Starting phenix.real_space_refine
on Sun Mar 10 18:59:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/03_2024/6cu7_7618.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/03_2024/6cu7_7618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/03_2024/6cu7_7618.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/03_2024/6cu7_7618.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/03_2024/6cu7_7618.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/03_2024/6cu7_7618.pdb"
  }
  resolution = 3.5
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
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: 3
    Type Number    sf(0)   Gaussians
     C    2600      2.51       5
     N     720      2.21       5
     O     820      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 4140
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "E"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "A"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "B"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "C"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "D"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "F"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "G"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "H"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "I"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "J"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 414
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
  Time building chain proxies: 2.54, per 1000 atoms: 0.61
  Number of scatterers: 4140
  At special positions: 0
  Unit cell: (84.53, 103.79, 42.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     820      8.00
     N     720      7.00
     C    2600      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.42
  Conformation dependent library (CDL) restraints added in 950.1 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 47.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 54
      removed outlier: 6.896A  pdb=" N   THR A  44 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   LYS C  45 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLU A  46 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY C  51 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL A  52 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA C  53 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR A  54 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 8.776A  pdb=" N   LYS E  43 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 9.694A  pdb=" N   GLU C  46 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LYS E  45 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   VAL C  48 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   GLY E  47 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   HIS C  50 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   VAL E  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   VAL C  52 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 8.828A  pdb=" N   GLY E  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 10.638A  pdb=" N   THR C  54 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 9.217A  pdb=" N   ALA E  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 10.047A  pdb=" N   LYS C  58 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU E  57 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   LYS C  60 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   THR E  59 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 8.519A  pdb=" N   GLN C  62 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU E  61 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   THR C  64 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   VAL E  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   LYS A  58 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   GLU C  61 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LYS A  60 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   VAL C  63 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   GLN A  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 54
      removed outlier: 6.896A  pdb=" N   THR A  44 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   LYS C  45 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLU A  46 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLY C  51 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL A  52 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA C  53 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR A  54 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 8.776A  pdb=" N   LYS E  43 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 9.694A  pdb=" N   GLU C  46 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LYS E  45 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   VAL C  48 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   GLY E  47 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   HIS C  50 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   VAL E  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   VAL C  52 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 8.828A  pdb=" N   GLY E  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 10.638A  pdb=" N   THR C  54 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 9.217A  pdb=" N   ALA E  