A  pdb=" N   CYS C  92 " --> pdb=" O   TRP C 102 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   TRP C 102 " --> pdb=" O   CYS C  92 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LYS C  94 " --> pdb=" O   ASP C 100C" (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7
    Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.535A  pdb=" N   THR D 102 " --> pdb=" O   TYR D  86 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 37
      removed outlier: 6.432A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN D  37 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.937A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU E  80 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 11
      removed outlier: 3.509A  pdb=" N   ALA E  93 " --> pdb=" O   HIS E  35 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   MET E  34 " --> pdb=" O   ILE E  50 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ILE E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 11
      removed outlier: 6.591A  pdb=" N   CYS E  92 " --> pdb=" O   TRP E 102 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TRP E 102 " --> pdb=" O   CYS E  92 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS E  94 " --> pdb=" O   ASP E 100C" (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 7
    Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13
    Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 54
      removed outlier: 6.481A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   TYR F  49 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LEU F  33 " --> pdb=" O   TYR F  49 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLN F  89 " --> pdb=" O   ALA F  34 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'M' and resid 3 through 7
      removed outlier: 3.776A  pdb=" N   SER M  21 " --> pdb=" O   SER M   7 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU M  80 " --> pdb=" O   LEU M  20 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 11
      removed outlier: 6.492A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 109 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   MET M  34 " --> pdb=" O   ILE M  50 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 11
      removed outlier: 6.492A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 109 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   CYS M  92 " --> pdb=" O   TRP M 102 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   TRP M 102 " --> pdb=" O   CYS M  92 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LYS M  94 " --> pdb=" O   ASP M 100C" (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7
    Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13
    Processing sheet with id=AD4, first strand: chain 'N' and resid 53 through 54
      removed outlier: 3.506A  pdb=" N   GLN N  37 " --> pdb=" O   LYS N  45 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU N  47 " --> pdb=" O   TRP N  35 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   TYR N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   LEU N  33 " --> pdb=" O   TYR N  49 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLN N  89 " --> pdb=" O   ALA N  34 " (cutoff:3.500A)

    335 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 2.68 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: 2879
        1.34 -     1.46: 2279
        1.46 -     1.58: 3956
        1.58 -     1.70: 0
        1.70 -     1.81: 50
  Bond restraints: 9164
  Sorted by residual:
  bond pdb=" N   GLY F  64 "
       pdb=" CA  GLY F  64 "
    ideal  model  delta    sigma   weight residual
    1.454  1.443  0.012 9.90e-03 1.02e+04 1.35e+00
  bond pdb=" CA  ASP C 100C"
       pdb=" C   ASP C 100C"
    ideal  model  delta    sigma   weight residual
    1.521  1.532 -0.011 9.90e-03 1.02e+04 1.35e+00
  bond pdb=" CB  ASP H 100C"
       pdb=" CG  ASP H 100C"
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  PRO I  50 "
       pdb=" CG  PRO I  50 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 5.00e-02 4.00e+02 1.07e+00
  bond pdb=" CB  GLU N  81 "
       pdb=" CG  GLU N  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.62e-01
  ... (remaining 9159 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 11832
        1.50 -     3.00: 498
        3.00 -     4.50: 76
        4.50 -     6.00: 16
        6.00 -     7.50: 5
  Bond angle restraints: 12427
  Sorted by residual:
  angle pdb=" CA  GLU N 105 "
        pdb=" CB  GLU N 105 "
        pdb=" CG  GLU N 105 "
      ideal   model   delta    sigma   weight residual
     114.10  121.39   -7.29 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" CA  GLU N  81 "
        pdb=" CB  GLU N  81 "
        pdb=" CG  GLU N  81 "
      ideal   model   delta    sigma   weight residual
     114.10  119.55   -5.45 2.00e+00 2.50e-01 7.44e+00
  angle pdb=" N   ILE F  29 "
        pdb=" CA  ILE F  29 "
        pdb=" CB  ILE F  29 "
      ideal   model   delta    sigma   weight residual
     111.64  109.47    2.17 8.20e-01 1.49e+00 7.02e+00
  angle pdb=" N   LYS D  50 "
