Starting phenix.real_space_refine (version: dev)
on Mon Dec 12 17:09:03 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/12_2022/7nci_12267.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/12_2022/7nci_12267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/12_2022/7nci_12267.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/12_2022/7nci_12267.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/12_2022/7nci_12267.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/12_2022/7nci_12267.pdb"
  }
  resolution = 3.55
  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=   0.001
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: 11292
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
  Time building chain proxies: 5.62, per 1000 atoms: 0.50
  Number of scatterers: 11292
  At special positions: 0
  Unit cell: (119.9, 95.7, 56.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O    1116      8.00
     N     972      7.00
     C    3408      6.00
     H    5796      1.00
    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: 9.29
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21
      removed outlier: 7.195A  pdb=" N   ALA A  18 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 9.452A  pdb=" N   LYS B  21 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   GLU A  20 " --> pdb=" O   LYS B  21 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ALA C  19 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS C  21 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41
      removed outlier: 5.672A  pdb=" N   TYR A  39 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   TYR B  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   TYR C  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY D  41 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 5.784A  pdb=" N   TYR E  39 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55
      removed outlier: 4.650A  pdb=" N   VAL A  49 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   GLY B  51 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   GLY A  51 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   ALA B  53 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ALA A  53 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   VAL B  55 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   VAL A  55 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 9.220A  pdb=" N   VAL B  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 10.372A  pdb=" N   VAL C  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   GLY B  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   THR C  54 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ALA B  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY D  51 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL C  52 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   ALA D  53 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   THR C  54 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   VAL D  55 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 9.025A  pdb=" N   HIS D  50 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   ALA E  53 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 9.108A  pdb=" N   VAL D  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 10.794A  pdb=" N   VAL E  55 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 9.009A  pdb=" N   THR D  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   HIS E  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   ALA F  53 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 9.024A  pdb=" N   VAL E  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 10.619A  pdb=" N   VAL F  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 8.793A  pdb=" N   THR E  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 64
      removed outlier: 7.057A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   VAL B  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 8.806A  pdb=" N   VAL C  66 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL D  66 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   VAL E  63 " --> pdb=" O   THR F  64 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 88
      removed outlier: 6.399A  pdb=" N   GLY B  86 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   GLY C  86 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
      removed outlier: 8.675A  pdb=" N   ALA D  89 " --> pdb=" O   GLY C  86 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE C  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLY D  86 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 8.770A  pdb=" N   ALA E  89 " --> pdb=" O   GLY D  86 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ILE D  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   GLY E  86 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 21
      removed outlier: 3.790A  pdb=" N   ALA E  19 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS E  21 " --> pdb=" O   GLU D  20 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA F  17 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS F  21 " --> pdb=" O   GLU E  20 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 18 through 21
      removed outlier: 7.012A  pdb=" N   ALA G  18 " --> pdb=" O   ALA H  19 " (cutoff:3.500A)
      removed outlier: 9.331A  pdb=" N   LYS H  21 " --> pdb=" O   ALA G  18 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   GLU G  20 " --> pdb=" O   LYS H  21 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA I  19 " --> pdb=" O   ALA H  18 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LYS I  21 " --> pdb=" O   GLU H  20 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ALA J  19 " --> pdb=" O   ALA I  18 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU I  20 " --> pdb=" O   ALA J  19 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS J  21 " --> pdb=" O   GLU I  20 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA K  19 " --> pdb=" O   ALA J  18 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS K  21 " --> pdb=" O   GLU J  20 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA L  19 " --> pdb=" O   ALA K  18 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLU K  20 " --> pdb=" O   ALA L  19 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS L  21 " --> pdb=" O   GLU K  20 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 39 through 41
      removed outlier: 5.540A  pdb=" N   TYR G  39 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   TYR H  39 " --> pdb=" O   VAL I  40 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   TYR I  39 " --> pdb=" O   VAL J  40 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   TYR J  39 " --> pdb=" O   VAL K  40 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 49 through 55
      removed outlier: 9.310A  pdb=" N   VAL G  49 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 10.589A  pdb=" N   VAL H  52 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   GLY G  51 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   THR H  54 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ALA G  53 " --> pdb=" O   THR H  54 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   HIS H  50 " --> pdb=" O   GLY I  51 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ALA I  53 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 8.845A  pdb=" N   VAL H  52 " --> pdb=" O   ALA I  53 " (cutoff:3.500A)
      removed outlier: 10.636A  pdb=" N   VAL I  55 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   THR H  54 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   HIS I  50 " --> pdb=" O   GLY J  51 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   ALA J  53 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
      removed outlier: 9.026A  pdb=" N   VAL I  52 " --> pdb=" O   ALA J  53 " (cutoff:3.500A)
      removed outlier: 10.661A  pdb=" N   VAL J  55 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 8.932A  pdb=" N   THR I  54 " --> pdb=" O   VAL J  55 " (cutoff:3.500A)
      removed outlier: 9.182A  pdb=" N   HIS J  50 " --> pdb=" O   GLY K  51 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ALA K  53 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 9.085A  pdb=" N   VAL J  52 " --> pdb=" O   ALA K  53 " (cutoff:3.500A)
      removed outlier: 10.710A  pdb=" N   VAL K  55 " --> pdb=" O   VAL J  52 " (cutoff:3.500A)
      removed outlier: 8.910A  pdb=" N   THR J  54 " --> pdb=" O   VAL K  55 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   HIS K  50 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   ALA L  53 " --> pdb=" O   HIS K  50 " (cutoff:3.500A)
      removed outlier: 9.215A  pdb=" N   VAL K  52 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 10.709A  pdb=" N   VAL L  55 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 8.950A  pdb=" N   THR K  54 " --> pdb=" O   VAL L  55 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 66
      removed outlier: 3.579A  pdb=" N   VAL H  66 " --> pdb=" O   ASN G  65 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   VAL I  63 " --> pdb=" O   THR J  64 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   VAL J  63 " --> pdb=" O   THR K  64 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   VAL K  63 " --> pdb=" O   THR L  64 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 86 through 90
      removed outlier: 6.516A  pdb=" N   GLY G  86 " --> pdb=" O   SER H  87 " (cutoff:3.500A)
      removed outlier: 8.594A  pdb=" N   ALA H  89 " --> pdb=" O   GLY G  86 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ILE G  88 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   GLY H  86 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   GLY I  86 " --> pdb=" O   SER J  87 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   GLY J  86 " --> pdb=" O   SER K  87 " (cutoff:3.500A)
      removed outlier: 8.569A  pdb=" N   ALA K  89 " --> pdb=" O   GLY J  86 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ILE J  88 " --> pdb=" O   ALA K  89 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   GLY K  86 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
      removed outlier: 9.036A  pdb=" N   ALA L  89 " --> pdb=" O   GLY K  86 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE K  88 " --> pdb=" O   ALA L  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    18 hydrogen bonds defined for protein.
    51 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: 3.46

