Starting phenix.real_space_refine (version: dev)
on Sun Dec 11 15:15:11 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/12_2022/6osj_20183.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/12_2022/6osj_20183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/12_2022/6osj_20183.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/12_2022/6osj_20183.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/12_2022/6osj_20183.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/12_2022/6osj_20183.pdb"
  }
  resolution = 2.8
  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=   0.000 sd=   0.009
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: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib"
  Total number of atoms: 4210
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "B"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "C"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "D"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "E"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "F"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "G"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "H"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "I"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
    Chain: "J"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
  Time building chain proxies: 2.64, per 1000 atoms: 0.63
  Number of scatterers: 4210
  At special positions: 0
  Unit cell: (92.22, 75.26, 40.28, 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     830      8.00
     N     730      7.00
     C    2650      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: 1.41
  Conformation dependent library (CDL) restraints added in 707.1 milliseconds
  

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49
      removed outlier: 5.687A  pdb=" N   GLU A  46 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   VAL C  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL A  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS C  45 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   VAL E  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   GLY C  47 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LYS E  45 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   VAL G  48 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   GLY E  47 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LYS G  45 " --> pdb=" O   GLU I  46 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   VAL I  48 " --> pdb=" O   LYS G  45 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   GLY G  47 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 58
      removed outlier: 6.572A  pdb=" N   ALA A  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.354A  pdb=" N   ALA C  56 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   LYS C  58 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   GLU A  57 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ALA C  53 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   ALA E  56 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL C  55 " --> pdb=" O   ALA E  56 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   LYS E  58 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   GLU C  57 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ALA E  53 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   ALA G  56 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   VAL E  55 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   LYS G  58 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   GLU E  57 " --> pdb=" O   LYS G  58 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ALA G  53 " --> pdb=" O   THR I  54 " (cutoff:3.500A)
      removed outlier: 8.347A  pdb=" N   ALA I  56 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL G  55 " --> pdb=" O   ALA I  56 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   LYS I  58 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   GLU G  57 " --> pdb=" O   LYS I  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 82
      removed outlier: 6.828A  pdb=" N   VAL A  70 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   VAL C  71 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   THR A  72 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   GLY C  73 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL C  77 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ALA A  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLN C  79 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LYS A  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   THR C  81 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   VAL A  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   VAL C  70 " --> pdb=" O   ALA E  69 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL E  71 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   THR C  72 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   GLY E  73 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL E  77 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ALA C  78 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN E  79 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   LYS C  80 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   THR E  81 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL C  82 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   VAL E  70 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL G  71 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   THR E  72 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   GLY G  73 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL G  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ALA E  78 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   GLN G  79 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LYS E  80 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   THR G  81 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL E  82 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL G  70 " --> pdb=" O   ALA I  69 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   VAL I  71 " --> pdb=" O   VAL G  70 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   THR G  72 " --> pdb=" O   VAL I  71 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   GLY I  73 " --> pdb=" O   THR G  72 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL I  77 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ALA G  78 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLN I  79 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LYS G  80 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   THR I  81 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL G  82 " --> pdb=" O   THR I  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 90
      removed outlier: 6.490A  pdb=" N   ALA A  89 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ALA C  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ALA E  89 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ALA G  89 " --> pdb=" O   ALA I  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49
      removed outlier: 5.625A  pdb=" N   GLU B  46 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 9.205A  pdb=" N   VAL D  49 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL B  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LYS D  45 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   VAL F  48 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   GLY D  47 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LYS F  45 " --> pdb=" O   GLU H  46 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   VAL H  48 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   GLY F  47 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LYS H  45 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   VAL J  48 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   GLY H  47 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 58
      removed outlier: 6.627A  pdb=" N   ALA B  53 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   ALA D  56 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   VAL B  55 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   LYS D  58 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   GLU B  57 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ALA D  53 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 8.295A  pdb=" N   ALA F  56 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   VAL D  55 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   LYS F  58 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   GLU D  57 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ALA F  53 " --> pdb=" O   THR H  54 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   ALA H  56 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   VAL F  55 " --> pdb=" O   ALA H  56 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   LYS H  58 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   GLU F  57 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 69 through 82
      removed outlier: 6.935A  pdb=" N   VAL B  70 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL D  71 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   THR B  72 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   GLY D  73 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL D  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ALA B  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLN D  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   LYS B  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   THR D  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   VAL B  82 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   VAL D  70 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL F  71 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   THR D  72 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLY F  73 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL F  77 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ALA D  78 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   GLN F  79 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   LYS D  80 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR F  81 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   VAL D  82 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL F  70 " --> pdb=" O   ALA H  69 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   VAL H  71 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   THR F  72 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLY H  73 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL H  77 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ALA F  78 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLN H  79 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LYS F  80 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR H  81 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL F  82 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL H  70 " --> pdb=" O   ALA J  69 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   VAL J  71 " --> pdb=" O   VAL H  70 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   THR H  72 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLY J  73 " --> pdb=" O   THR H  72 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   VAL J  77 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ALA H  78 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   GLN J  79 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LYS H  80 " --> pdb=" O   GLN J  79 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   THR J  81 " --> pdb=" O   LYS H  80 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL H  82 " --> pdb=" O   THR J  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 90
      removed outlier: 6.464A  pdb=" N   ALA B  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ALA D  89 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ALA F  89 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA H  89 " --> pdb=" O   ALA J  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    29 hydrogen bonds defined for protein.
    87 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: 0.95

