Starting phenix.real_space_refine
on Fri Dec  8 07:08:30 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/12_2023/8ehs_28151.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/12_2023/8ehs_28151.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/12_2023/8ehs_28151.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/12_2023/8ehs_28151.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/12_2023/8ehs_28151.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehs_28151/12_2023/8ehs_28151.pdb"
  }
  resolution = 3.3
  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=   0.014
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: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    4676      2.51       5
     N    1253      2.21       5
     O    1596      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "G GLU  129": "OE1" <-> "OE2"
    Residue "A ASP   53": "OD1" <-> "OD2"
    Residue "A ASP   93": "OD1" <-> "OD2"
    Residue "B ASP   21": "OD1" <-> "OD2"
    Residue "B ASP   53": "OD1" <-> "OD2"
    Residue "B GLU   95": "OE1" <-> "OE2"
    Residue "B GLU  109": "OE1" <-> "OE2"
    Residue "C ASP   99": "OD1" <-> "OD2"
    Residue "D ASP   21": "OD1" <-> "OD2"
    Residue "D GLU  129": "OE1" <-> "OE2"
    Residue "E GLU   41": "OE1" <-> "OE2"
    Residue "E GLU  129": "OE1" <-> "OE2"
    Residue "F ASP   21": "OD1" <-> "OD2"
    Residue "F ASP   93": "OD1" <-> "OD2"
    Residue "F GLU   95": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7546
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1078
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "A"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1078
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "B"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1078
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "C"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1078
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "D"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1078
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "E"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1078
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "F"
      Number of atoms: 1078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1078
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
  Time building chain proxies: 4.52, per 1000 atoms: 0.60
  Number of scatterers: 7546
  At special positions: 0
  Unit cell: (85.162, 85.162, 99.176, 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)
     S      21     16.00
     O    1596      8.00
     N    1253      7.00
     C    4676      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: 2.79
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1904

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 26 sheets defined
      3.6% alpha, 54.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'G' and resid 97 through 101
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'D' and resid 97 through 102
      removed outlier: 3.622A  pdb=" N   ASN D 102 " --> pdb=" O   VAL D  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 101
    Processing helix  chain 'F' and resid 97 through 102
      removed outlier: 3.654A  pdb=" N   ASN F 102 " --> pdb=" O   VAL F  98 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40
      removed outlier: 8.254A  pdb=" N   ILE A  29 " --> pdb=" O   ASN G   4 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   THR G   6 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   LEU A  31 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ARG G   8 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   TYR A  33 " --> pdb=" O   ARG G   8 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   SER G  10 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   ILE A 136 " --> pdb=" O   VAL A  67 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   VAL A  67 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40
      removed outlier: 8.254A  pdb=" N   ILE A  29 " --> pdb=" O   ASN G   4 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   THR G   6 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   LEU A  31 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ARG G   8 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   TYR A  33 " --> pdb=" O   ARG G   8 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   SER G  10 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 15 through 19
      removed outlier: 4.385A  pdb=" N   ILE G  49 " --> pdb=" O   SER G 113 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   SER G 113 " --> pdb=" O   ILE G  49 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   THR G  51 " --> pdb=" O   VAL G 111 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   VAL G 111 " --> pdb=" O   THR G  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 33 through 34
      removed outlier: 3.507A  pdb=" N   SER G  34 " --> pdb=" O   ASN G  39 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ASN G  39 " --> pdb=" O   SER G  34 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'G' and resid 94 through 96
      removed outlier: 3.621A  pdb=" N   GLY G  57 " --> pdb=" O   LYS G 144 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 79
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30
      removed outlier: 8.165A  pdb=" N   ILE B  29 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   THR A   6 " --> pdb=" O   ILE B  29 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   ILE B 136 " --> pdb=" O   VAL B  67 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   VAL B  67 " --> pdb=" O   ILE B 136 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 30
      removed outlier: 8.165A  pdb=" N   ILE B  29 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   THR A   6 " --> pdb=" O   ILE B  29 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 15 through 19
      removed outlier: 4.587A  pdb=" N   ILE A  49 " --> pdb=" O   SER A 113 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   SER A 113 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   THR A  51 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   VAL A 111 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 15 through 19