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 9.221A  pdb=" N   THR E  44 " --> pdb=" O   LYS G  45 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   GLY G  47 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   GLU E  46 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   VAL G  49 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL E  48 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   GLY G  51 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   HIS E  50 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 10.244A  pdb=" N   ALA G  53 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   VAL E  52 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 10.266A  pdb=" N   VAL G  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 9.100A  pdb=" N   THR E  54 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 9.861A  pdb=" N   GLU G  57 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   ALA E  56 " --> pdb=" O   GLU G  57 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   THR G  59 " --> pdb=" O   ALA E  56 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   LYS E  58 " --> pdb=" O   THR G  59 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   GLU G  61 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LYS E  60 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   VAL G  63 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   GLN E  62 " --> pdb=" O   VAL G  63 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   THR G  44 " --> pdb=" O   LYS I  43 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   LYS I  45 " --> pdb=" O   THR G  44 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   GLU G  46 " --> pdb=" O   LYS I  45 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   GLY I  51 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL G  52 " --> pdb=" O   GLY I  51 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ALA I  53 " --> pdb=" O   VAL G  52 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   THR G  54 " --> pdb=" O   ALA I  53 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   VAL I  55 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ALA G  56 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   GLU I  57 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 73
      removed outlier: 7.015A  pdb=" N   GLY A  73 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   VAL E  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   GLY C  73 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   THR E  72 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   GLY E  73 " --> pdb=" O   THR G  72 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   GLY G  73 " --> pdb=" O   THR I  72 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77
      removed outlier: 6.082A  pdb=" N   ALA E  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81
      removed outlier: 5.940A  pdb=" N   LYS E  80 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 91 through 92
      removed outlier: 6.328A  pdb=" N   ALA A  91 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ALA E  91 " --> pdb=" O   THR G  92 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ALA G  91 " --> pdb=" O   THR I  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 54
      removed outlier: 6.890A  pdb=" N   THR B  44 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   LYS D  45 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   GLU B  46 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   GLY D  51 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   VAL B  52 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ALA D  53 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   THR B  54 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   THR D  44 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LYS F  45 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   GLU D  46 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLY F  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   VAL D  52 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ALA F  53 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   THR D  54 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   THR F  44 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   LYS H  45 " --> pdb=" O   THR F  44 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   GLU F  46 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   GLY H  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL F  52 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ALA H  53 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   THR F  54 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   THR H  44 " --> pdb=" O   LYS J  43 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LYS J  45 " --> pdb=" O   THR H  44 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLU H  46 " --> pdb=" O   LYS J  45 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   GLY J  51 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   VAL H  52 " --> pdb=" O   GLY J  51 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ALA J  53 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   THR H  54 " --> pdb=" O   ALA J  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 64
