Starting phenix.real_space_refine (version: 1.21rc1)
on Tue Oct  3 05:55:28 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyv_27085/10_2023/8cyv_27085.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyv_27085/10_2023/8cyv_27085.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyv_27085/10_2023/8cyv_27085.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyv_27085/10_2023/8cyv_27085.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyv_27085/10_2023/8cyv_27085.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyv_27085/10_2023/8cyv_27085.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    3744      2.51       5
     N    1044      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "I PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib"
  Total number of atoms: 5964
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
  Time building chain proxies: 3.47, per 1000 atoms: 0.58
  Number of scatterers: 5964
  At special positions: 0
  Unit cell: (81, 114.48, 48.6, 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    1176      8.00
     N    1044      7.00
     C    3744      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: 2.04
  Conformation dependent library (CDL) restraints added in 914.9 milliseconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 33.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 23
      removed outlier: 6.520A  pdb=" N   VAL C  16 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ALA B  19 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ALA C  18 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   LYS B  21 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLU C  20 " --> pdb=" O   LYS B  21 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   LYS B  23 " --> pdb=" O   GLU C  20 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   THR C  22 " --> pdb=" O   LYS B  23 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL D  16 " --> pdb=" O   ALA C  17 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ALA C  19 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ALA D  18 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   LYS C  21 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLU D  20 " --> pdb=" O   LYS C  21 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   LYS C  23 " --> pdb=" O   GLU D  20 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR D  22 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL F  16 " --> pdb=" O   ALA E  17 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   ALA E  19 " --> pdb=" O   VAL F  16 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ALA F  18 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   LYS E  21 " --> pdb=" O   ALA F  18 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   GLU F  20 " --> pdb=" O   LYS E  21 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LYS E  23 " --> pdb=" O   GLU F  20 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   THR F  22 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42
      removed outlier: 6.475A  pdb=" N   LEU A  38 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   GLY B  41 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   VAL A  40 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU D  38 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   GLY E  41 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   VAL D  40 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.266A  pdb=" N   VAL A  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL D  49 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55
      removed outlier: 6.950A  pdb=" N   ALA C  53 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ALA D  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ALA F  53 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66
      removed outlier: 6.778A  pdb=" N   VAL C  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL B  66 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASN C  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL D  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL C  66 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASN D  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL F  63 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   VAL E  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ASN F  65 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71
      removed outlier: 6.521A  pdb=" N   VAL A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL D  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 79
      removed outlier: 6.393A  pdb=" N   ALA C  78 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ALA D  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ALA F  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 90 through 91
      removed outlier: 6.643A  pdb=" N   ALA C  90 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA D  90 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ALA F  90 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 95 through 96
      removed outlier: 6.609A  pdb=" N   VAL A  95 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D  95 " --> pdb=" O   LYS E  96 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 17 through 23
      removed outlier: 6.795A  pdb=" N   ALA K  18 " --> pdb=" O   ALA J  19 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LYS J  21 " --> pdb=" O   ALA K  18 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLU K  20 " --> pdb=" O   LYS J  21 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   LYS J  23 " --> pdb=" O   GLU K  20 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   THR K  22 " --> pdb=" O   LYS J  23 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ALA L  18 " --> pdb=" O   ALA K  19 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LYS K  21 " --> pdb=" O   ALA L  18 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLU L  20 " --> pdb=" O   LYS K  21 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   LYS K  23 " --> pdb=" O   GLU L  20 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR L  22 " --> pdb=" O   LYS K  23 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ALA N  18 " --> pdb=" O   ALA M  19 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   LYS M  21 " --> pdb=" O   ALA N  18 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLU N  20 " --> pdb=" O   LYS M  21 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   LYS M  23 " --> pdb=" O   GLU N  20 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR N  22 " --> pdb=" O   LYS M  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 38 through 42
      removed outlier: 6.147A  pdb=" N   LEU I  38 " --> pdb=" O   TYR J  39 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   GLY J  41 " --> pdb=" O   LEU I  38 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL I  40 " --> pdb=" O   GLY J  41 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU L  38 " --> pdb=" O   TYR M  39 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   GLY M  41 " --> pdb=" O   LEU L  38 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL L  40 " --> pdb=" O   GLY M  41 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'I' and resid 48 through 49
      removed outlier: 6.453A  pdb=" N   VAL K  48 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL L  48 " --> pdb=" O   VAL K  49 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL N  48 " --> pdb=" O   VAL M  49 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'I' and resid 62 through 64
      removed outlier: 6.485A  pdb=" N   VAL K  63 " --> pdb=" O   THR J  64 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL L  63 " --> pdb=" O   THR K  64 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL N  63 " --> pdb=" O   THR M  64 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 70 through 71
      removed outlier: 6.107A  pdb=" N   VAL I  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   VAL L  70 " --> pdb=" O   VAL M  71 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 75 through 79
      removed outlier: 6.226A  pdb=" N   ALA K  76 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   GLN J  79 " --> pdb=" O   ALA K  76 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ALA K  78 " --> pdb=" O   GLN J  79 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ALA L  76 " --> pdb=" O   VAL K  77 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   GLN K  79 " --> pdb=" O   ALA L  76 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ALA L  78 " --> pdb=" O   GLN K  79 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ALA N  76 " --> pdb=" O   VAL M  77 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   GLN M  79 " --> pdb=" O   ALA N  76 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ALA N  78 " --> pdb=" O   GLN M  79 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 86 through 91
      removed outlier: 6.365A  pdb=" N   SER I  87 " --> pdb=" O   ILE J  88 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   ALA J  90 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA I  89 " --> pdb=" O   ALA J  90 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   SER L  87 " --> pdb=" O   ILE M  88 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   ALA M  90 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ALA L  89 " --> pdb=" O   ALA M  90 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'I' and resid 94 through 95
      removed outlier: 5.970A  pdb=" N   PHE K  94 " --> pdb=" O   VAL J  95 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   PHE L  94 " --> pdb=" O   VAL K  95 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   PHE N  94 " --> pdb=" O   VAL M  95 " (cutoff:3.500A)