      removed outlier: 4.621A  pdb=" N   ILE C  49 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   SER C 113 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   THR C  51 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   VAL C 111 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   VAL C  67 " --> pdb=" O   ILE C 136 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   ILE C 136 " --> pdb=" O   VAL C  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 31
      removed outlier: 8.083A  pdb=" N   ILE C  29 " --> pdb=" O   ASN B   4 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   THR B   6 " --> pdb=" O   ILE C  29 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   LEU C  31 " --> pdb=" O   THR B   6 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG B   8 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   ILE C 136 " --> pdb=" O   VAL C  67 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   VAL C  67 " --> pdb=" O   ILE C 136 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 77 through 84
    current: chain 'C' and resid 94 through 96
    Processing sheet with id=AB3, first strand: chain 'B' and resid 15 through 19
    Processing sheet with id=AB4, first strand: chain 'B' and resid 33 through 34
      removed outlier: 3.575A  pdb=" N   ASN B  39 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 28 through 31
      removed outlier: 8.466A  pdb=" N   ILE D  29 " --> pdb=" O   ASN C   4 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   THR C   6 " --> pdb=" O   ILE D  29 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   LEU D  31 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ARG C   8 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ILE D 136 " --> pdb=" O   VAL D  67 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   VAL D  67 " --> pdb=" O   ILE D 136 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 31
      removed outlier: 8.466A  pdb=" N   ILE D  29 " --> pdb=" O   ASN C   4 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   THR C   6 " --> pdb=" O   ILE D  29 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   LEU D  31 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ARG C   8 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 34
      removed outlier: 3.591A  pdb=" N   ASN C  39 " --> pdb=" O   SER C  34 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 28 through 31
      removed outlier: 8.424A  pdb=" N   ILE E  29 " --> pdb=" O   ASN D   4 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   THR D   6 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   LEU E  31 " --> pdb=" O   THR D   6 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ARG D   8 " --> pdb=" O   LEU E  31 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   ILE E 136 " --> pdb=" O   VAL E  67 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   VAL E  67 " --> pdb=" O   ILE E 136 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 28 through 31
      removed outlier: 8.424A  pdb=" N   ILE E  29 " --> pdb=" O   ASN D   4 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   THR D   6 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   LEU E  31 " --> pdb=" O   THR D   6 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ARG D   8 " --> pdb=" O   LEU E  31 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 19
      removed outlier: 4.482A  pdb=" N   ILE D  49 " --> pdb=" O   SER D 113 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   SER D 113 " --> pdb=" O   ILE D  49 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   THR D  51 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   VAL D 111 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 33 through 34
      removed outlier: 3.501A  pdb=" N   SER D  34 " --> pdb=" O   ASN D  39 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASN D  39 " --> pdb=" O   SER D  34 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'F' and resid 28 through 30
      removed outlier: 8.400A  pdb=" N   ILE F  29 " --> pdb=" O   ASN E   4 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   THR E   6 " --> pdb=" O   ILE F  29 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY F 131 " --> pdb=" O   VAL E  11 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   ILE F 136 " --> pdb=" O   VAL F  67 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   VAL F  67 " --> pdb=" O   ILE F 136 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 28 through 30
      removed outlier: 8.400A  pdb=" N   ILE F  29 " --> pdb=" O   ASN E   4 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   THR E   6 " --> pdb=" O   ILE F  29 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY F 131 " --> pdb=" O   VAL E  11 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 15 through 19
      removed outlier: 4.239A  pdb=" N   ILE E  49 " --> pdb=" O   SER E 113 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   SER E 113 " --> pdb=" O   ILE E  49 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   THR E  51 " --> pdb=" O   VAL E 111 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   VAL E 111 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 33 through 34
      removed outlier: 3.580A  pdb=" N   ASN E  39 " --> pdb=" O   SER E  34 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'F' and resid 15 through 19
      removed outlier: 4.370A  pdb=" N   ILE F  49 " --> pdb=" O   SER F 113 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   SER F 113 " --> pdb=" O   ILE F  49 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   THR F  51 " --> pdb=" O   VAL F 111 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   VAL F 111 " --> pdb=" O   THR F  51 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 33 through 34
      removed outlier: 3.533A  pdb=" N   SER F  34 " --> pdb=" O   ASN F  39 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASN F  39 " --> pdb=" O   SER F  34 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8

    306 hydrogen bonds defined for protein.