        pdb=" CA  LYS D  50 "
        pdb=" C   LYS D  50 "
      ideal   model   delta    sigma   weight residual
     112.86  109.71    3.15 1.22e+00 6.72e-01 6.68e+00
  angle pdb=" C   ASP F  17 "
        pdb=" CA  ASP F  17 "
        pdb=" CB  ASP F  17 "
      ideal   model   delta    sigma   weight residual
     109.76  114.84   -5.08 1.99e+00 2.53e-01 6.53e+00
  ... (remaining 12422 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 4789
       17.78 -    35.56: 459
       35.56 -    53.34: 98
       53.34 -    71.11: 26
       71.11 -    88.89: 12
  Dihedral angle restraints: 5384
    sinusoidal: 2100
      harmonic: 3284
  Sorted by residual:
  dihedral pdb=" CB  CYS B  23 "
           pdb=" SG  CYS B  23 "
           pdb=" SG  CYS B  88 "
           pdb=" CB  CYS B  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.94   42.94     1      1.00e+01 1.00e-02 2.57e+01
  dihedral pdb=" CB  CYS F  23 "
           pdb=" SG  CYS F  23 "
           pdb=" SG  CYS F  88 "
           pdb=" CB  CYS F  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.77   40.77     1      1.00e+01 1.00e-02 2.33e+01
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  88 "
           pdb=" CB  CYS D  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.86   37.86     1      1.00e+01 1.00e-02 2.02e+01
  ... (remaining 5381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 823
       0.029 -    0.059: 332
       0.059 -    0.088: 81
       0.088 -    0.117: 77
       0.117 -    0.147: 22
  Chirality restraints: 1335
  Sorted by residual:
  chirality pdb=" CA  VAL A  40 "
            pdb=" N   VAL A  40 "
            pdb=" C   VAL A  40 "
            pdb=" CB  VAL A  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" CA  ASP C 100C"
            pdb=" N   ASP C 100C"
            pdb=" C   ASP C 100C"
            pdb=" CB  ASP C 100C"
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CG  LEU D  33 "
            pdb=" CB  LEU D  33 "
            pdb=" CD1 LEU D  33 "
            pdb=" CD2 LEU D  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 4.82e-01
  ... (remaining 1332 not shown)

  Planarity restraints: 1594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  40 "   -0.054 5.00e-02 4.00e+02   8.11e-02 1.05e+01
        pdb=" N   PRO A  41 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A  41 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A  41 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR N  91 "    0.016 2.00e-02 2.50e+03   1.29e-02 3.33e+00
        pdb=" CG  TYR N  91 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR N  91 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR N  91 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR N  91 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR N  91 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR N  91 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR N  91 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  39 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.33e+00
        pdb=" N   PRO B  40 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B  40 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  40 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1591 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 431
        2.71 -     3.26: 8584
        3.26 -     3.81: 14663
        3.81 -     4.35: 17872
        4.35 -     4.90: 30731
  Nonbonded interactions: 72281
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 100C"
            pdb=" N   TYR C 101 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" O   TYR H  32 "
            pdb=" NH1 ARG H  71 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   TYR C  32 "
            pdb=" NH1 ARG C  71 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" ND2 ASN I  43 "
            pdb=" O   TYR L  91 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OG1 THR E  28 "
            pdb=" OD2 ASP N   1 "
     model   vdw
     2.247 3.040
  ... (remaining 72276 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 'C'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'L'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.580
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
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      :  0.003   0.052   9164  Z= 0.189
  Angle     :  0.713   7.497  12427  Z= 0.399
  Chirality :  0.042   0.147   1335
  Planarity :  0.004   0.081   1594
  Dihedral  : 15.288  88.892   3274
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 18.34 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.63 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.97 (0.23), residues: 495
  loop :  0.25 (0.28), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 102 
 HIS   0.005   0.002   HIS M  35 
 PHE   0.016   0.002   PHE A  79 
 TYR   0.028   0.002   TYR N  91 
 ARG   0.011   0.001   ARG F  18 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.7682 (ptpp) cc_final: 0.7476 (ptpp)
REVERT: A   80 LEU cc_start: 0.7136 (tt) cc_final: 0.6845 (tt)
