Starting phenix.real_space_refine
on Fri Dec  8 02:29:28 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/12_2023/6dso_8910.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/12_2023/6dso_8910.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/12_2023/6dso_8910.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/12_2023/6dso_8910.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/12_2023/6dso_8910.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/12_2023/6dso_8910.pdb"
  }
  resolution = 3.0
  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=   0.001 sd=   0.011
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      24      5.16       5
     C    4212      2.51       5
     N    1128      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "B"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "C"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "D"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "E"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "F"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "G"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "H"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "I"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "J"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "K"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "L"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
  Time building chain proxies: 4.04, per 1000 atoms: 0.61
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (128.25, 81, 54, 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      24     16.00
     O    1224      8.00
     N    1128      7.00
     C    4212      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: 2.35
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1392

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 31.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8
      removed outlier: 6.241A  pdb=" N   PHE A   2 " --> pdb=" O   PHE C   3 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   PHE C   5 " --> pdb=" O   PHE A   2 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   SER A   4 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   GLY C   7 " --> pdb=" O   SER A   4 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE A   6 " --> pdb=" O   GLY C   7 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   PHE C   2 " --> pdb=" O   PHE E   3 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   PHE E   5 " --> pdb=" O   PHE C   2 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   SER C   4 " --> pdb=" O   PHE E   5 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   GLY E   7 " --> pdb=" O   SER C   4 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ILE C   6 " --> pdb=" O   GLY E   7 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   PHE E   2 " --> pdb=" O   PHE G   3 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   PHE G   5 " --> pdb=" O   PHE E   2 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   SER E   4 " --> pdb=" O   PHE G   5 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   GLY G   7 " --> pdb=" O   SER E   4 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE E   6 " --> pdb=" O   GLY G   7 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   PHE G   2 " --> pdb=" O   PHE I   3 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   PHE I   5 " --> pdb=" O   PHE G   2 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   SER G   4 " --> pdb=" O   PHE I   5 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   GLY I   7 " --> pdb=" O   SER G   4 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE G   6 " --> pdb=" O   GLY I   7 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   PHE I   2 " --> pdb=" O   PHE K   3 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   PHE K   5 " --> pdb=" O   PHE I   2 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   SER I   4 " --> pdb=" O   PHE K   5 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   GLY K   7 " --> pdb=" O   SER I   4 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE I   6 " --> pdb=" O   GLY K   7 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21
      removed outlier: 6.332A  pdb=" N   TYR A  20 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   TYR C  20 " --> pdb=" O   THR E  21 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   TYR E  20 " --> pdb=" O   THR G  21 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   TYR G  20 " --> pdb=" O   THR I  21 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   TYR I  20 " --> pdb=" O   THR K  21 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.808A  pdb=" N   TRP A  28 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   TRP C  28 " --> pdb=" O   LYS E  29 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   TRP E  28 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   TRP G  28 " --> pdb=" O   LYS I  29 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   TRP I  28 " --> pdb=" O   LYS K  29 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 38
      removed outlier: 6.555A  pdb=" N   LYS C  33 " --> pdb=" O   TYR E  34 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   HIS E  36 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   PHE C  35 " --> pdb=" O   HIS E  36 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ARG E  38 " --> pdb=" O   PHE C  35 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA C  37 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LYS I  33 " --> pdb=" O   TYR K  34 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   HIS K  36 " --> pdb=" O   LYS I  33 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   PHE I  35 " --> pdb=" O   HIS K  36 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   ARG K  38 " --> pdb=" O   PHE I  35 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ALA I  37 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 46
    Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 53
      removed outlier: 6.145A  pdb=" N   VAL A  51 " --> pdb=" O   TRP C  52 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL C  51 " --> pdb=" O   TRP E  52 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   VAL E  51 " --> pdb=" O   TRP G  52 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   VAL G  51 " --> pdb=" O   TRP I  52 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   VAL I  51 " --> pdb=" O   TRP K  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.416A  pdb=" N   LYS A  56 " --> pdb=" O   ILE C  57 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LYS G  56 " --> pdb=" O   ILE I  57 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 65 through 68
    Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 8
      removed outlier: 6.237A  pdb=" N   PHE B   2 " --> pdb=" O   PHE D   3 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   PHE D   5 " --> pdb=" O   PHE B   2 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   SER B   4 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   GLY D   7 " --> pdb=" O   SER B   4 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ILE B   6 " --> pdb=" O   GLY D   7 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   PHE D   2 " --> pdb=" O   PHE F   3 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   PHE F   5 " --> pdb=" O   PHE D   2 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   SER D   4 " --> pdb=" O   PHE F   5 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   GLY F   7 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ILE D   6 " --> pdb=" O   GLY F   7 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   PHE F   2 " --> pdb=" O   PHE H   3 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   PHE H   5 " --> pdb=" O   PHE F   2 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   SER F   4 " --> pdb=" O   PHE H   5 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   GLY H   7 " --> pdb=" O   SER F   4 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE F   6 " --> pdb=" O   GLY H   7 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   PHE H   2 " --> pdb=" O   PHE J   3 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   PHE J   5 " --> pdb=" O   PHE H   2 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   SER H   4 " --> pdb=" O   PHE J   5 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   GLY J   7 " --> pdb=" O   SER H   4 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ILE H   6 " --> pdb=" O   GLY J   7 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   PHE J   2 " --> pdb=" O   PHE L   3 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   PHE L   5 " --> pdb=" O   PHE J   2 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   SER J   4 " --> pdb=" O   PHE L   5 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   GLY L   7 " --> pdb=" O   SER J   4 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE J   6 " --> pdb=" O   GLY L   7 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 21
      removed outlier: 6.296A  pdb=" N   TYR B  20 " --> pdb=" O   THR D  21 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   TYR D  20 " --> pdb=" O   THR F  21 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   TYR F  20 " --> pdb=" O   THR H  21 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   TYR H  20 " --> pdb=" O   THR J  21 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   TYR J  20 " --> pdb=" O   THR L  21 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 28 through 29
      removed outlier: 6.805A  pdb=" N   TRP B  28 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   TRP D  28 " --> pdb=" O   LYS F  29 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   TRP F  28 " --> pdb=" O   LYS H  29 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   TRP H  28 " --> pdb=" O   LYS J  29 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   TRP J  28 " --> pdb=" O   LYS L  29 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 38
      removed outlier: 6.566A  pdb=" N   LYS D  33 " --> pdb=" O   TYR F  34 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   HIS F  36 " --> pdb=" O   LYS D  33 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   PHE D  35 " --> pdb=" O   HIS F  36 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ARG F  38 " --> pdb=" O   PHE D  35 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ALA D  37 " --> pdb=" O   ARG F  38 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LYS J  33 " --> pdb=" O   TYR L  34 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   HIS L  36 " --> pdb=" O   LYS J  33 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   PHE J  35 " --> pdb=" O   HIS L  36 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   ARG L  38 " --> pdb=" O   PHE J  35 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA J  37 " --> pdb=" O   ARG L  38 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 46
    Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 53
      removed outlier: 6.134A  pdb=" N   VAL B  51 " --> pdb=" O   TRP D  52 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL D  51 " --> pdb=" O   TRP F  52 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL F  51 " --> pdb=" O   TRP H  52 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   VAL H  51 " --> pdb=" O   TRP J  52 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   VAL J  51 " --> pdb=" O   TRP L  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 56 through 58
      removed outlier: 6.414A  pdb=" N   LYS B  56 " --> pdb=" O   ILE D  57 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   LYS H  56 " --> pdb=" O   ILE J  57 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 68

    82 hydrogen bonds defined for protein.