    762 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: 2.54

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2506
        1.34 -     1.46: 1474
        1.46 -     1.58: 3615
        1.58 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 7637
  Sorted by residual:
  bond pdb=" N   VAL G   1 "
       pdb=" CA  VAL G   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.90e-02 2.77e+03 3.39e+00
  bond pdb=" N   VAL E   1 "
       pdb=" CA  VAL E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  bond pdb=" N   VAL C   1 "
       pdb=" CA  VAL C   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  bond pdb=" N   VAL B   1 "
       pdb=" CA  VAL B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.98e+00
  bond pdb=" N   VAL F   1 "
       pdb=" CA  VAL F   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.98e+00
  ... (remaining 7632 not shown)

  Histogram of bond angle deviations from ideal:
      100.69 -   106.82: 204
      106.82 -   112.94: 4494
      112.94 -   119.06: 1903
      119.06 -   125.18: 3752
      125.18 -   131.31: 56
  Bond angle restraints: 10409
  Sorted by residual:
  angle pdb=" C   ASP A  93 "
        pdb=" CA  ASP A  93 "
        pdb=" CB  ASP A  93 "
      ideal   model   delta    sigma   weight residual
     109.54  112.42   -2.88 1.84e+00 2.95e-01 2.45e+00
  angle pdb=" N   MET E  72 "
        pdb=" CA  MET E  72 "
        pdb=" C   MET E  72 "
      ideal   model   delta    sigma   weight residual
     111.36  113.00   -1.64 1.09e+00 8.42e-01 2.27e+00
  angle pdb=" N   MET D  72 "
        pdb=" CA  MET D  72 "
        pdb=" C   MET D  72 "
      ideal   model   delta    sigma   weight residual
     111.36  112.98   -1.62 1.09e+00 8.42e-01 2.20e+00
  angle pdb=" N   MET G  72 "
        pdb=" CA  MET G  72 "
        pdb=" C   MET G  72 "
      ideal   model   delta    sigma   weight residual
     111.36  112.97   -1.61 1.09e+00 8.42e-01 2.18e+00
  angle pdb=" CA  GLN A 124 "
        pdb=" C   GLN A 124 "
        pdb=" N   GLY A 125 "
      ideal   model   delta    sigma   weight residual
     114.90  116.86   -1.96 1.37e+00 5.33e-01 2.04e+00
  ... (remaining 10404 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4342
       17.95 -    35.90: 264
       35.90 -    53.85: 42
       53.85 -    71.80: 19
       71.80 -    89.75: 16
  Dihedral angle restraints: 4683
    sinusoidal: 1750
      harmonic: 2933
  Sorted by residual:
  dihedral pdb=" CA  ASP C  99 "
           pdb=" CB  ASP C  99 "
           pdb=" CG  ASP C  99 "
           pdb=" OD1 ASP C  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -91.71   61.71     1      2.00e+01 2.50e-03 1.26e+01
  dihedral pdb=" CB  GLU E  95 "
           pdb=" CG  GLU E  95 "
           pdb=" CD  GLU E  95 "
           pdb=" OE1 GLU E  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.75  -89.75     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU D 129 "
           pdb=" CG  GLU D 129 "
           pdb=" CD  GLU D 129 "
           pdb=" OE1 GLU D 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.38  -89.38     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 4680 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 758
       0.029 -    0.057: 386
       0.057 -    0.086: 38
       0.086 -    0.114: 111
       0.114 -    0.143: 30
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CA  VAL D   1 "
            pdb=" N   VAL D   1 "
            pdb=" C   VAL D   1 "
            pdb=" CB  VAL D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  VAL B   1 "
            pdb=" N   VAL B   1 "
            pdb=" C   VAL B   1 "
            pdb=" CB  VAL B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  VAL E   1 "
            pdb=" N   VAL E   1 "
            pdb=" C   VAL E   1 "
            pdb=" CB  VAL E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 1320 not shown)

  Planarity restraints: 1337
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E 142 "    0.023 2.00e-02 2.50e+03   4.65e-02 2.16e+01
        pdb=" C   THR E 142 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   THR E 142 "    0.031 2.00e-02 2.50e+03
        pdb=" N   GLN E 143 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 142 "    0.023 2.00e-02 2.50e+03   4.60e-02 2.12e+01
        pdb=" C   THR B 142 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   THR B 142 "    0.030 2.00e-02 2.50e+03
        pdb=" N   GLN B 143 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 142 "   -0.023 2.00e-02 2.50e+03   4.55e-02 2.07e+01
        pdb=" C   THR C 142 "    0.079 2.00e-02 2.50e+03