  outliers start: 6
  outliers final: 5
  residues processed: 138
  average time/residue: 0.2795
  time to fit residues: 50.2051
Evaluate side-chains
  122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  106 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 28 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 63 optimal weight:    8.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN
D  90 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.087856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.068158 restraints weight = 21946.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.070493 restraints weight = 13808.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.072074 restraints weight = 9969.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9164  Z= 0.355
  Angle     :  0.659   6.904  12427  Z= 0.353
  Chirality :  0.045   0.166   1335
  Planarity :  0.004   0.050   1594
  Dihedral  :  5.667  49.351   1263
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.58 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -1.03 (0.22), residues: 535
  loop :  0.05 (0.28), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 102 
 HIS   0.005   0.002   HIS M  96 
 PHE   0.016   0.002   PHE A  79 
 TYR   0.018   0.002   TYR E  90 
 ARG   0.004   0.001   ARG C  19 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 120
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.7434 (m-10) cc_final: 0.6518 (m-10)
REVERT: B   27 GLN cc_start: 0.7068 (mm110) cc_final: 0.6846 (mm-40)
REVERT: C   45 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7397 (mt)
REVERT: C  100 ASP cc_start: 0.8099 (p0) cc_final: 0.7603 (p0)
REVERT: C  102 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.8645 (m100)
REVERT: E  100 ASP cc_start: 0.7872 (p0) cc_final: 0.7428 (t0)
REVERT: N  105 GLU cc_start: 0.7152 (tp30) cc_final: 0.6394 (tm-30)
  outliers start: 39
  outliers final: 19
  residues processed: 146
  average time/residue: 0.2443
  time to fit residues: 48.0435
Evaluate side-chains
  131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   32 SER
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain C residue  102 TRP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0770
   chunk 60 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M   3 GLN
N  89 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.091626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.072086 restraints weight = 21513.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.074707 restraints weight = 14251.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.075694 restraints weight = 9376.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9164  Z= 0.152
  Angle     :  0.580   7.780  12427  Z= 0.307
  Chirality :  0.043   0.141   1335
  Planarity :  0.003   0.038   1594
  Dihedral  :  5.306  58.120   1260
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.41 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.48 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.63 (0.23), residues: 510
  loop :  0.14 (0.28), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP M 102 
 HIS   0.002   0.001   HIS M  35 
 PHE   0.012   0.001   PHE B  71 
 TYR   0.012   0.001   TYR E 101 
 ARG   0.005   0.000   ARG F  18 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   90 TYR cc_start: 0.8095 (m-80) cc_final: 0.7857 (m-10)
REVERT: A   19 ARG cc_start: 0.7223 (ttt-90) cc_final: 0.7022 (ttt-90)
REVERT: A   67 PHE cc_start: 0.7355 (m-10) cc_final: 0.7109 (m-10)
REVERT: B   11 LEU cc_start: 0.7719 (tt) cc_final: 0.7461 (tt)
REVERT: C   45 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7086 (mt)
REVERT: C   53 ASP cc_start: 0.7227 (p0) cc_final: 0.6989 (p0)
REVERT: C  100 ASP cc_start: 0.8087 (p0) cc_final: 0.7814 (p0)
REVERT: E   53 ASP cc_start: 0.8186 (p0) cc_final: 0.7660 (p0)
REVERT: N  105 GLU cc_start: 0.7402 (tp30) cc_final: 0.6952 (tm-30)
  outliers start: 26
  outliers final: 15
  residues processed: 146
  average time/residue: 0.2696
  time to fit residues: 51.8542
Evaluate side-chains
  130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain B residue   32 SER
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   91 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 94 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.092133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.072692 restraints weight = 21688.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.075102 restraints weight = 13207.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.076667 restraints weight = 9382.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9164  Z= 0.174
  Angle     :  0.574   8.461  12427  Z= 0.299
  Chirality :  0.042   0.139   1335
  Planarity :  0.003   0.033   1594
  Dihedral  :  5.234  58.155   1260
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.62 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.39 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.69 (0.23), residues: 530
  loop :  0.36 (0.28), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 102 