    114 hydrogen bonds defined for protein.
    342 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 1032
        1.29 -     1.36: 924
        1.36 -     1.43: 204
        1.43 -     1.49: 1080
        1.49 -     1.56: 2736
  Bond restraints: 5976
  Sorted by residual:
  bond pdb=" N   LYS N  58 "
       pdb=" CA  LYS N  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.476 -0.014 1.52e-02 4.33e+03 8.97e-01
  bond pdb=" N   LYS J  58 "
       pdb=" CA  LYS J  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.475 -0.014 1.52e-02 4.33e+03 8.82e-01
  bond pdb=" N   LYS I  58 "
       pdb=" CA  LYS I  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.475 -0.014 1.52e-02 4.33e+03 8.40e-01
  bond pdb=" N   LYS L  58 "
       pdb=" CA  LYS L  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.475 -0.014 1.52e-02 4.33e+03 8.37e-01
  bond pdb=" C   GLU M  57 "
       pdb=" N   LYS M  58 "
    ideal  model  delta    sigma   weight residual
    1.332  1.345 -0.013 1.40e-02 5.10e+03 8.21e-01
  ... (remaining 5971 not shown)

  Histogram of bond angle deviations from ideal:
      105.92 -   110.98: 2338
      110.98 -   116.05: 1964
      116.05 -   121.12: 1852
      121.12 -   126.18: 1880
      126.18 -   131.25: 18
  Bond angle restraints: 8052
  Sorted by residual:
  angle pdb=" C   THR D  81 "
        pdb=" N   VAL D  82 "
        pdb=" CA  VAL D  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.12   -5.15 1.80e+00 3.09e-01 8.18e+00
  angle pdb=" C   THR E  81 "
        pdb=" N   VAL E  82 "
        pdb=" CA  VAL E  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.12   -5.15 1.80e+00 3.09e-01 8.18e+00
  angle pdb=" C   THR F  81 "
        pdb=" N   VAL F  82 "
        pdb=" CA  VAL F  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.11   -5.14 1.80e+00 3.09e-01 8.16e+00
  angle pdb=" C   THR A  81 "
        pdb=" N   VAL A  82 "
        pdb=" CA  VAL A  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.11   -5.14 1.80e+00 3.09e-01 8.16e+00
  angle pdb=" C   THR C  81 "
        pdb=" N   VAL C  82 "
        pdb=" CA  VAL C  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.11   -5.14 1.80e+00 3.09e-01 8.14e+00
  ... (remaining 8047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.63: 3184
       11.63 -    23.26: 271
       23.26 -    34.89: 49
       34.89 -    46.52: 12
       46.52 -    58.15: 12
  Dihedral angle restraints: 3528
    sinusoidal: 1188
      harmonic: 2340
  Sorted by residual:
  dihedral pdb=" CA  GLY M  73 "
           pdb=" C   GLY M  73 "
           pdb=" N   VAL M  74 "
           pdb=" CA  VAL M  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  GLY K  73 "
           pdb=" C   GLY K  73 "
           pdb=" N   VAL K  74 "
           pdb=" CA  VAL K  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  GLY I  73 "
           pdb=" C   GLY I  73 "
           pdb=" N   VAL I  74 "
           pdb=" CA  VAL I  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.06   17.94     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 3525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 449
       0.025 -    0.050: 309
       0.050 -    0.075: 103
       0.075 -    0.099: 84
       0.099 -    0.124: 123
  Chirality restraints: 1068
  Sorted by residual:
  chirality pdb=" CA  ILE I  88 "
            pdb=" N   ILE I  88 "
            pdb=" C   ILE I  88 "
            pdb=" CB  ILE I  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ILE L  88 "
            pdb=" N   ILE L  88 "
            pdb=" C   ILE L  88 "
            pdb=" CB  ILE L  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  VAL K  40 "
            pdb=" N   VAL K  40 "
            pdb=" C   VAL K  40 "
            pdb=" CB  VAL K  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 1065 not shown)