      removed outlier: 6.318A  pdb=" N   LYS B  58 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   GLU D  61 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LYS B  60 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   VAL D  63 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   GLN B  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   LYS D  58 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   GLU F  61 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS D  60 " --> pdb=" O   GLU F  61 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   VAL F  63 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLN D  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LYS F  58 " --> pdb=" O   THR H  59 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   GLU H  61 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LYS F  60 " --> pdb=" O   GLU H  61 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   VAL H  63 " --> pdb=" O   LYS F  60 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   GLN F  62 " --> pdb=" O   VAL H  63 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LYS H  58 " --> pdb=" O   THR J  59 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   GLU J  61 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LYS H  60 " --> pdb=" O   GLU J  61 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   VAL J  63 " --> pdb=" O   LYS H  60 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLN H  62 " --> pdb=" O   VAL J  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 73
      removed outlier: 7.014A  pdb=" N   GLY B  73 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLY D  73 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   GLY F  73 " --> pdb=" O   THR H  72 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   GLY H  73 " --> pdb=" O   THR J  72 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 76 through 77
    Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 92
      removed outlier: 6.322A  pdb=" N   ALA B  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ALA D  91 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ALA F  91 " --> pdb=" O   THR H  92 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ALA H  91 " --> pdb=" O   THR J  92 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    64 hydrogen bonds defined for protein.
    192 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: 0.99

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 710
        1.28 -     1.35: 640
        1.35 -     1.42: 180
        1.42 -     1.49: 728
        1.49 -     1.55: 1902
  Bond restraints: 4160
  Sorted by residual:
  bond pdb=" CB  ASN B  65 "
       pdb=" CG  ASN B  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.76e+00
  bond pdb=" CB  ASN A  65 "
       pdb=" CG  ASN A  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.76e+00
  bond pdb=" CB  ASN G  65 "
       pdb=" CG  ASN G  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.73e+00
  bond pdb=" CB  ASN D  65 "
       pdb=" CG  ASN D  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.70e+00
  bond pdb=" CB  ASN C  65 "
       pdb=" CG  ASN C  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.69e+00
  ... (remaining 4155 not shown)

  Histogram of bond angle deviations from ideal:
      105.15 -   110.37: 1175
      110.37 -   115.58: 1749
      115.58 -   120.79: 1335
      120.79 -   126.01: 1351
      126.01 -   131.22: 10
  Bond angle restraints: 5620
  Sorted by residual:
  angle pdb=" N   VAL D  40 "
        pdb=" CA  VAL D  40 "
        pdb=" C   VAL D  40 "
      ideal   model   delta    sigma   weight residual
     113.42  110.46    2.96 1.17e+00 7.31e-01 6.39e+00
  angle pdb=" N   VAL C  40 "
        pdb=" CA  VAL C  40 "
        pdb=" C   VAL C  40 "
      ideal   model   delta    sigma   weight residual
     113.42  110.46    2.96 1.17e+00 7.31e-01 6.38e+00
  angle pdb=" N   VAL J  40 "
        pdb=" CA  VAL J  40 "
        pdb=" C   VAL J  40 "
      ideal   model   delta    sigma   weight residual
     113.42  110.48    2.94 1.17e+00 7.31e-01 6.33e+00
  angle pdb=" N   VAL F  40 "
        pdb=" CA  VAL F  40 "
        pdb=" C   VAL F  40 "
      ideal   model   delta    sigma   weight residual
     113.42  110.48    2.94 1.17e+00 7.31e-01 6.30e+00
  angle pdb=" N   VAL G  40 "
        pdb=" CA  VAL G  40 "
        pdb=" C   VAL G  40 "
      ideal   model   delta    sigma   weight residual
     113.42  110.49    2.93 1.17e+00 7.31e-01 6.27e+00
  ... (remaining 5615 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.92: 1720
        5.92 -    11.83: 450
       11.83 -    17.75: 158
       17.75 -    23.67: 82
       23.67 -    29.58: 20
  Dihedral angle restraints: 2430
    sinusoidal: 810
      harmonic: 1620
  Sorted by residual:
  dihedral pdb=" CA  TYR I  39 "
           pdb=" C   TYR I  39 "
           pdb=" N   VAL I  40 "
           pdb=" CA  VAL I  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.76   22.24     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  TYR H  39 "
           pdb=" C   TYR H  39 "
           pdb=" N   VAL H  40 "
           pdb=" CA  VAL H  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.79   22.21     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  TYR A  39 "
           pdb=" C   TYR A  39 "
           pdb=" N   VAL A  40 "