  Time building geometry restraints manager: 9.61 seconds

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

  Histogram of bond lengths:
        0.81 -     0.97: 1817
        0.97 -     1.12: 3979
        1.12 -     1.28: 984
        1.28 -     1.43: 1075
        1.43 -     1.59: 3437
  Bond restraints: 11292
  Sorted by residual:
  bond pdb=" N   VAL G  40 "
       pdb=" CA  VAL G  40 "
    ideal  model  delta    sigma   weight residual
    1.460  1.501 -0.041 1.44e-02 4.82e+03 8.11e+00
  bond pdb=" N   VAL J  40 "
       pdb=" CA  VAL J  40 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.44e-02 4.82e+03 7.85e+00
  bond pdb=" CA  ILE A  88 "
       pdb=" CB  ILE A  88 "
    ideal  model  delta    sigma   weight residual
    1.548  1.587 -0.040 1.46e-02 4.69e+03 7.35e+00
  bond pdb=" N   VAL B  40 "
       pdb=" CA  VAL B  40 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.44e-02 4.82e+03 5.53e+00
  bond pdb=" N   VAL A  40 "
       pdb=" CA  VAL A  40 "
    ideal  model  delta    sigma   weight residual
    1.460  1.490 -0.030 1.35e-02 5.49e+03 4.93e+00
  ... (remaining 11287 not shown)