    246 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: 1.91

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2142
        1.34 -     1.45: 1472
        1.45 -     1.56: 3142
        1.56 -     1.68: 0
        1.68 -     1.79: 48
  Bond restraints: 6804
  Sorted by residual:
  bond pdb=" CG  ARG E  46 "
       pdb=" CD  ARG E  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.60e+00
  bond pdb=" CG  ARG G  46 "
       pdb=" CD  ARG G  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.59e+00
  bond pdb=" CG  ARG A  46 "
       pdb=" CD  ARG A  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.58e+00
  bond pdb=" CG  ARG I  46 "
       pdb=" CD  ARG I  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.56e+00
  bond pdb=" CG  ARG K  46 "
       pdb=" CD  ARG K  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.55e+00
  ... (remaining 6799 not shown)

  Histogram of bond angle deviations from ideal:
       99.13 -   106.10: 84
      106.10 -   113.07: 3070
      113.07 -   120.04: 2424
      120.04 -   127.01: 3422
      127.01 -   133.98: 108
  Bond angle restraints: 9108
  Sorted by residual:
  angle pdb=" C   GLY B  27 "
        pdb=" N   TRP B  28 "
        pdb=" CA  TRP B  28 "
      ideal   model   delta    sigma   weight residual
     121.75  116.64    5.11 1.73e+00 3.34e-01 8.73e+00
  angle pdb=" C   GLY J  27 "
        pdb=" N   TRP J  28 "
        pdb=" CA  TRP J  28 "
      ideal   model   delta    sigma   weight residual
     121.75  116.67    5.08 1.73e+00 3.34e-01 8.63e+00
  angle pdb=" C   GLY F  27 "
        pdb=" N   TRP F  28 "
        pdb=" CA  TRP F  28 "
      ideal   model   delta    sigma   weight residual
     121.75  116.67    5.08 1.73e+00 3.34e-01 8.62e+00
  angle pdb=" C   GLY H  27 "
        pdb=" N   TRP H  28 "
        pdb=" CA  TRP H  28 "
      ideal   model   delta    sigma   weight residual
     121.75  116.67    5.08 1.73e+00 3.34e-01 8.61e+00
  angle pdb=" C   GLY C  27 "
        pdb=" N   TRP C  28 "
        pdb=" CA  TRP C  28 "
      ideal   model   delta    sigma   weight residual
     121.75  116.68    5.07 1.73e+00 3.34e-01 8.59e+00
  ... (remaining 9103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.30: 3138
        7.30 -    14.61: 483
       14.61 -    21.91: 63
       21.91 -    29.21: 0
       29.21 -    36.52: 24
  Dihedral angle restraints: 3708
    sinusoidal: 1464
      harmonic: 2244
  Sorted by residual:
  dihedral pdb=" CA  THR J  21 "
           pdb=" C   THR J  21 "
           pdb=" N   ASP J  22 "
           pdb=" CA  ASP J  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.33   19.67     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  THR D  21 "
           pdb=" C   THR D  21 "
           pdb=" N   ASP D  22 "
           pdb=" CA  ASP D  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.33   19.67     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  THR B  21 "
           pdb=" C   THR B  21 "
           pdb=" N   ASP B  22 "
           pdb=" CA  ASP B  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.34   19.66     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 3705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 240
       0.027 -    0.054: 208
       0.054 -    0.080: 134
       0.080 -    0.107: 142
       0.107 -    0.134: 20
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CA  TRP A  28 "
            pdb=" N   TRP A  28 "
            pdb=" C   TRP A  28 "
            pdb=" CB  TRP A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  TRP L  28 "
            pdb=" N   TRP L  28 "
            pdb=" C   TRP L  28 "
            pdb=" CB  TRP L  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  TRP I  28 "
            pdb=" N   TRP I  28 "
            pdb=" C   TRP I  28 "
            pdb=" CB  TRP I  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 741 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU J  66 "    0.006 2.00e-02 2.50e+03   1.30e-02 1.69e+00
        pdb=" C   GLU J  66 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   GLU J  66 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE J  67 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  66 "    0.006 2.00e-02 2.50e+03   1.30e-02 1.69e+00
        pdb=" C   GLU B  66 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   GLU B  66 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE B  67 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  66 "    0.006 2.00e-02 2.50e+03   1.30e-02 1.68e+00
        pdb=" C   GLU D  66 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   GLU D  66 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PHE D  67 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 2815
        2.93 -     3.42: 5523
        3.42 -     3.91: 11466
        3.91 -     4.41: 13343
        4.41 -     4.90: 24345
  Nonbonded interactions: 57492
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  49 "
            pdb=" NH2 ARG C  46 "
     model   vdw
     2.431 2.520
  nonbonded pdb=" O   GLY B  49 "
            pdb=" NH2 ARG D  46 "
     model   vdw
     2.435 2.520
  nonbonded pdb=" O   GLY E  49 "
            pdb=" NH2 ARG G  46 "
     model   vdw
     2.436 2.520
  nonbonded pdb=" O   GLY I  49 "
            pdb=" NH2 ARG K  46 "
     model   vdw
     2.437 2.520
  nonbonded pdb=" O   GLY C  49 "
            pdb=" NH2 ARG E  46 "
     model   vdw
     2.437 2.520
  ... (remaining 57487 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  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:          2.200
  Check model and map are aligned:         0.090
  Set scattering table:                    0.060
  Process input model:                     22.070
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.060
  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:12.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