           pdb=" CA  VAL A  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.80   22.20     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 2427 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 370
       0.041 -    0.082: 228
       0.082 -    0.124: 98
       0.124 -    0.165: 34
       0.165 -    0.206: 10
  Chirality restraints: 740
  Sorted by residual:
  chirality pdb=" CB  THR G  92 "
            pdb=" CA  THR G  92 "
            pdb=" OG1 THR G  92 "
            pdb=" CG2 THR G  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  THR E  92 "
            pdb=" CA  THR E  92 "
            pdb=" OG1 THR E  92 "
            pdb=" CG2 THR E  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  THR J  92 "
            pdb=" CA  THR J  92 "
            pdb=" OG1 THR J  92 "
            pdb=" CG2 THR J  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 737 not shown)

  Planarity restraints: 690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL G  40 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.37e+00
        pdb=" C   VAL G  40 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL G  40 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY G  41 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  40 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.35e+00
        pdb=" C   VAL A  40 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A  40 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY A  41 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  40 "    0.010 2.00e-02 2.50e+03   2.08e-02 4.32e+00
        pdb=" C   VAL B  40 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL B  40 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY B  41 "    0.012 2.00e-02 2.50e+03
  ... (remaining 687 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1379
        2.86 -     3.37: 3314
        3.37 -     3.88: 7138
        3.88 -     4.39: 6647
        4.39 -     4.90: 14750
  Nonbonded interactions: 33228
  Sorted by model distance:
  nonbonded pdb=" O   LEU E  38 "
            pdb=" N   LEU G  38 "
     model   vdw
     2.346 2.520
  nonbonded pdb=" N   ASN H  65 "
            pdb=" OD1 ASN H  65 "
     model   vdw
     2.374 2.520
  nonbonded pdb=" N   ASN B  65 "
            pdb=" OD1 ASN B  65 "
     model   vdw
     2.374 2.520
  nonbonded pdb=" N   ASN G  65 "
            pdb=" OD1 ASN G  65 "
     model   vdw
     2.374 2.520
  nonbonded pdb=" N   ASN D  65 "
            pdb=" OD1 ASN D  65 "
     model   vdw
     2.375 2.520
  ... (remaining 33223 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             0.330
  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:          1.730
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     15.770
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
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      :  0.007   0.047   4160  Z= 0.443
  Angle     :  0.993   6.263   5620  Z= 0.571
  Chirality :  0.065   0.206    740
  Planarity :  0.004   0.021    690
  Dihedral  :  9.610  29.582   1410
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.52 %
    Favored  : 84.48 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  4.76 %
    Favored  : 92.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.74 (0.27), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.60 (0.21), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.004   HIS H  50 
 PHE   0.017   0.005   PHE H  94 
 TYR   0.007   0.002   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 THR cc_start: 0.8549 (m) cc_final: 0.8217 (m)
REVERT: A   80 LYS cc_start: 0.6865 (tttt) cc_final: 0.6520 (pttm)
REVERT: B   38 LEU cc_start: 0.7694 (pp) cc_final: 0.7390 (mt)
REVERT: B   52 VAL cc_start: 0.8818 (t) cc_final: 0.8567 (m)
REVERT: B   75 THR cc_start: 0.8216 (m) cc_final: 0.7809 (p)
REVERT: B   80 LYS cc_start: 0.7081 (tttt) cc_final: 0.6580 (pttp)
REVERT: C   75 THR cc_start: 0.8433 (m) cc_final: 0.8050 (p)
REVERT: D   75 THR cc_start: 0.8360 (m) cc_final: 0.8067 (p)
REVERT: D   97 LYS cc_start: 0.8561 (mttt) cc_final: 0.8294 (mttp)
REVERT: F   75 THR cc_start: 0.8307 (m) cc_final: 0.7995 (p)
REVERT: G   75 THR cc_start: 0.8423 (m) cc_final: 0.8100 (p)
REVERT: H   52 VAL cc_start: 0.9092 (t) cc_final: 0.8875 (m)
REVERT: H   75 THR cc_start: 0.8233 (m) cc_final: 0.7924 (p)
REVERT: I   52 VAL cc_start: 0.8900 (t) cc_final: 0.8533 (m)
REVERT: I   95 VAL cc_start: 0.7914 (t) cc_final: 0.7603 (m)
REVERT: J   38 LEU cc_start: 0.7576 (pp) cc_final: 0.7219 (mt)
REVERT: J   52 VAL cc_start: 0.8887 (t) cc_final: 0.8680 (m)
  outliers start: 10
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1454
  time to fit residues: 25.6282
Evaluate side-chains
  76 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 45 optimal weight:   30.0000
   chunk 25 optimal weight:   30.0000
   chunk 15 optimal weight:   10.0000
   chunk 30 optimal weight:   40.0000
   chunk 24 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   chunk 28 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 54 optimal weight:   40.0000
   overall best weight:   12.5996

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

Flipped N/Q/H residues before XYZ refinement:
** E  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   4160  Z= 0.402
  Angle     :  0.787   4.514   5620  Z= 0.466
  Chirality :  0.056   0.146    740