 HIS   0.003   0.001   HIS A  35 
 PHE   0.011   0.001   PHE B  71 
 TYR   0.013   0.001   TYR H  32 
 ARG   0.005   0.000   ARG F  18 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 LEU cc_start: 0.7748 (tt) cc_final: 0.7514 (tt)
REVERT: B   17 ASP cc_start: 0.7196 (t0) cc_final: 0.6216 (m-30)
REVERT: B   24 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7720 (ttm-80)
REVERT: C   53 ASP cc_start: 0.7280 (p0) cc_final: 0.7068 (p0)
REVERT: E   53 ASP cc_start: 0.8201 (p0) cc_final: 0.7709 (p0)
REVERT: E   82 MET cc_start: 0.8524 (tpp) cc_final: 0.8192 (mmt)
REVERT: E  100 ASP cc_start: 0.7766 (p0) cc_final: 0.7507 (t0)
REVERT: F   36 TYR cc_start: 0.8723 (m-80) cc_final: 0.8219 (m-10)
REVERT: M   11 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8408 (m)
REVERT: N   46 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8666 (tt)
REVERT: N   90 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7589 (pm20)
  outliers start: 31
  outliers final: 22
  residues processed: 143
  average time/residue: 0.2565
  time to fit residues: 48.9898
Evaluate side-chains
  137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   11 VAL
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   42 LYS
Chi-restraints excluded: chain N residue   46 LEU
Chi-restraints excluded: chain N residue   90 GLN
Chi-restraints excluded: chain N residue   91 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   chunk 82 optimal weight:    0.8980
   chunk 105 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   overall best weight:    2.7784

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 GLN
C  39 GLN
D  90 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.089840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.070291 restraints weight = 21859.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.072629 restraints weight = 13535.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.074228 restraints weight = 9705.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9164  Z= 0.295
  Angle     :  0.617   7.414  12427  Z= 0.323
  Chirality :  0.043   0.208   1335
  Planarity :  0.004   0.031   1594
  Dihedral  :  5.385  57.927   1260
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 17.72 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.48 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.73 (0.23), residues: 530
  loop :  0.28 (0.28), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 102 
 HIS   0.004   0.002   HIS A  35 
 PHE   0.011   0.001   PHE B  71 
 TYR   0.017   0.002   TYR M  91 
 ARG   0.004   0.000   ARG B  24 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 115
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ASP cc_start: 0.6952 (t0) cc_final: 0.5937 (m-30)
REVERT: B  105 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7852 (mm-30)
REVERT: C   53 ASP cc_start: 0.7325 (p0) cc_final: 0.7108 (p0)
REVERT: C  100 ASP cc_start: 0.7875 (p0) cc_final: 0.7594 (p0)
REVERT: E   53 ASP cc_start: 0.8243 (p0) cc_final: 0.7724 (p0)
REVERT: E   82 MET cc_start: 0.8616 (tpp) cc_final: 0.8243 (mmt)
REVERT: M   11 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8453 (m)
  outliers start: 41
  outliers final: 27
  residues processed: 145
  average time/residue: 0.2482
  time to fit residues: 48.4388
Evaluate side-chains
  138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   88 CYS
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    7 SER
Chi-restraints excluded: chain M residue   11 VAL
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 105 optimal weight:    8.9990
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0270
   chunk 80 optimal weight:    7.9990
   chunk 94 optimal weight:    0.0370
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN
F  27 GLN
M   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.092959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.073552 restraints weight = 21382.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.076016 restraints weight = 12993.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.077678 restraints weight = 9181.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9164  Z= 0.151
  Angle     :  0.597  10.609  12427  Z= 0.303
  Chirality :  0.042   0.157   1335
  Planarity :  0.003   0.028   1594
  Dihedral  :  4.892  59.519   1258
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.45 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.26 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.61 (0.23), residues: 530
  loop :  0.45 (0.28), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  47 
 HIS   0.002   0.001   HIS M  35 
 PHE   0.009   0.001   PHE H  52A
 TYR   0.014   0.001   TYR N  36 
 ARG   0.003   0.000   ARG F  18 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.7613 (t60) cc_final: 0.7410 (t60)
REVERT: B   17 ASP cc_start: 0.7107 (t0) cc_final: 0.6189 (m-30)
REVERT: C   53 ASP cc_start: 0.7324 (p0) cc_final: 0.7058 (p0)
REVERT: E   53 ASP cc_start: 0.8239 (p0) cc_final: 0.7756 (p0)
REVERT: E   82 MET cc_start: 0.8527 (tpp) cc_final: 0.8066 (mmt)
