Starting phenix.real_space_refine (version: dev)
on Tue Nov 29 13:18:28 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/11_2022/6cu7_7618.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/11_2022/6cu7_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_7618/11_2022/6cu7_7618.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/11_2022/6cu7_7618.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/11_2022/6cu7_7618.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu7_7618/11_2022/6cu7_7618.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.68, per 1000 atoms: 0.65
  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: 1.54
  Conformation dependent library (CDL) restraints added in 852.2 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: 0.36
  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: 1.02

  Time building geometry restraints manager: 1.67 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
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.
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:             0.290
  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:          1.850
  Check model and map are aligned:         0.060
  Convert atoms to be neutral:             0.040
  Process input model:                     15.700
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
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 %
  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

*********************** 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  : 0.463 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1405
  time to fit residues: 24.7686
Evaluate side-chains
  63 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.520 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6079
-------------------------------------------------------------------------------
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:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 30 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   chunk 28 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:   40.0000
   overall best weight:    7.9990

-------------------------------------------------------------------------------
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
** 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: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4160  Z= 0.281
  Angle     :  0.673   4.278   5620  Z= 0.397
  Chirality :  0.053   0.140    740
  Planarity :  0.003   0.012    690
  Dihedral  :  8.028  21.793    600
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.31 %
    Favored  : 85.69 %
  Rotamer Outliers :  5.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.35 (0.28), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.22), residues: 580

*********************** 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
  86 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0985
  time to fit residues: 11.3884
Evaluate side-chains
  53 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.504 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0422
  time to fit residues: 1.2142
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:   40.0000
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:   40.0000
   chunk 37 optimal weight:   20.0000
   chunk 15 optimal weight:    0.0670
   chunk 54 optimal weight:   30.0000
   chunk 58 optimal weight:   20.0000
   chunk 48 optimal weight:   30.0000
   chunk 18 optimal weight:   50.0000
   chunk 43 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    5.9326

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

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS
C  65 ASN
D  50 HIS
F  50 HIS
H  50 HIS
J  50 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4160  Z= 0.209
  Angle     :  0.607   4.251   5620  Z= 0.360
  Chirality :  0.052   0.143    740
  Planarity :  0.002   0.009    690
  Dihedral  :  7.506  21.757    600
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.97 %
    Favored  : 86.03 %
  Rotamer Outliers :  5.71 %
  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: -4.30 (0.28), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.21), residues: 580

*********************** 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
  90 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.524 
Fit side-chains
  outliers start: 24
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0949
  time to fit residues: 11.8761
Evaluate side-chains
  64 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.514 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0392
  time to fit residues: 1.5787
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    9.9990
   chunk 6 optimal weight:   40.0000
   chunk 26 optimal weight:   30.0000
   chunk 36 optimal weight:   50.0000
   chunk 54 optimal weight:   30.0000
   chunk 57 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   overall best weight:   11.5996

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

Flipped N/Q/H residues before XYZ refinement:
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.4326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4160  Z= 0.356
  Angle     :  0.734   4.579   5620  Z= 0.434
  Chirality :  0.055   0.141    740
  Planarity :  0.003   0.011    690
  Dihedral  :  8.019  23.962    600
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.03 %
    Favored  : 83.97 %
  Rotamer Outliers :  2.14 %
  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: -4.66 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.19), residues: 580

*********************** 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
  61 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.491 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0933
  time to fit residues: 8.2724
Evaluate side-chains
  49 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.496 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0414
  time to fit residues: 1.2141
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 49 optimal weight:   20.0000
   chunk 40 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   chunk 52 optimal weight:    8.9990
   chunk 14 optimal weight:   30.0000
   chunk 19 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    8.3990

-------------------------------------------------------------------------------
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: 0.7198
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4160  Z= 0.263
  Angle     :  0.649   4.723   5620  Z= 0.385
  Chirality :  0.053   0.140    740
  Planarity :  0.002   0.011    690
  Dihedral  :  7.680  21.955    600
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer Outliers :  2.14 %
  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: -4.69 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.19), residues: 580

*********************** 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
  52 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.515 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0843
  time to fit residues: 6.6790
Evaluate side-chains
  47 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.488 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0901
  time to fit residues: 1.3506
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 58 optimal weight:   20.0000
   chunk 48 optimal weight:   40.0000
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:   30.0000
   chunk 30 optimal weight:   40.0000
   chunk 55 optimal weight:    8.9990
   chunk 6 optimal weight:   40.0000
   chunk 33 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   overall best weight:   10.9992