  Planarity :  0.003   0.012    690
  Dihedral  :  8.522  22.508    600
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.90 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  :  9.52 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.55 (0.27), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.21), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J  50 
 PHE   0.008   0.002   PHE J  94 
 TYR   0.008   0.002   TYR C  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.487 
Fit side-chains
REVERT: E   46 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6879 (mm-30)
REVERT: E   59 THR cc_start: 0.8608 (m) cc_final: 0.7916 (p)
REVERT: E   75 THR cc_start: 0.8104 (m) cc_final: 0.7683 (p)
REVERT: A   75 THR cc_start: 0.8273 (m) cc_final: 0.7999 (p)
REVERT: C   59 THR cc_start: 0.8622 (m) cc_final: 0.8185 (p)
REVERT: D   59 THR cc_start: 0.8560 (m) cc_final: 0.7870 (p)
REVERT: F   59 THR cc_start: 0.8434 (m) cc_final: 0.7914 (p)
REVERT: F   61 GLU cc_start: 0.8161 (mp0) cc_final: 0.7955 (mp0)
REVERT: F   75 THR cc_start: 0.8150 (m) cc_final: 0.7793 (p)
REVERT: F   77 VAL cc_start: 0.8286 (t) cc_final: 0.8068 (t)
REVERT: H   59 THR cc_start: 0.8432 (m) cc_final: 0.7559 (p)
REVERT: J   61 GLU cc_start: 0.8098 (mp0) cc_final: 0.7396 (mp0)
  outliers start: 27
  outliers final: 13
  residues processed: 90
  average time/residue: 0.1279
  time to fit residues: 15.2438
Evaluate side-chains
  61 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain J residue   65 ASN
Chi-restraints excluded: chain J residue   66 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:   30.0000
   chunk 16 optimal weight:   10.0000
   chunk 45 optimal weight:   30.0000
   chunk 37 optimal weight:    0.9990
   chunk 15 optimal weight:   30.0000
   chunk 54 optimal weight:   30.0000
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:   30.0000
   chunk 18 optimal weight:   40.0000
   chunk 43 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   overall best weight:    8.7994

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

Flipped N/Q/H residues before XYZ refinement:
E  50 HIS
A  50 HIS
** B  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  50 HIS
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  50 HIS
** H  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  50 HIS
** J  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4160  Z= 0.290
  Angle     :  0.699   5.369   5620  Z= 0.412
  Chirality :  0.054   0.138    740
  Planarity :  0.002   0.010    690
  Dihedral  :  8.159  22.149    600
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 20.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.76 %
    Favored  : 87.24 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 10.00 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.60 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  50 
 PHE   0.005   0.001   PHE J  94 
 TYR   0.007   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 55
  time to evaluate  : 0.395 
Fit side-chains
REVERT: E   38 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7494 (mp)
REVERT: B   61 GLU cc_start: 0.4446 (pm20) cc_final: 0.4190 (pm20)
REVERT: C   59 THR cc_start: 0.8398 (m) cc_final: 0.8171 (p)
REVERT: D   38 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7480 (mp)
REVERT: D   75 THR cc_start: 0.8323 (m) cc_final: 0.8019 (p)
REVERT: F   59 THR cc_start: 0.8359 (m) cc_final: 0.7996 (p)
REVERT: F   75 THR cc_start: 0.8319 (m) cc_final: 0.8079 (p)
REVERT: F   77 VAL cc_start: 0.8313 (t) cc_final: 0.8104 (t)
REVERT: J   61 GLU cc_start: 0.7834 (mp0) cc_final: 0.7542 (mp0)
  outliers start: 28
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0866
  time to fit residues: 10.0165
Evaluate side-chains
  64 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain J residue   65 ASN
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:   40.0000
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 26 optimal weight:   30.0000
   chunk 36 optimal weight:   40.0000
   chunk 54 optimal weight:   30.0000
   chunk 57 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 15 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    8.1992

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

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS
D  50 HIS
F  50 HIS
H  50 HIS
J  50 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4160  Z= 0.273
  Angle     :  0.655   4.392   5620  Z= 0.386
  Chirality :  0.053   0.142    740
  Planarity :  0.002   0.009    690
  Dihedral  :  7.839  21.827    600
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 20.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.79 %
    Favored  : 86.21 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 11.90 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.73 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.60 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I  50 
 PHE   0.005   0.001   PHE I  94 
 TYR   0.007   0.001   TYR C  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 54
  time to evaluate  : 0.498 
Fit side-chains
REVERT: E   38 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7517 (mt)
REVERT: D   38 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7473 (mp)
REVERT: D   61 GLU cc_start: 0.8066 (mp0) cc_final: 0.7613 (mp0)