        pdb=" O   THR C 142 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   GLN C 143 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1334 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 101
        2.65 -     3.21: 6867
        3.21 -     3.77: 10358
        3.77 -     4.34: 15566
        4.34 -     4.90: 26430
  Nonbonded interactions: 59322
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  63 "
            pdb=" OG  SER G 138 "
     model   vdw
     2.082 2.440
  nonbonded pdb=" OG  SER D  63 "
            pdb=" OG  SER D 138 "
     model   vdw
     2.090 2.440
  nonbonded pdb=" OG  SER F  63 "
            pdb=" OG  SER F 138 "
     model   vdw
     2.117 2.440
  nonbonded pdb=" OG  SER E  63 "
            pdb=" OG  SER E 138 "
     model   vdw
     2.122 2.440
  nonbonded pdb=" OG  SER B  63 "
            pdb=" OG  SER B 138 "
     model   vdw
     2.146 2.440
  ... (remaining 59317 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'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:             0.010
  Extract box with map and model:          2.110
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     25.050
  Find NCS groups from input model:        0.500
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
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      :  0.002   0.035   7637  Z= 0.156
  Angle     :  0.471   3.830  10409  Z= 0.263
  Chirality :  0.044   0.143   1323
  Planarity :  0.004   0.047   1337
  Dihedral  : 14.122  89.752   2779
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.50 (0.27), residues: 1001
  helix:  None (None), residues: 0
  sheet:  0.86 (0.24), residues: 406
  loop :  1.29 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.000   HIS A 120 
   PHE   0.004   0.001   PHE E  96 
   TYR   0.004   0.001   TYR C 133 
   ARG   0.001   0.000   ARG D   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.898 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2102
  time to fit residues: 33.4427
Evaluate side-chains
  90 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.831 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2336
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
G 134 GLN
A 110 ASN
B 115 GLN
D  38 ASN
D 115 GLN
E  38 ASN
E 115 GLN
F 115 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7637  Z= 0.342
  Angle     :  0.618   5.523  10409  Z= 0.331
  Chirality :  0.050   0.177   1323
  Planarity :  0.004   0.032   1337
  Dihedral  :  7.227  74.650   1043
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  5.96 %
    Favored  : 92.80 %
  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:  0.62 (0.25), residues: 1001
  helix: -3.39 (0.54), residues: 42
  sheet:  1.02 (0.26), residues: 350
  loop :  0.44 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS C  50 
   PHE   0.012   0.002   PHE D  40 
   TYR   0.008   0.002   TYR A 133 
   ARG   0.003   0.001   ARG D   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.833 
Fit side-chains
  outliers start: 11
  outliers final: 10
  residues processed: 105
  average time/residue: 0.2037
  time to fit residues: 29.0542
Evaluate side-chains
  90 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.764 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0685
  time to fit residues: 2.3528
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 89 optimal weight:    8.9990
   chunk 96 optimal weight:    9.9990
   chunk 79 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
G 120 HIS
A 116 GLN
B 143 GLN
E  38 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7637  Z= 0.322
  Angle     :  0.573   5.763  10409  Z= 0.306
  Chirality :  0.049   0.158   1323
  Planarity :  0.003   0.034   1337
  Dihedral  :  6.938  77.898   1043
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.69 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.25), residues: 1001
  helix: -3.63 (0.46), residues: 42
  sheet:  1.07 (0.27), residues: 329
  loop :  0.38 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS F 120 
   PHE   0.011   0.001   PHE D  40 
   TYR   0.006   0.002   TYR F 133 
   ARG   0.002   0.001   ARG A   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.900 
Fit side-chains
  outliers start: 14
  outliers final: 9
  residues processed: 97
  average time/residue: 0.1775
  time to fit residues: 24.4736
Evaluate side-chains
  90 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.878 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0684
  time to fit residues: 2.3621
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 42 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0970
   chunk 84 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