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      :  0.009   0.048   6804  Z= 0.561
  Angle     :  0.942   5.111   9108  Z= 0.582
  Chirality :  0.057   0.134    744
  Planarity :  0.005   0.031   1236
  Dihedral  :  7.347  36.516   2316
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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: -4.46 (0.13), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.10), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.003   TRP K  17 
   HIS   0.002   0.001   HIS D  36 
   PHE   0.021   0.005   PHE E  10 
   TYR   0.015   0.003   TYR C  20 
   ARG   0.005   0.001   ARG C  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 1.6656
  time to fit residues: 337.7846
Evaluate side-chains
  133 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.681 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9360
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  40 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6804  Z= 0.168
  Angle     :  0.519   5.480   9108  Z= 0.294
  Chirality :  0.042   0.118    744
  Planarity :  0.003   0.029   1236
  Dihedral  :  4.645  17.499    900
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.93 %
    Favored  : 82.47 %
  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: -4.38 (0.14), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.11), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP H  17 
   HIS   0.001   0.001   HIS H  36 
   PHE   0.013   0.001   PHE B   5 
   TYR   0.009   0.001   TYR K  34 
   ARG   0.003   0.000   ARG J  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 0
  residues processed: 168
  average time/residue: 1.8033
  time to fit residues: 312.7459
Evaluate side-chains
  145 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.712 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9263
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0070
   chunk 22 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.5404

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
B  11 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  11 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   6804  Z= 0.245
  Angle     :  0.537   5.955   9108  Z= 0.306
  Chirality :  0.042   0.118    744
  Planarity :  0.003   0.019   1236
  Dihedral  :  4.429  15.503    900
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.84 %
    Favored  : 80.03 %
  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: -4.23 (0.15), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.22 (0.11), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP H  52 
   HIS   0.002   0.001   HIS H  36 
   PHE   0.014   0.002   PHE G   5 
   TYR   0.012   0.001   TYR A  34 
   ARG   0.003   0.001   ARG G  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 1
  residues processed: 160
  average time/residue: 1.7956
  time to fit residues: 296.5614
Evaluate side-chains
  145 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.715 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 1.0489
  time to fit residues: 2.0103
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    0.0770
   chunk 49 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0000
   chunk 69 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.6146

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
B  11 GLN
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  45 GLN
** K  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  11 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   6804  Z= 0.252
  Angle     :  0.540   6.087   9108  Z= 0.306
  Chirality :  0.042   0.120    744
  Planarity :  0.002   0.023   1236
  Dihedral  :  4.393  15.832    900
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.27 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.15), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP G  17 
   HIS   0.002   0.001   HIS L  36 
   PHE   0.016   0.002   PHE F  67 
   TYR   0.012   0.001   TYR F  34 
   ARG   0.006   0.001   ARG K  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 2
  residues processed: 164
  average time/residue: 1.7251
  time to fit residues: 292.2734
Evaluate side-chains
  155 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.632 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 1.0285
  time to fit residues: 3.0536
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
B  11 GLN
B  40 ASN
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  40 ASN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  40 ASN
G  45 GLN
K  40 ASN
** L  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
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      :  0.009   0.052   6804  Z= 0.603
  Angle     :  0.720   5.483   9108  Z= 0.410
  Chirality :  0.047   0.129    744
  Planarity :  0.004   0.032   1236
  Dihedral  :  5.049  14.888    900
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 19.62 %
    Favored  : 76.04 %
  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: -4.18 (0.15), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP A  17 
   HIS   0.005   0.002   HIS L  36 
   PHE   0.022   0.003   PHE E   3 
   TYR   0.018   0.002   TYR B  34 
   ARG   0.012   0.001   ARG K  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 6
  residues processed: 160
  average time/residue: 1.9540
  time to fit residues: 323.6155
Evaluate side-chains
  155 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 149
  time to evaluate  : 0.737 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 1
  residues processed: 5
  average time/residue: 0.7394
  time to fit residues: 4.9559
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
B  11 GLN
B  45 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  45 GLN
** L  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6804  Z= 0.187
  Angle     :  0.545   5.635   9108  Z= 0.306
  Chirality :  0.042   0.133    744
  Planarity :  0.003   0.027   1236