  Planarity restraints: 984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  81 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.08e+00
        pdb=" C   THR A  81 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR A  81 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A  82 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D  81 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   THR D  81 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR D  81 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL D  82 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  81 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   THR E  81 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR E  81 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL E  82 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 981 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 2394
        2.92 -     3.41: 4632
        3.41 -     3.91: 9727
        3.91 -     4.40: 9551
        4.40 -     4.90: 21742
  Nonbonded interactions: 48046
  Sorted by model distance:
  nonbonded pdb=" O   THR D  75 "
            pdb=" OG1 THR D  75 "
     model   vdw
     2.423 2.440
  nonbonded pdb=" O   THR B  75 "
            pdb=" OG1 THR B  75 "
     model   vdw
     2.423 2.440
  nonbonded pdb=" O   THR A  75 "
            pdb=" OG1 THR A  75 "
     model   vdw
     2.424 2.440
  nonbonded pdb=" O   THR E  75 "
            pdb=" OG1 THR E  75 "
     model   vdw
     2.424 2.440
  nonbonded pdb=" O   THR F  75 "
            pdb=" OG1 THR F  75 "
     model   vdw
     2.424 2.440
  ... (remaining 48041 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 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.770
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     20.110
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5976  Z= 0.199
  Angle     :  0.611   5.149   8052  Z= 0.358
  Chirality :  0.053   0.124   1068
  Planarity :  0.003   0.018    984
  Dihedral  : 10.014  58.153   2040
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  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: -4.11 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.18), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.705 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2197
  time to fit residues: 40.2075
Evaluate side-chains
  118 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.687 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 63 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    7.1994

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
F  79 GLN
D  62 GLN
E  62 GLN
I  24 GLN
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  62 GLN
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  62 GLN
M  62 GLN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  62 GLN
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  79 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   5976  Z= 0.465
  Angle     :  0.716   5.749   8052  Z= 0.400
  Chirality :  0.050   0.135   1068
  Planarity :  0.004   0.018    984
  Dihedral  :  6.193  20.022    852
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.67 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.27 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.17), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 15
  residues processed: 152
  average time/residue: 0.2360
  time to fit residues: 43.9601
Evaluate side-chains
  147 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.634 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0590
  time to fit residues: 2.4542
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 82 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   overall best weight:    3.8986

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
E  79 GLN
C  62 GLN
I  65 ASN
L  62 GLN
L  65 ASN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  65 ASN
J  65 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5976  Z= 0.273
  Angle     :  0.542   7.908   8052  Z= 0.300
  Chirality :  0.050   0.163   1068
  Planarity :  0.002   0.032    984
  Dihedral  :  5.337  24.517    852
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.00 %
    Favored  : 80.83 %
  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: -4.27 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.17), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.670 
Fit side-chains
  outliers start: 13
  outliers final: 7
  residues processed: 150
  average time/residue: 0.2334
  time to fit residues: 43.1480
Evaluate side-chains
  145 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 0.658 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0969
  time to fit residues: 1.9079
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   chunk 76 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   overall best weight:    8.7990

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  62 GLN
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  79 GLN
N  62 GLN
N  65 ASN
N  79 GLN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  79 GLN
K  62 GLN
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  79 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.4959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.072   5976  Z= 0.551
  Angle     :  0.779   9.254   8052  Z= 0.432
  Chirality :  0.053   0.150   1068
  Planarity :  0.004   0.025    984
  Dihedral  :  6.502  31.383    852
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 19.50 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -4.70 (0.20), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.16), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.710 
Fit side-chains
  outliers start: 32
  outliers final: 20
  residues processed: 167
  average time/residue: 0.2754
  time to fit residues: 58.3724
Evaluate side-chains
  165 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.833 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0588
  time to fit residues: 3.1215
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 72 optimal weight:    8.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
D  65 ASN
C  62 GLN
I  65 ASN
L  65 ASN
N  65 ASN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  65 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.5019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5976  Z= 0.273
  Angle     :  0.573   6.937   8052  Z= 0.318
  Chirality :  0.051   0.179   1068
  Planarity :  0.002   0.020    984
  Dihedral  :  5.547  26.213    852
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.33 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.50 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.16), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.735 
Fit side-chains
  outliers start: 26
  outliers final: 14
  residues processed: 158
  average time/residue: 0.2232
  time to fit residues: 44.4174
Evaluate side-chains
  156 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.689 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0635
  time to fit residues: 2.5026
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 6 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:   20.0000
   overall best weight:    6.1992