E  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7637  Z= 0.145
  Angle     :  0.449   3.607  10409  Z= 0.242
  Chirality :  0.044   0.142   1323
  Planarity :  0.003   0.027   1337
  Dihedral  :  6.108  74.707   1043
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.27 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1001
  helix: -3.40 (0.52), residues: 42
  sheet:  1.26 (0.27), residues: 329
  loop :  0.50 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS B  50 
   PHE   0.005   0.001   PHE E  96 
   TYR   0.003   0.001   TYR E  33 
   ARG   0.002   0.000   ARG D   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.870 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 95
  average time/residue: 0.1660
  time to fit residues: 22.6303
Evaluate side-chains
  87 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.820 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0689
  time to fit residues: 2.2222
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0070
   chunk 31 optimal weight:    9.9990
   overall best weight:    3.2006

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

Flipped N/Q/H residues before XYZ refinement:
G 134 GLN
A 143 GLN
B  50 HIS
D 143 GLN
F  50 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7637  Z= 0.344
  Angle     :  0.583   5.710  10409  Z= 0.308
  Chirality :  0.049   0.156   1323
  Planarity :  0.003   0.035   1337
  Dihedral  :  6.637  80.392   1043
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.84 %
    Favored  : 84.25 %
  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:  0.45 (0.26), residues: 1001
  helix: -3.46 (0.50), residues: 42
  sheet:  0.92 (0.27), residues: 329
  loop :  0.32 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS F 120 
   PHE   0.009   0.001   PHE D  40 
   TYR   0.008   0.002   TYR E 133 
   ARG   0.002   0.000   ARG A   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.857 
Fit side-chains
  outliers start: 17
  outliers final: 12
  residues processed: 91
  average time/residue: 0.1819
  time to fit residues: 23.5097
Evaluate side-chains
  92 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.762 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0750
  time to fit residues: 2.8330
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 78 optimal weight:    0.1980
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0970
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7637  Z= 0.135
  Angle     :  0.437   3.325  10409  Z= 0.235
  Chirality :  0.044   0.139   1323
  Planarity :  0.003   0.026   1337
  Dihedral  :  5.872  77.877   1043
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.62 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1001
  helix: -3.29 (0.55), residues: 42
  sheet:  1.06 (0.27), residues: 329
  loop :  0.44 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS F  50 
   PHE   0.006   0.001   PHE E  96 
   TYR   0.003   0.001   TYR D  33 
   ARG   0.001   0.000   ARG A   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.717 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 88
  average time/residue: 0.1672
  time to fit residues: 21.5772
Evaluate side-chains
  84 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.826 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0681
  time to fit residues: 2.0929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 69 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0030
   overall best weight:    0.9394

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

Flipped N/Q/H residues before XYZ refinement:
G 134 GLN
G 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7637  Z= 0.146
  Angle     :  0.445   9.021  10409  Z= 0.235
  Chirality :  0.044   0.139   1323
  Planarity :  0.003   0.025   1337
  Dihedral  :  5.610  79.192   1043
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 16.54 %
    Favored  : 83.01 %
  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:  0.70 (0.26), residues: 1001
  helix: -3.19 (0.56), residues: 42
  sheet:  0.72 (0.26), residues: 364
  loop :  0.74 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS C  50 
   PHE   0.005   0.001   PHE E  96 
   TYR   0.004   0.001   TYR D  33 
   ARG   0.001   0.000   ARG F   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.855 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 79
  average time/residue: 0.1664
  time to fit residues: 19.2858
Evaluate side-chains
  76 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.853 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0726
  time to fit residues: 1.3328