REVERT: D   75 THR cc_start: 0.8239 (m) cc_final: 0.7923 (p)
REVERT: J   61 GLU cc_start: 0.7894 (mp0) cc_final: 0.7640 (mp0)
  outliers start: 27
  outliers final: 20
  residues processed: 76
  average time/residue: 0.0763
  time to fit residues: 9.0766
Evaluate side-chains
  70 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   65 ASN
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 43 optimal weight:   20.0000
   chunk 23 optimal weight:   30.0000
   chunk 49 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 29 optimal weight:   30.0000
   chunk 52 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 11 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    6.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4160  Z= 0.216
  Angle     :  0.602   4.435   5620  Z= 0.355
  Chirality :  0.052   0.137    740
  Planarity :  0.002   0.012    690
  Dihedral  :  7.461  20.770    600
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.43 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.63 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS I  50 
 PHE   0.003   0.001   PHE E  94 
 TYR   0.006   0.001   TYR C  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: E   38 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7539 (mt)
REVERT: D   38 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7488 (mp)
REVERT: D   61 GLU cc_start: 0.8136 (mp0) cc_final: 0.7716 (mm-30)
REVERT: D   75 THR cc_start: 0.8460 (m) cc_final: 0.8114 (p)
REVERT: J   61 GLU cc_start: 0.7984 (mp0) cc_final: 0.7713 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 78
  average time/residue: 0.0830
  time to fit residues: 9.8247
Evaluate side-chains
  69 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   65 ASN
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:   30.0000
   chunk 58 optimal weight:    0.3980
   chunk 48 optimal weight:   30.0000
   chunk 26 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:   40.0000
   chunk 55 optimal weight:    0.5980
   chunk 6 optimal weight:   20.0000
   chunk 33 optimal weight:   40.0000
   chunk 42 optimal weight:    9.9990
   overall best weight:    5.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4160  Z= 0.198
  Angle     :  0.574   4.026   5620  Z= 0.338
  Chirality :  0.052   0.143    740
  Planarity :  0.002   0.010    690
  Dihedral  :  7.215  20.384    600
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.28 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 17.62 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.53 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I  50 
 PHE   0.003   0.001   PHE E  94 
 TYR   0.006   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
REVERT: E   38 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7546 (mp)
REVERT: A   71 VAL cc_start: 0.7604 (t) cc_final: 0.7182 (p)
REVERT: D   38 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7458 (pp)
REVERT: D   61 GLU cc_start: 0.8106 (mp0) cc_final: 0.7742 (mm-30)
REVERT: D   75 THR cc_start: 0.8429 (m) cc_final: 0.8142 (p)
  outliers start: 26
  outliers final: 21
  residues processed: 79
  average time/residue: 0.0887
  time to fit residues: 10.3362
Evaluate side-chains
  75 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   65 ASN
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:   40.0000
   chunk 48 optimal weight:   40.0000
   chunk 57 optimal weight:   30.0000
   chunk 36 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 23 optimal weight:   40.0000
   chunk 34 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   overall best weight:    8.3994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.4682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4160  Z= 0.267
  Angle     :  0.637   4.792   5620  Z= 0.376
  Chirality :  0.053   0.141    740
  Planarity :  0.002   0.008    690
  Dihedral  :  7.529  21.182    600
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.28 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 18.81 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.56 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS I  50 
 PHE   0.006   0.001   PHE I  94 
 TYR   0.006   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: E   38 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7516 (mp)
REVERT: A   71 VAL cc_start: 0.7663 (t) cc_final: 0.7258 (p)
REVERT: C   77 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8039 (t)
REVERT: D   38 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7444 (mp)
REVERT: D   75 THR cc_start: 0.8428 (m) cc_final: 0.8205 (p)
  outliers start: 26
  outliers final: 22
  residues processed: 75
  average time/residue: 0.0827
  time to fit residues: 9.3961
Evaluate side-chains
  73 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 48
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   65 ASN
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0040
   chunk 55 optimal weight:   40.0000
   chunk 50 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 32 optimal weight:   40.0000
   chunk 23 optimal weight:    5.9990
   chunk 42 optimal weight:   40.0000
   chunk 16 optimal weight:   20.0000
   overall best weight:    4.6000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4160  Z= 0.177
  Angle     :  0.555   3.960   5620  Z= 0.327
  Chirality :  0.052   0.140    740
  Planarity :  0.002   0.009    690