  Histogram of bond angle deviations from ideal:
       73.18 -    84.57: 6
       84.57 -    95.96: 0
       95.96 -   107.35: 1333
      107.35 -   118.74: 15344
      118.74 -   130.13: 3849
  Bond angle restraints: 20532
  Sorted by residual:
  angle pdb=" N   THR C  44 "
        pdb=" CA  THR C  44 "
        pdb=" HA  THR C  44 "
      ideal   model   delta    sigma   weight residual
     110.00   73.18   36.82 3.00e+00 1.11e-01 1.51e+02
  angle pdb=" C   THR I  44 "
        pdb=" CA  THR I  44 "
        pdb=" HA  THR I  44 "
      ideal   model   delta    sigma   weight residual
     109.00   73.72   35.28 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" C   THR C  44 "
        pdb=" CA  THR C  44 "
        pdb=" HA  THR C  44 "
      ideal   model   delta    sigma   weight residual
     109.00   74.54   34.46 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" N   THR I  44 "
        pdb=" CA  THR I  44 "
        pdb=" HA  THR I  44 "
      ideal   model   delta    sigma   weight residual
     110.00   75.68   34.32 3.00e+00 1.11e-01 1.31e+02
  angle pdb=" CB  THR I  44 "
        pdb=" CA  THR I  44 "
        pdb=" HA  THR I  44 "
      ideal   model   delta    sigma   weight residual
     109.00   80.08   28.92 3.00e+00 1.11e-01 9.29e+01
  ... (remaining 20527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3611
       17.86 -    35.72: 306
       35.72 -    53.58: 47
       53.58 -    71.44: 222
       71.44 -    89.30: 26
  Dihedral angle restraints: 4212
    sinusoidal: 1956
      harmonic: 2256
  Sorted by residual:
  dihedral pdb=" C   THR I  44 "
           pdb=" N   THR I  44 "
           pdb=" CA  THR I  44 "
           pdb=" CB  THR I  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.89   14.89     0      2.50e+00 1.60e-01 3.55e+01
  dihedral pdb=" CA  VAL E  74 "
           pdb=" C   VAL E  74 "
           pdb=" N   THR E  75 "
           pdb=" CA  THR E  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.91   29.09     0      5.00e+00 4.00e-02 3.39e+01
  dihedral pdb=" CA  SER A  87 "
           pdb=" C   SER A  87 "
           pdb=" N   ILE A  88 "
           pdb=" CA  ILE A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.03   28.97     0      5.00e+00 4.00e-02 3.36e+01
  ... (remaining 4209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 740
       0.107 -    0.213: 208
       0.213 -    0.320: 34
       0.320 -    0.427: 0
       0.427 -    0.533: 2
  Chirality restraints: 984
  Sorted by residual:
  chirality pdb=" CA  THR I  44 "
            pdb=" N   THR I  44 "
            pdb=" C   THR I  44 "
            pdb=" CB  THR I  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.99    0.53 2.00e-01 2.50e+01 7.11e+00
  chirality pdb=" CA  THR C  44 "
            pdb=" N   THR C  44 "
            pdb=" C   THR C  44 "
            pdb=" CB  THR C  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.05    0.48 2.00e-01 2.50e+01 5.77e+00
  chirality pdb=" CB  VAL J  40 "
            pdb=" CA  VAL J  40 "
            pdb=" CG1 VAL J  40 "
            pdb=" CG2 VAL J  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 981 not shown)