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
G 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7637  Z= 0.335
  Angle     :  0.562   5.779  10409  Z= 0.297
  Chirality :  0.048   0.152   1323
  Planarity :  0.003   0.030   1337
  Dihedral  :  6.391  83.371   1043
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.42 %
    Favored  : 82.45 %
  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:  0.43 (0.26), residues: 1001
  helix: -3.30 (0.53), residues: 42
  sheet:  0.84 (0.27), residues: 329
  loop :  0.35 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS F 120 
   PHE   0.008   0.001   PHE D  40 
   TYR   0.007   0.002   TYR E 133 
   ARG   0.002   0.000   ARG A   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.850 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1865
  time to fit residues: 23.6786
Evaluate side-chains
  91 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.772 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0682
  time to fit residues: 2.1450
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 88 optimal weight:    8.9990
   chunk 90 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
G 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7637  Z= 0.179
  Angle     :  0.459   3.801  10409  Z= 0.246
  Chirality :  0.044   0.142   1323
  Planarity :  0.003   0.026   1337
  Dihedral  :  5.989  86.667   1043
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 16.54 %
    Favored  : 82.79 %
  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:  0.55 (0.26), residues: 1001
  helix: -3.21 (0.54), residues: 42
  sheet:  0.57 (0.26), residues: 364
  loop :  0.67 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.001   HIS C  50 
   PHE   0.005   0.001   PHE E  96 
   TYR   0.003   0.001   TYR G 133 
   ARG   0.001   0.000   ARG A   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.843 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1730
  time to fit residues: 19.8891
Evaluate side-chains
  80 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.827 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0705
  time to fit residues: 1.7263
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0770
   chunk 64 optimal weight:    0.2980
   chunk 97 optimal weight:    6.9990
   chunk 89 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 47 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
G 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7637  Z= 0.122
  Angle     :  0.420   3.367  10409  Z= 0.224
  Chirality :  0.043   0.135   1323
  Planarity :  0.003   0.023   1337
  Dihedral  :  5.511  89.494   1043
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 17.10 %
    Favored  : 82.56 %
  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:  0.75 (0.27), residues: 1001
  helix: -3.09 (0.57), residues: 42
  sheet:  0.73 (0.26), residues: 364
  loop :  0.79 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS C  50 
   PHE   0.005   0.001   PHE E  96 
   TYR   0.003   0.000   TYR F  33 
   ARG   0.000   0.000   ARG C   8 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.850 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 84
  average time/residue: 0.1768
  time to fit residues: 21.4564
Evaluate side-chains
  84 residues out of total 889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.819 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0699
  time to fit residues: 1.3579
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 11 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 79 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
G 134 GLN
D 102 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.113377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.105802 restraints weight = 8707.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 0.86
r_work: 0.2977 rms_B_bonded: 1.38 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7637  Z= 0.327
  Angle     :  0.549   5.560  10409  Z= 0.290
  Chirality :  0.047   0.150   1323
  Planarity :  0.003   0.027   1337
  Dihedral  :  6.140  82.654   1043
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 17.32 %
    Favored  : 82.11 %
  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:  0.52 (0.26), residues: 1001
  helix: -3.16 (0.54), residues: 42
  sheet:  0.89 (0.27), residues: 329
  loop :  0.41 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS F 120 
   PHE   0.008   0.001   PHE D  40 
   TYR   0.006   0.002   TYR E 133 
   ARG   0.002   0.000   ARG A   8 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1582.12 seconds
wall clock time: 29 minutes 44.98 seconds (1784.98 seconds total)