  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 -     1.29: 720
        1.29 -     1.35: 660
        1.35 -     1.42: 170
        1.42 -     1.48: 781
        1.48 -     1.55: 1899
  Bond restraints: 4230
  Sorted by residual:
  bond pdb=" CA  ALA F  89 "
       pdb=" CB  ALA F  89 "
    ideal  model  delta    sigma   weight residual
    1.531  1.466  0.065 3.12e-02 1.03e+03 4.33e+00
  bond pdb=" CA  ALA C  89 "
       pdb=" CB  ALA C  89 "
    ideal  model  delta    sigma   weight residual
    1.531  1.466  0.065 3.12e-02 1.03e+03 4.29e+00
  bond pdb=" CA  ALA D  89 "
       pdb=" CB  ALA D  89 "
    ideal  model  delta    sigma   weight residual
    1.531  1.466  0.065 3.12e-02 1.03e+03 4.29e+00
  bond pdb=" CA  ALA I  89 "
       pdb=" CB  ALA I  89 "
    ideal  model  delta    sigma   weight residual
    1.531  1.466  0.064 3.12e-02 1.03e+03 4.27e+00
  bond pdb=" CA  ALA B  89 "
       pdb=" CB  ALA B  89 "
    ideal  model  delta    sigma   weight residual
    1.531  1.466  0.064 3.12e-02 1.03e+03 4.23e+00
  ... (remaining 4225 not shown)