-------------------------------------------------------------------------------
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: 0.7224
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4160  Z= 0.323
  Angle     :  0.701   4.463   5620  Z= 0.416
  Chirality :  0.055   0.141    740
  Planarity :  0.003   0.010    690
  Dihedral  :  7.865  23.175    600
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.48 %
    Favored  : 85.52 %
  Rotamer Outliers :  0.95 %
  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: -4.83 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.68 (0.19), residues: 580

*********************** 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
  48 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.493 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0728
  time to fit residues: 5.6827
Evaluate side-chains
  42 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.503 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0419
  time to fit residues: 0.8676
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:   50.0000
   chunk 48 optimal weight:   40.0000
   chunk 57 optimal weight:   40.0000
   chunk 36 optimal weight:   20.0000
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 23 optimal weight:   30.0000
   chunk 34 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    5.3186

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

Flipped N/Q/H residues before XYZ refinement:
F  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.4877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4160  Z= 0.189
  Angle     :  0.569   3.860   5620  Z= 0.339
  Chirality :  0.052   0.140    740
  Planarity :  0.002   0.009    690
  Dihedral  :  7.254  20.564    600
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.55 %
    Favored  : 88.45 %
  Rotamer Outliers :  1.67 %
  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: -4.68 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.19), residues: 580

*********************** 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
  51 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.487 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0874
  time to fit residues: 7.0333
Evaluate side-chains
  44 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.501 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0423
  time to fit residues: 0.9393
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 52 optimal weight:   30.0000
   chunk 55 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:   40.0000
   chunk 23 optimal weight:    7.9990
   chunk 42 optimal weight:   40.0000
   chunk 16 optimal weight:    3.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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: 0.7152
moved from start:          0.4993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4160  Z= 0.197
  Angle     :  0.565   3.772   5620  Z= 0.336
  Chirality :  0.052   0.141    740
  Planarity :  0.002   0.008    690
  Dihedral  :  7.109  21.255    600
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer Outliers :  0.95 %
  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

*********************** 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
  53 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.499 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 53
  average time/residue: 0.0840
  time to fit residues: 6.9135
Evaluate side-chains
  43 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.499 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0385
  time to fit residues: 0.7896
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:   40.0000
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0020
   chunk 35 optimal weight:   30.0000
   chunk 56 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 27 optimal weight:   30.0000
   chunk 39 optimal weight:   40.0000
   chunk 59 optimal weight:   20.0000
   chunk 55 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   overall best weight:    7.1998

-------------------------------------------------------------------------------
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: 0.7166
moved from start:          0.5090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4160  Z= 0.229
  Angle     :  0.599   3.928   5620  Z= 0.357
  Chirality :  0.053   0.139    740
  Planarity :  0.002   0.009    690
  Dihedral  :  7.240  21.869    600
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer Outliers :  0.95 %
  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: -4.64 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.53 (0.19), residues: 580

*********************** 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
  44 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.525 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.0803
  time to fit residues: 5.6768
Evaluate side-chains
  42 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.501 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0406
  time to fit residues: 0.8303
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:   40.0000
   chunk 29 optimal weight:   40.0000
   chunk 37 optimal weight:   20.0000
   chunk 50 optimal weight:    0.0040
   chunk 14 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 7 optimal weight:   40.0000
   chunk 13 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    5.2000

-------------------------------------------------------------------------------
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: 0.7129
moved from start:          0.5179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4160  Z= 0.182
  Angle     :  0.553   3.665   5620  Z= 0.329
  Chirality :  0.052   0.144    740
  Planarity :  0.002   0.009    690
  Dihedral  :  6.927  21.587    600
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer Outliers :  0.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.55 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.20), residues: 580

********************** 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
  47 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.488 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0715
  time to fit residues: 5.4837
Evaluate side-chains
  44 residues out of total 420 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.407 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0345
  time to fit residues: 0.5866
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:   30.0000
   chunk 6 optimal weight:   40.0000
   chunk 8 optimal weight:   20.0000
   chunk 41 optimal weight:   40.0000
   chunk 2 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   chunk 40 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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 = 0.4507 r_free = 0.4507 target = 0.145082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.135121 restraints weight = 11133.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.137250 restraints weight = 6416.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.138718 restraints weight = 4191.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4160  Z= 0.227
  Angle     :  0.594   3.683   5620  Z= 0.354
  Chirality :  0.053   0.143    740
  Planarity :  0.002   0.009    690
  Dihedral  :  7.115  22.064    600
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.28 %
    Favored  : 86.72 %
  Rotamer Outliers :  0.48 %
  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: -4.59 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.19), residues: 580

===============================================================================
Job complete
usr+sys time: 829.21 seconds
wall clock time: 16 minutes 31.99 seconds (991.99 seconds total)