  Planarity restraints: 1716
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  39 "    0.077 2.00e-02 2.50e+03   3.32e-02 3.32e+01
        pdb=" CG  TYR L  39 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  39 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  39 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  39 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  39 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR L  39 "    0.021 2.00e-02 2.50e+03
        pdb=" HD1 TYR L  39 "   -0.038 2.00e-02 2.50e+03
        pdb=" HD2 TYR L  39 "   -0.021 2.00e-02 2.50e+03
        pdb=" HE1 TYR L  39 "    0.025 2.00e-02 2.50e+03
        pdb=" HE2 TYR L  39 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  39 "   -0.025 2.00e-02 2.50e+03   3.16e-02 2.99e+01
        pdb=" CG  TYR B  39 "    0.076 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  39 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  39 "    0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  39 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  39 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  39 "    0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR B  39 "   -0.017 2.00e-02 2.50e+03
        pdb=" HD1 TYR B  39 "   -0.030 2.00e-02 2.50e+03
        pdb=" HD2 TYR B  39 "   -0.040 2.00e-02 2.50e+03
        pdb=" HE1 TYR B  39 "   -0.009 2.00e-02 2.50e+03
        pdb=" HE2 TYR B  39 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR K  39 "    0.004 2.00e-02 2.50e+03   2.79e-02 2.33e+01
        pdb=" CG  TYR K  39 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD1 TYR K  39 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR K  39 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR K  39 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR K  39 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR K  39 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR K  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD1 TYR K  39 "    0.027 2.00e-02 2.50e+03
        pdb=" HD2 TYR K  39 "    0.047 2.00e-02 2.50e+03
        pdb=" HE1 TYR K  39 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR K  39 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1713 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.22: 665
        2.22 -     2.79: 22320
        2.79 -     3.36: 26919
        3.36 -     3.93: 34152
        3.93 -     4.50: 52195
  Nonbonded interactions: 136251
  Sorted by model distance:
  nonbonded pdb=" H   THR C  44 "
            pdb=" HA  THR C  44 "
     model   vdw
     1.651 1.816
  nonbonded pdb=" HG1 THR C  44 "
            pdb=" O   THR D  44 "
     model   vdw
     1.680 1.850
  nonbonded pdb=" HG1 THR I  44 "
            pdb=" O   THR J  44 "
     model   vdw
     1.691 1.850
  nonbonded pdb=" H   THR I  44 "
            pdb=" HA  THR I  44 "
     model   vdw
     1.692 1.816
  nonbonded pdb=" HG1 THR H  44 "
            pdb=" O   THR I  44 "
     model   vdw
     1.695 1.850
  ... (remaining 136246 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'
  selection = chain 'K'
  selection = chain 'L'
}

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: 4
    Type Number    sf(0)   Gaussians
     C    3408      2.51       5
     N     972      2.21       5
     O    1116      1.98       5
     H    5796      0.53       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:             1.050
  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:             0.190
  Extract box with map and model:          4.380
  Check model and map are aligned:         0.180
  Convert atoms to be neutral:             0.090
  Process input model:                     38.270
  Find NCS groups from input model:        0.620
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5901
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      :  0.012   0.068   5496  Z= 0.789
  Angle     :  1.574   9.424   7416  Z= 0.948
  Chirality :  0.101   0.533    984
  Planarity :  0.005   0.034    924
  Dihedral  : 15.566  89.302   1848
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 0.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.29 %
  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: -3.74 (0.16), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.13), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.3952
  time to fit residues: 104.9943
Evaluate side-chains
  111 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.920 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1308
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  50 HIS
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6072
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5496  Z= 0.239
  Angle     :  0.652   5.871   7416  Z= 0.379
  Chirality :  0.053   0.387    984
  Planarity :  0.002   0.010    924
  Dihedral  :  8.346  23.401    804
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer Outliers :  2.41 %
  Cbeta Deviations :  0.29 %
  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: -4.13 (0.16), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.12), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 11
  residues processed: 136
  average time/residue: 0.3359
  time to fit residues: 59.8415
Evaluate side-chains
  124 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.811 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1281
  time to fit residues: 3.3899
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 64 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6117
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5496  Z= 0.212
  Angle     :  0.579   5.784   7416  Z= 0.335
  Chirality :  0.054   0.387    984
  Planarity :  0.002   0.008    924
  Dihedral  :  7.136  20.497    804
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer Outliers :  3.89 %
  Cbeta Deviations :  0.29 %
  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 (0.21), residues: 768
  helix:  None (None), residues: 0
  sheet: -1.50 (0.43), residues: 120
  loop : -3.06 (0.16), residues: 648

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 18
  residues processed: 132
  average time/residue: 0.3722
  time to fit residues: 64.6113
Evaluate side-chains
  131 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.948 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 0
  residues processed: 18
  average time/residue: 0.1311
  time to fit residues: 5.3504
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6096
moved from start:          0.5553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5496  Z= 0.170
  Angle     :  0.509   5.608   7416  Z= 0.297
  Chirality :  0.053   0.383    984
  Planarity :  0.001   0.008    924
  Dihedral  :  6.476  18.792    804
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer Outliers :  1.67 %
  Cbeta Deviations :  0.29 %
  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: -3.62 (0.22), residues: 768
  helix:  None (None), residues: 0
  sheet: -1.41 (0.44), residues: 120
  loop : -2.90 (0.17), residues: 648