  Histogram of bond angle deviations from ideal:
      105.69 -   110.72: 1629
      110.72 -   115.76: 1379
      115.76 -   120.80: 1279
      120.80 -   125.83: 1393
      125.83 -   130.87: 40
  Bond angle restraints: 5720
  Sorted by residual:
  angle pdb=" C   VAL A  49 "
        pdb=" N   HIS A  50 "
        pdb=" CA  HIS A  50 "
      ideal   model   delta    sigma   weight residual
     121.41  112.57    8.84 1.83e+00 2.99e-01 2.33e+01
  angle pdb=" C   VAL H  49 "
        pdb=" N   HIS H  50 "
        pdb=" CA  HIS H  50 "
      ideal   model   delta    sigma   weight residual
     121.41  112.58    8.83 1.83e+00 2.99e-01 2.33e+01
  angle pdb=" C   VAL J  49 "
        pdb=" N   HIS J  50 "
        pdb=" CA  HIS J  50 "
      ideal   model   delta    sigma   weight residual
     121.41  112.58    8.83 1.83e+00 2.99e-01 2.33e+01
  angle pdb=" C   VAL D  49 "
        pdb=" N   HIS D  50 "
        pdb=" CA  HIS D  50 "
      ideal   model   delta    sigma   weight residual
     121.41  112.59    8.82 1.83e+00 2.99e-01 2.32e+01
  angle pdb=" C   VAL F  49 "
        pdb=" N   HIS F  50 "
        pdb=" CA  HIS F  50 "
      ideal   model   delta    sigma   weight residual
     121.41  112.59    8.82 1.83e+00 2.99e-01 2.32e+01
  ... (remaining 5715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.29: 2170
       13.29 -    26.57: 220
       26.57 -    39.85: 40
       39.85 -    53.14: 20
       53.14 -    66.42: 20
  Dihedral angle restraints: 2470
    sinusoidal: 820
      harmonic: 1650
  Sorted by residual:
  dihedral pdb=" CA  GLY F  51 "
           pdb=" C   GLY F  51 "
           pdb=" N   VAL F  52 "
           pdb=" CA  VAL F  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.64  -16.36     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  GLY H  51 "
           pdb=" C   GLY H  51 "
           pdb=" N   VAL H  52 "
           pdb=" CA  VAL H  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.70  -16.30     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  GLY C  51 "
           pdb=" C   GLY C  51 "
           pdb=" N   VAL C  52 "
           pdb=" CA  VAL C  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.71  -16.29     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 2467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 533
       0.064 -    0.128: 187
       0.128 -    0.192: 20
       0.192 -    0.256: 10
       0.256 -    0.320: 10
  Chirality restraints: 760
  Sorted by residual:
  chirality pdb=" CA  HIS A  50 "
            pdb=" N   HIS A  50 "
            pdb=" C   HIS A  50 "
            pdb=" CB  HIS A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  HIS I  50 "
            pdb=" N   HIS I  50 "
            pdb=" C   HIS I  50 "
            pdb=" CB  HIS I  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  HIS G  50 "
            pdb=" N   HIS G  50 "
            pdb=" C   HIS G  50 "
            pdb=" CB  HIS G  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 757 not shown)

  Planarity restraints: 700
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  39 "    0.020 2.00e-02 2.50e+03   1.09e-02 2.37e+00
        pdb=" CG  TYR A  39 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  39 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  39 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  39 "    0.020 2.00e-02 2.50e+03   1.08e-02 2.35e+00
        pdb=" CG  TYR F  39 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  39 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR F  39 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  39 "    0.019 2.00e-02 2.50e+03   1.07e-02 2.29e+00
        pdb=" CG  TYR E  39 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  39 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR E  39 "    0.006 2.00e-02 2.50e+03
  ... (remaining 697 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 712
        2.76 -     3.30: 3943
        3.30 -     3.83: 6750
        3.83 -     4.37: 7647
        4.37 -     4.90: 15935
  Nonbonded interactions: 34987
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU F  57 "
            pdb=" ND1 HIS G  50 "
     model   vdw
     2.227 2.520
  nonbonded pdb=" OE2 GLU D  57 "
            pdb=" ND1 HIS E  50 "
     model   vdw
     2.258 2.520
  nonbonded pdb=" OE2 GLU H  57 "
            pdb=" ND1 HIS I  50 "
     model   vdw
     2.260 2.520
  nonbonded pdb=" OE2 GLU B  57 "
            pdb=" ND1 HIS C  50 "
     model   vdw
     2.264 2.520
  nonbonded pdb=" O   SER A  42 "
            pdb=" OG1 THR A  44 "
     model   vdw
     2.329 2.440
  ... (remaining 34982 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    2650      2.51       5
     N     730      2.21       5
     O     830      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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:          2.070
  Check model and map are aligned:         0.060
  Convert atoms to be neutral:             0.040
  Process input model:                     14.790
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    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:12.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
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      :  0.011   0.065   4230  Z= 0.772
  Angle     :  1.127   8.838   5720  Z= 0.666
  Chirality :  0.072   0.320    760
  Planarity :  0.004   0.012    700
  Dihedral  : 13.688  66.424   1430
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  1.69 %
    Allowed  : 18.64 %
    Favored  : 79.66 %
  Rotamer Outliers :  0.00 %
  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: -4.71 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.22), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.492 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 1.0413
  time to fit residues: 54.4282
Evaluate side-chains
  36 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.489 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6578
-------------------------------------------------------------------------------
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:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    4.3990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4230  Z= 0.346
  Angle     :  0.851   7.843   5720  Z= 0.494
  Chirality :  0.063   0.292    760
  Planarity :  0.003   0.015    700
  Dihedral  :  6.352  19.139    610
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.27 %
    Favored  : 83.73 %
  Rotamer Outliers :  5.35 %
  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: -4.44 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.38 (0.22), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 48
  time to evaluate  : 0.473 
Fit side-chains
  outliers start: 23
  outliers final: 9
  residues processed: 66
  average time/residue: 0.6701
  time to fit residues: 46.9327
Evaluate side-chains
  48 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.351 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 4
  residues processed: 5
  average time/residue: 0.0323
  time to fit residues: 0.8270
-------------------------------------------------------------------------------
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:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0020
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0570
   overall best weight:    2.8112