  Dihedral  :  7.105  20.520    600
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 19.52 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.42 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  50 
 PHE   0.005   0.001   PHE E  94 
 TYR   0.006   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 56
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: E   38 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7593 (mp)
REVERT: A   71 VAL cc_start: 0.7517 (t) cc_final: 0.7086 (p)
REVERT: D   38 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7492 (pp)
REVERT: D   75 THR cc_start: 0.8408 (m) cc_final: 0.8066 (p)
  outliers start: 25
  outliers final: 20
  residues processed: 78
  average time/residue: 0.0862
  time to fit residues: 10.1413
Evaluate side-chains
  70 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   65 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:   30.0000
   chunk 50 optimal weight:    7.9990
   chunk 53 optimal weight:   30.0000
   chunk 35 optimal weight:    8.9990
   chunk 56 optimal weight:   30.0000
   chunk 34 optimal weight:   10.0000
   chunk 27 optimal weight:   20.0000
   chunk 39 optimal weight:   40.0000
   chunk 59 optimal weight:   20.0000
   chunk 55 optimal weight:    2.9990
   chunk 47 optimal weight:   20.0000
   overall best weight:    9.9994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.4859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4160  Z= 0.304
  Angle     :  0.668   5.342   5620  Z= 0.394
  Chirality :  0.054   0.141    740
  Planarity :  0.002   0.011    690
  Dihedral  :  7.590  21.616    600
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.83 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 18.33 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.60 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS I  50 
 PHE   0.008   0.002   PHE I  94 
 TYR   0.006   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 45
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: E   38 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7515 (mp)
REVERT: A   71 VAL cc_start: 0.7662 (t) cc_final: 0.7263 (p)
REVERT: C   77 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8062 (t)
REVERT: D   38 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7376 (mp)
  outliers start: 28
  outliers final: 22
  residues processed: 71
  average time/residue: 0.0824
  time to fit residues: 9.1139
Evaluate side-chains
  68 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   65 ASN
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:   40.0000
   chunk 29 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.4918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4160  Z= 0.219
  Angle     :  0.603   4.763   5620  Z= 0.355
  Chirality :  0.052   0.140    740
  Planarity :  0.002   0.015    690
  Dihedral  :  7.330  20.891    600
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.28 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 19.52 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.53 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I  50 
 PHE   0.004   0.001   PHE I  94 
 TYR   0.006   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 44
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: E   38 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7491 (mp)
REVERT: A   71 VAL cc_start: 0.7567 (t) cc_final: 0.7143 (p)
REVERT: C   77 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8007 (t)
REVERT: D   38 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7558 (pp)
  outliers start: 24
  outliers final: 19
  residues processed: 65
  average time/residue: 0.0765
  time to fit residues: 7.8286
Evaluate side-chains
  63 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 41
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   38 LEU
Chi-restraints excluded: chain G residue   65 ASN
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   65 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:   40.0000
   chunk 6 optimal weight:   30.0000
   chunk 8 optimal weight:   20.0000
   chunk 41 optimal weight:   40.0000
   chunk 2 optimal weight:   20.0000
   chunk 34 optimal weight:   30.0000
   chunk 54 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   overall best weight:   10.5996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.143783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.133035 restraints weight = 10875.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.135390 restraints weight = 5913.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.136869 restraints weight = 3736.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4160  Z= 0.320
  Angle     :  0.688   5.510   5620  Z= 0.405
  Chirality :  0.054   0.141    740
  Planarity :  0.002   0.009    690
  Dihedral  :  7.712  22.188    600
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.83 %
    Favored  : 85.17 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 19.05 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.71 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  50 
 PHE   0.009   0.002   PHE I  94 
 TYR   0.006   0.001   TYR I  39 

===============================================================================
Job complete
usr+sys time: 927.92 seconds
wall clock time: 19 minutes 59.95 seconds (1199.95 seconds total)