  outliers start: 30
  outliers final: 22
  residues processed: 156
  average time/residue: 0.2586
  time to fit residues: 53.5706
Evaluate side-chains
  147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   88 CYS
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
F  27 GLN
M   3 GLN
N  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.091360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.071622 restraints weight = 21910.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.073931 restraints weight = 13543.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.075599 restraints weight = 9763.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9164  Z= 0.222
  Angle     :  0.613   7.157  12427  Z= 0.317
  Chirality :  0.043   0.240   1335
  Planarity :  0.004   0.041   1594
  Dihedral  :  4.974  56.597   1258
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.55 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.32 (0.27), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.66 (0.23), residues: 530
  loop :  0.43 (0.28), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 102 
 HIS   0.004   0.001   HIS A  35 
 PHE   0.009   0.001   PHE B  71 
 TYR   0.023   0.002   TYR B  91 
 ARG   0.009   0.001   ARG M  83 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 ASP cc_start: 0.7194 (t0) cc_final: 0.6088 (m-30)
REVERT: C   53 ASP cc_start: 0.7363 (p0) cc_final: 0.7133 (p0)
REVERT: E   53 ASP cc_start: 0.8272 (p0) cc_final: 0.7763 (p0)
REVERT: E   82 MET cc_start: 0.8580 (tpp) cc_final: 0.8143 (mmt)
REVERT: N  105 GLU cc_start: 0.7152 (tp30) cc_final: 0.6474 (tm-30)
  outliers start: 31
  outliers final: 27
  residues processed: 148
  average time/residue: 0.2616
  time to fit residues: 52.2745
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   88 CYS
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 106 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   3 GLN
** N  90 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 = 0.3526 r_free = 0.3526 target = 0.095989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.075886 restraints weight = 22355.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.077204 restraints weight = 18240.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.077902 restraints weight = 14895.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   9164  Z= 0.402
  Angle     :  0.692  12.643  12427  Z= 0.360
  Chirality :  0.045   0.235   1335
  Planarity :  0.004   0.031   1594
  Dihedral  :  5.483  54.672   1258
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.13 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.66 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.85 (0.23), residues: 535
  loop :  0.17 (0.28), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  35 
 HIS   0.005   0.002   HIS M  96 
 PHE   0.017   0.002   PHE F  62 
 TYR   0.020   0.002   TYR M  91 
 ARG   0.009   0.001   ARG M  83 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 112
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8744 (pttt) cc_final: 0.8294 (pttm)
REVERT: A   57 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7529 (ptmt)
REVERT: B   17 ASP cc_start: 0.7229 (t0) cc_final: 0.6441 (m-30)
REVERT: C   46 GLU cc_start: 0.7520 (pm20) cc_final: 0.7253 (pm20)
REVERT: E   53 ASP cc_start: 0.8268 (p0) cc_final: 0.7645 (p0)
REVERT: E   82 MET cc_start: 0.8537 (tpp) cc_final: 0.8097 (mmt)
REVERT: M    3 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8572 (pp30)
REVERT: N  105 GLU cc_start: 0.7171 (tp30) cc_final: 0.6400 (tm-30)
  outliers start: 42
  outliers final: 33
  residues processed: 148
  average time/residue: 0.2601
  time to fit residues: 50.9731
Evaluate side-chains
  141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   88 CYS
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   34 MET
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   88 CYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue    3 GLN
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   99 GLU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
M   3 GLN
** N  90 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 = 0.3551 r_free = 0.3551 target = 0.096604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.075507 restraints weight = 21331.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.077630 restraints weight = 14154.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.079114 restraints weight = 10739.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9164  Z= 0.307
  Angle     :  0.674  11.990  12427  Z= 0.349
  Chirality :  0.044   0.222   1335
  Planarity :  0.004   0.033   1594
  Dihedral  :  5.324  52.808   1258
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.27 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.67 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.75 (0.23), residues: 525
  loop :  0.03 (0.28), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  35 
 HIS   0.005   0.001   HIS A  35 
 PHE   0.009   0.001   PHE F  62 