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4230  Z= 0.240
  Angle     :  0.719   6.487   5720  Z= 0.417
  Chirality :  0.058   0.252    760
  Planarity :  0.002   0.011    700
  Dihedral  :  5.751  17.469    610
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.59 %
    Favored  : 84.41 %
  Rotamer Outliers :  6.28 %
  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: -4.22 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.22), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 43
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
  outliers start: 27
  outliers final: 18
  residues processed: 62
  average time/residue: 0.6914
  time to fit residues: 45.6041
Evaluate side-chains
  59 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.479 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 12
  residues processed: 6
  average time/residue: 0.0419
  time to fit residues: 1.1114
-------------------------------------------------------------------------------
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:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 6 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 54 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    5.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.031   4230  Z= 0.411
  Angle     :  0.881   8.297   5720  Z= 0.513
  Chirality :  0.064   0.298    760
  Planarity :  0.003   0.013    700
  Dihedral  :  6.263  18.324    610
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.49 %
    Favored  : 80.51 %
  Rotamer Outliers :  9.30 %
  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: -4.16 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.22), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 43
  time to evaluate  : 0.479 
Fit side-chains
  outliers start: 40
  outliers final: 28
  residues processed: 73
  average time/residue: 0.6981
  time to fit residues: 54.0248
Evaluate side-chains
  70 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 42
  time to evaluate  : 0.471 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 19
  residues processed: 9
  average time/residue: 0.0404
  time to fit residues: 1.2697
-------------------------------------------------------------------------------
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:   20.0000
   chunk 43 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    3.7990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4230  Z= 0.296
  Angle     :  0.771   7.291   5720  Z= 0.449
  Chirality :  0.060   0.280    760
  Planarity :  0.003   0.012    700
  Dihedral  :  5.934  17.771    610
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.46 %
    Favored  : 82.54 %
  Rotamer Outliers :  7.44 %
  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: -4.04 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.23), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 39
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 25
  residues processed: 60
  average time/residue: 0.6356
  time to fit residues: 40.7574
Evaluate side-chains
  63 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 38
  time to evaluate  : 0.472 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 15
  residues processed: 10
  average time/residue: 0.0391
  time to fit residues: 1.3292
-------------------------------------------------------------------------------
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:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 48 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:   20.0000
   chunk 55 optimal weight:    0.0980
   chunk 6 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    6.2190

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.043   4230  Z= 0.450
  Angle     :  0.911   8.616   5720  Z= 0.532
  Chirality :  0.065   0.310    760
  Planarity :  0.003   0.014    700
  Dihedral  :  6.365  18.817    610
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.85 %
    Favored  : 79.15 %
  Rotamer Outliers :  8.37 %
  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: -4.07 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.23), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 41
  time to evaluate  : 0.481 
Fit side-chains
  outliers start: 36
  outliers final: 30
  residues processed: 67
  average time/residue: 0.5894
  time to fit residues: 42.4374
Evaluate side-chains
  70 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 40
  time to evaluate  : 0.465 
Switching outliers to nearest non-outliers
  outliers start: 30
  outliers final: 21
  residues processed: 9
  average time/residue: 0.0414
  time to fit residues: 1.3056
-------------------------------------------------------------------------------
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:    0.1980
   chunk 48 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    2.7984