  Dihedral  :  4.402  15.044    900
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 21.53 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP E  28 
   HIS   0.002   0.001   HIS L  36 
   PHE   0.016   0.001   PHE F  67 
   TYR   0.015   0.001   TYR F  34 
   ARG   0.003   0.000   ARG J  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 1
  residues processed: 162
  average time/residue: 1.7287
  time to fit residues: 288.6938
Evaluate side-chains
  151 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.708 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 1.3226
  time to fit residues: 2.2054
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 58 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
B  45 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  45 GLN
** H  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  45 GLN
** L  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.050   6804  Z= 0.588
  Angle     :  0.720   7.673   9108  Z= 0.406
  Chirality :  0.048   0.121    744
  Planarity :  0.004   0.036   1236
  Dihedral  :  4.972  14.559    900
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.74 %
    Favored  : 74.65 %
  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: -4.37 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP A  17 
   HIS   0.005   0.002   HIS L  36 
   PHE   0.020   0.003   PHE E   3 
   TYR   0.015   0.002   TYR B  34 
   ARG   0.014   0.001   ARG K  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 3
  residues processed: 152
  average time/residue: 1.8987
  time to fit residues: 297.8119
Evaluate side-chains
  150 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 147
  time to evaluate  : 0.792 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 1.1231
  time to fit residues: 4.4621
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
B  45 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  11 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6804  Z= 0.188
  Angle     :  0.556   6.865   9108  Z= 0.311
  Chirality :  0.043   0.123    744
  Planarity :  0.002   0.025   1236
  Dihedral  :  4.406  14.680    900
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 25.00 %
    Favored  : 73.78 %
  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: -4.28 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP E  28 
   HIS   0.002   0.001   HIS H  36 
   PHE   0.016   0.001   PHE F  67 
   TYR   0.012   0.001   TYR D  34 
   ARG   0.004   0.000   ARG J  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 149
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 0
  residues processed: 150
  average time/residue: 1.8651
  time to fit residues: 288.6913
Evaluate side-chains
  143 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.726 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9530
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 68 optimal weight:    0.1980
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  45 GLN
** L  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6804  Z= 0.287
  Angle     :  0.602   6.979   9108  Z= 0.334
  Chirality :  0.043   0.121    744
  Planarity :  0.003   0.038   1236
  Dihedral  :  4.536  14.901    900
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 24.83 %
    Favored  : 73.78 %
  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: -4.31 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP B  17 
   HIS   0.002   0.001   HIS L  36 
   PHE   0.016   0.001   PHE F  67 
   TYR   0.015   0.001   TYR F  34 
   ARG   0.006   0.001   ARG F  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 2
  residues processed: 150
  average time/residue: 1.8984
  time to fit residues: 293.6598
Evaluate side-chains
  147 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 145
  time to evaluate  : 0.766 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 1.0702
  time to fit residues: 3.2333
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6804  Z= 0.233
  Angle     :  0.594   7.076   9108  Z= 0.328
  Chirality :  0.043   0.123    744
  Planarity :  0.002   0.025   1236
  Dihedral  :  4.497  15.164    900
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 26.91 %
    Favored  : 72.92 %
  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: -4.29 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP H  28 
   HIS   0.002   0.001   HIS H  36 
   PHE   0.014   0.001   PHE F  67 
   TYR   0.011   0.001   TYR D  34 
   ARG   0.003   0.000   ARG J  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 150
  average time/residue: 1.7915
  time to fit residues: 277.4032
Evaluate side-chains
  146 residues out of total 576 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.731 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9474
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0970
   chunk 50 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   overall best weight:    1.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  40 ASN
** L  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.106046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.092531 restraints weight = 10070.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.62
r_work: 0.3542 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6804  Z= 0.260
  Angle     :  0.613   7.166   9108  Z= 0.339
  Chirality :  0.043   0.123    744
  Planarity :  0.002   0.024   1236
  Dihedral  :  4.607  15.156    900
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 27.08 %
    Favored  : 72.57 %
  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: -4.29 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP B  17 
   HIS   0.002   0.001   HIS L  36 
   PHE   0.016   0.001   PHE F  67 
   TYR   0.011   0.001   TYR D  34 
   ARG   0.003   0.000   ARG J  46 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4355.14 seconds
wall clock time: 78 minutes 27.77 seconds (4707.77 seconds total)