 TYR   0.019   0.002   TYR B  91 
 ARG   0.009   0.001   ARG M  83 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8843 (pttt) cc_final: 0.8407 (pttm)
REVERT: A   57 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7369 (ptmt)
REVERT: B   17 ASP cc_start: 0.7418 (t0) cc_final: 0.6318 (m-30)
REVERT: C   45 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7504 (mt)
REVERT: C   46 GLU cc_start: 0.7646 (pm20) cc_final: 0.7348 (pm20)
REVERT: C   53 ASP cc_start: 0.7658 (p0) cc_final: 0.7373 (p0)
REVERT: E   17 SER cc_start: 0.9054 (m) cc_final: 0.8820 (p)
REVERT: E   53 ASP cc_start: 0.8337 (p0) cc_final: 0.8022 (p0)
REVERT: E   82 MET cc_start: 0.8598 (tpp) cc_final: 0.8125 (mmt)
REVERT: M   82 SER cc_start: 0.9317 (m) cc_final: 0.9077 (p)
REVERT: N  105 GLU cc_start: 0.7339 (tp30) cc_final: 0.6480 (tm-30)
  outliers start: 33
  outliers final: 28
  residues processed: 142
  average time/residue: 0.2515
  time to fit residues: 47.5460
Evaluate side-chains
  140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   57 LYS
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   88 CYS
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   99 GLU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0370
   chunk 107 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0070
   chunk 108 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 26 optimal weight:   20.0000
   overall best weight:    0.9278

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
M   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.093147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.073396 restraints weight = 21856.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.075710 restraints weight = 13577.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.077391 restraints weight = 9832.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9164  Z= 0.181
  Angle     :  0.651  11.811  12427  Z= 0.330
  Chirality :  0.043   0.200   1335
  Planarity :  0.003   0.034   1594
  Dihedral  :  4.982  54.096   1258
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.31 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.38 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.56 (0.23), residues: 520
  loop :  0.21 (0.28), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  35 
 HIS   0.003   0.001   HIS A  35 
 PHE   0.010   0.001   PHE H  52A
 TYR   0.026   0.001   TYR B  91 
 ARG   0.009   0.001   ARG M  83 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   45 LYS cc_start: 0.8751 (pttt) cc_final: 0.8397 (pttm)
REVERT: B   17 ASP cc_start: 0.7309 (t0) cc_final: 0.6301 (m-30)
REVERT: C   45 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7233 (mt)
REVERT: C   46 GLU cc_start: 0.7486 (pm20) cc_final: 0.7256 (pm20)
REVERT: C   53 ASP cc_start: 0.7431 (p0) cc_final: 0.7131 (p0)
REVERT: E   17 SER cc_start: 0.9081 (m) cc_final: 0.8836 (p)
REVERT: E   53 ASP cc_start: 0.8272 (p0) cc_final: 0.7956 (p0)
REVERT: E   82 MET cc_start: 0.8596 (tpp) cc_final: 0.8165 (mmt)
REVERT: F   18 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.8153 (ttp80)
REVERT: M   82 SER cc_start: 0.9338 (m) cc_final: 0.9075 (p)
REVERT: N  105 GLU cc_start: 0.7072 (tp30) cc_final: 0.6375 (tm-30)
  outliers start: 27
  outliers final: 22
  residues processed: 148
  average time/residue: 0.2315
  time to fit residues: 45.9550
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   91 TYR
Chi-restraints excluded: chain D residue  102 THR
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   91 TYR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain M residue    2 VAL
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain N residue   33 LEU
Chi-restraints excluded: chain N residue   58 VAL
Chi-restraints excluded: chain N residue   91 TYR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN
F  27 GLN
** F  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   3 GLN
** N  90 GLN ** 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 = 0.3507 r_free = 0.3507 target = 0.089038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.069235 restraints weight = 22587.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.071468 restraints weight = 14282.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.073002 restraints weight = 10417.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9164  Z= 0.367
  Angle     :  0.704  11.667  12427  Z= 0.364
  Chirality :  0.045   0.221   1335
  Planarity :  0.004   0.036   1594
  Dihedral  :  5.378  50.870   1258
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.79 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -0.67 (0.26), residues: 1133
  helix:  None (None), residues: 0
  sheet: -0.74 (0.23), residues: 525
  loop :  0.00 (0.27), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  35 
 HIS   0.005   0.002   HIS M  96 
 PHE   0.013   0.002   PHE A  79 
 TYR   0.021   0.002   TYR B  91 
 ARG   0.008   0.001   ARG M  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2757.86 seconds
wall clock time: 50 minutes 34.66 seconds (3034.66 seconds total)