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4230  Z= 0.241
  Angle     :  0.708   6.571   5720  Z= 0.412
  Chirality :  0.059   0.261    760
  Planarity :  0.002   0.012    700
  Dihedral  :  5.738  17.364    610
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.39 %
    Favored  : 86.61 %
  Rotamer Outliers :  7.21 %
  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: -3.92 (0.31), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.23), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 39
  time to evaluate  : 0.618 
Fit side-chains
  outliers start: 31
  outliers final: 23
  residues processed: 62
  average time/residue: 0.5327
  time to fit residues: 35.6652
Evaluate side-chains
  60 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 37
  time to evaluate  : 0.440 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 16
  residues processed: 7
  average time/residue: 0.0391
  time to fit residues: 1.0846
-------------------------------------------------------------------------------
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:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0570
   chunk 23 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   overall best weight:    3.9504

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4230  Z= 0.310
  Angle     :  0.783   7.456   5720  Z= 0.455
  Chirality :  0.060   0.280    760
  Planarity :  0.003   0.013    700
  Dihedral  :  5.866  17.370    610
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.81 %
    Favored  : 81.19 %
  Rotamer Outliers :  6.74 %
  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: -3.90 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.23), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 36
  time to evaluate  : 0.423 
Fit side-chains
  outliers start: 29
  outliers final: 27
  residues processed: 56
  average time/residue: 0.6327
  time to fit residues: 37.8789
Evaluate side-chains
  63 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 36
  time to evaluate  : 0.423 
Switching outliers to nearest non-outliers
  outliers start: 27
  outliers final: 18
  residues processed: 9
  average time/residue: 0.0382
  time to fit residues: 1.1976
-------------------------------------------------------------------------------
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:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0670
   chunk 35 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    4.6126

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4230  Z= 0.347
  Angle     :  0.819   8.001   5720  Z= 0.478
  Chirality :  0.062   0.293    760
  Planarity :  0.003   0.013    700
  Dihedral  :  6.002  17.482    610
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.64 %
    Favored  : 81.36 %
  Rotamer Outliers :  6.05 %
  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: -3.92 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.23), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 39
  time to evaluate  : 0.422 
Fit side-chains
  outliers start: 26
  outliers final: 25
  residues processed: 59
  average time/residue: 0.6130
  time to fit residues: 38.7852
Evaluate side-chains
  64 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 39
  time to evaluate  : 0.464 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 19
  residues processed: 6
  average time/residue: 0.0390
  time to fit residues: 1.0375
-------------------------------------------------------------------------------
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:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   overall best weight:    6.1990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4230  Z= 0.444
  Angle     :  0.917   8.712   5720  Z= 0.535
  Chirality :  0.066   0.316    760
  Planarity :  0.003   0.014    700
  Dihedral  :  6.314  18.226    610
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.19 %
    Favored  : 78.81 %
  Rotamer Outliers :  6.05 %
  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: -3.97 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.23), residues: 590

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 37
  time to evaluate  : 0.476 
Fit side-chains
  outliers start: 26
  outliers final: 25
  residues processed: 58
  average time/residue: 0.5908
  time to fit residues: 36.9360
Evaluate side-chains
  62 residues out of total 430 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 0.492 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 20
  residues processed: 5
  average time/residue: 0.0385
  time to fit residues: 0.9805
-------------------------------------------------------------------------------
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:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    2.5386

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.204895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.182150 restraints weight = 4726.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.4490 rms_B_bonded: 2.01
r_work: 0.4427 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.4336 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4230  Z= 0.221
  Angle     :  0.698   6.244   5720  Z= 0.403
  Chirality :  0.058   0.254    760
  Planarity :  0.002   0.011    700
  Dihedral  :  5.635  16.703    610
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.39 %
    Favored  : 86.61 %
  Rotamer Outliers :  5.81 %
  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: -3.82 (0.31), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.23), residues: 590

===============================================================================
Job complete
usr+sys time: 1374.49 seconds
wall clock time: 25 minutes 26.80 seconds (1526.80 seconds total)