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 126
  average time/residue: 0.3256
  time to fit residues: 54.8609
Evaluate side-chains
  121 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.870 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1221
  time to fit residues: 2.3774
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.5972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5496  Z= 0.273
  Angle     :  0.573   6.024   7416  Z= 0.333
  Chirality :  0.054   0.393    984
  Planarity :  0.002   0.009    924
  Dihedral  :  6.914  20.992    804
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer Outliers :  4.81 %
  Cbeta Deviations :  0.29 %
  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: -4.13 (0.20), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 20
  residues processed: 119
  average time/residue: 0.3281
  time to fit residues: 51.7176
Evaluate side-chains
  127 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.830 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1179
  time to fit residues: 5.2438
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6148
moved from start:          0.6165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5496  Z= 0.166
  Angle     :  0.490   5.651   7416  Z= 0.286
  Chirality :  0.053   0.380    984
  Planarity :  0.001   0.008    924
  Dihedral  :  6.262  19.884    804
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer Outliers :  1.11 %
  Cbeta Deviations :  0.29 %
  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 (0.20), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 119
  average time/residue: 0.3135
  time to fit residues: 50.6128
Evaluate side-chains
  112 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 0.746 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1047
  time to fit residues: 1.4877
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0170
   overall best weight:    1.1022

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6205
moved from start:          0.6441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5496  Z= 0.207
  Angle     :  0.508   5.718   7416  Z= 0.296
  Chirality :  0.053   0.389    984
  Planarity :  0.002   0.007    924
  Dihedral  :  6.305  19.578    804
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  Rotamer Outliers :  3.89 %
  Cbeta Deviations :  0.29 %
  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: -4.19 (0.20), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 17
  residues processed: 110
  average time/residue: 0.3462
  time to fit residues: 51.0470
Evaluate side-chains
  120 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.823 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1699
  time to fit residues: 6.5478
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 63 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6230
moved from start:          0.6644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5496  Z= 0.219
  Angle     :  0.519   5.715   7416  Z= 0.304
  Chirality :  0.053   0.389    984
  Planarity :  0.002   0.007    924
  Dihedral  :  6.385  19.713    804
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.24 %
    Favored  : 87.76 %
  Rotamer Outliers :  1.30 %
  Cbeta Deviations :  0.29 %
  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: -4.24 (0.20), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.22 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 109
  average time/residue: 0.3473
  time to fit residues: 49.9987
Evaluate side-chains
  104 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1171
  time to fit residues: 1.8068
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6155
moved from start:          0.6816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5496  Z= 0.149
  Angle     :  0.459   5.463   7416  Z= 0.268
  Chirality :  0.053   0.377    984
  Planarity :  0.001   0.005    924
  Dihedral  :  5.709  18.057    804
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer Outliers :  1.67 %
  Cbeta Deviations :  0.29 %
  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: -4.09 (0.20), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 8
  residues processed: 109
  average time/residue: 0.3382
  time to fit residues: 49.6401
Evaluate side-chains
  114 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.943 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1293
  time to fit residues: 2.9588
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.0770
   chunk 47 optimal weight:    0.0970
   chunk 71 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 57 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6124
moved from start:          0.6953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5496  Z= 0.144
  Angle     :  0.443   5.250   7416  Z= 0.257
  Chirality :  0.053   0.378    984
  Planarity :  0.001   0.006    924
  Dihedral  :  5.343  17.098    804
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer Outliers :  0.56 %
  Cbeta Deviations :  0.29 %
  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: -3.93 (0.21), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.16), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 111
  average time/residue: 0.3323
  time to fit residues: 49.5192
Evaluate side-chains
  110 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.929 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1239
  time to fit residues: 1.4992
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** 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 = 0.5335 r_free = 0.5335 target = 0.245665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.5095 r_free = 0.5095 target = 0.188586 restraints weight = 25268.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5184 r_free = 0.5184 target = 0.198422 restraints weight = 12656.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.5249 r_free = 0.5249 target = 0.205677 restraints weight = 7558.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.5177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5663
moved from start:          0.7042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5496  Z= 0.195
  Angle     :  0.476   5.612   7416  Z= 0.277
  Chirality :  0.053   0.387    984
  Planarity :  0.002   0.007    924
  Dihedral  :  5.701  18.204    804
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer Outliers :  0.37 %
  Cbeta Deviations :  0.29 %
  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: -4.08 (0.21), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.16), residues: 768

===============================================================================
Job complete
usr+sys time: 3450.98 seconds
wall clock time: 61 minutes 35.41 seconds (3695.41 seconds total)