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN
I  65 ASN
L  65 ASN
N  65 ASN
M  65 ASN
** K  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  65 ASN
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.5287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   5976  Z= 0.402
  Angle     :  0.659   7.567   8052  Z= 0.364
  Chirality :  0.052   0.186   1068
  Planarity :  0.003   0.022    984
  Dihedral  :  6.008  28.913    852
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.64 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 19.00 %
    Favored  : 75.50 %
  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: -4.50 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.16), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.720 
Fit side-chains
  outliers start: 33
  outliers final: 17
  residues processed: 160
  average time/residue: 0.2240
  time to fit residues: 44.4812
Evaluate side-chains
  157 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.647 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1346
  time to fit residues: 3.9086
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 49 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN
I  65 ASN
L  65 ASN
N  65 ASN
M  65 ASN
** K  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  65 ASN
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.5305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5976  Z= 0.259
  Angle     :  0.589   7.975   8052  Z= 0.324
  Chirality :  0.052   0.210   1068
  Planarity :  0.002   0.022    984
  Dihedral  :  5.464  24.582    852
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.67 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.35 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.17), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.612 
Fit side-chains
  outliers start: 18
  outliers final: 6
  residues processed: 162
  average time/residue: 0.2297
  time to fit residues: 46.0457
Evaluate side-chains
  148 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.611 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0568
  time to fit residues: 1.5436
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 24 optimal weight:    0.4980
   chunk 15 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   chunk 63 optimal weight:   20.0000
   chunk 73 optimal weight:   20.0000
   chunk 77 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    7.0988

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN
I  65 ASN
L  65 ASN
N  65 ASN
** K  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.5584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   5976  Z= 0.451
  Angle     :  0.720   7.790   8052  Z= 0.397
  Chirality :  0.053   0.178   1068
  Planarity :  0.003   0.025    984
  Dihedral  :  6.188  30.200    852
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 12.13 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 22.17 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.16), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.671 
Fit side-chains
  outliers start: 24
  outliers final: 16
  residues processed: 157
  average time/residue: 0.2045
  time to fit residues: 40.3961
Evaluate side-chains
  159 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.614 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0536
  time to fit residues: 2.4127
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 49 optimal weight:   20.0000
   chunk 79 optimal weight:   10.0000
   chunk 48 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN
I  65 ASN
L  65 ASN
N  65 ASN
M  65 ASN
K  65 ASN
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.5592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5976  Z= 0.330
  Angle     :  0.672   8.301   8052  Z= 0.367
  Chirality :  0.052   0.206   1068
  Planarity :  0.003   0.023    984
  Dihedral  :  5.866  24.860    852
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  8.58 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.17 %
    Favored  : 74.83 %
  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: -4.33 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.17), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.677 
Fit side-chains
  outliers start: 12
  outliers final: 2
  residues processed: 146
  average time/residue: 0.2191
  time to fit residues: 39.9247
Evaluate side-chains
  141 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.628 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0565
  time to fit residues: 1.0966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN
I  65 ASN
L  65 ASN
N  65 ASN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  65 ASN
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   5976  Z= 0.397
  Angle     :  0.715   9.150   8052  Z= 0.393
  Chirality :  0.053   0.194   1068
  Planarity :  0.003   0.028    984
  Dihedral  :  6.127  27.771    852
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 11.89 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 24.83 %
    Favored  : 73.83 %
  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: -4.36 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.17), residues: 816

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.700 
Fit side-chains
  outliers start: 8
  outliers final: 2
  residues processed: 148
  average time/residue: 0.2123
  time to fit residues: 39.6809
Evaluate side-chains
  144 residues out of total 600 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.642 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0585
  time to fit residues: 1.0499
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.2980
   chunk 9 optimal weight:    0.3980
   chunk 18 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 58 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 48 optimal weight:   20.0000
   overall best weight:    3.5384

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  62 GLN
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  65 ASN
N  65 ASN
K  65 ASN
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.138730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.120257 restraints weight = 8460.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.123340 restraints weight = 4315.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.125378 restraints weight = 2679.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.5637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5976  Z= 0.263
  Angle     :  0.622   8.579   8052  Z= 0.339
  Chirality :  0.052   0.218   1068
  Planarity :  0.002   0.022    984
  Dihedral  :  5.623  23.865    852
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  6.99 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 24.33 %
    Favored  : 73.50 %
  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: -4.20 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.17), residues: 816
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1360.48 seconds
wall clock time: 25 minutes 36.11 seconds (1536.11 seconds total)