Starting phenix.real_space_refine
on Wed Mar 12 13:49:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zrh_60396/03_2025/8zrh_60396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zrh_60396/03_2025/8zrh_60396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zrh_60396/03_2025/8zrh_60396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zrh_60396/03_2025/8zrh_60396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zrh_60396/03_2025/8zrh_60396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zrh_60396/03_2025/8zrh_60396.cif"
  }
  resolution = 3.6
  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=   0.004 sd=   0.044
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      35      5.16       5
     C    5151      2.51       5
     N    1357      2.21       5
     O    1493      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8036
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1111
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 11, 'TRANS': 127}
    Chain: "A"
      Number of atoms: 1119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1119
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 11, 'TRANS': 128}
    Chain: "D"
      Number of atoms: 1045
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1045
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 10, 'TRANS': 119}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1119
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 11, 'TRANS': 128}
    Chain: "h"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 941
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "l"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 880
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106}
    Chain: "H"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 941
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "L"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 880
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106}
  Time building chain proxies: 4.76, per 1000 atoms: 0.59
  Number of scatterers: 8036
  At special positions: 0
  Unit cell: (110.622, 120.288, 123.51, 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      35     16.00
     O    1493      8.00
     N    1357      7.00
     C    5151      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS h  22 " - pdb=" SG  CYS h  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS l  23 " - pdb=" SG  CYS l  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  93 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 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:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      44.6% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'B' and resid 12 through 18
      removed outlier: 3.850A  pdb=" N   LEU B  16 " --> pdb=" O   SER B  12 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE B  18 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 43
      removed outlier: 6.667A  pdb=" N   GLU B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ALA B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 75
      removed outlier: 3.799A  pdb=" N   LEU B  55 " --> pdb=" O   HIS B  51 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LEU B  60 " --> pdb=" O   ARG B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 110
      removed outlier: 3.745A  pdb=" N   ARG B  82 " --> pdb=" O   ASP B  78 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   MET B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   GLY B  94 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LYS B  96 " --> pdb=" O   ASN B  92 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE B  97 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 127
    Processing helix  chain 'A' and resid 12 through 17
    Processing helix  chain 'A' and resid 20 through 24
      removed outlier: 3.783A  pdb=" N   PHE A  24 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 44
      removed outlier: 3.846A  pdb=" N   LEU A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU A  37 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ARG A  39 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   GLU A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ALA A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 75
      removed outlier: 3.597A  pdb=" N   ARG A  56 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 92
      removed outlier: 3.786A  pdb=" N   ARG A  82 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 4.312A  pdb=" N   ILE A  97 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 4.021A  pdb=" N   GLY A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   VAL A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TRP A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 10
    Processing helix  chain 'D' and resid 12 through 18
    Processing helix  chain 'D' and resid 19 through 24
      removed outlier: 6.373A  pdb=" N   ASP D  22 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 39
      removed outlier: 3.638A  pdb=" N   ASP D  32 " --> pdb=" O   ARG D  28 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   THR D  33 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA D  34 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.751A  pdb=" N   LEU D  55 " --> pdb=" O   HIS D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 92
      removed outlier: 4.080A  pdb=" N   ARG D  82 " --> pdb=" O   ASP D  78 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU D  83 " --> pdb=" O   PRO D  79 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   LEU D  84 " --> pdb=" O   ALA D  80 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL D  85 " --> pdb=" O   SER D  81 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR D  88 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 110
      removed outlier: 3.736A  pdb=" N   CYS D 107 " --> pdb=" O   PHE D 103 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU D 108 " --> pdb=" O   HIS D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 128
      removed outlier: 3.869A  pdb=" N   GLY D 123 " --> pdb=" O   LEU D 119 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL D 124 " --> pdb=" O   VAL D 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 19
      removed outlier: 4.008A  pdb=" N   LEU C  19 " --> pdb=" O   LEU C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 24
    Processing helix  chain 'C' and resid 26 through 38
      removed outlier: 3.672A  pdb=" N   LEU C  30 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 44
    Processing helix  chain 'C' and resid 49 through 75
      removed outlier: 3.767A  pdb=" N   LEU C  60 " --> pdb=" O   ARG C  56 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   CYS C  61 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   TRP C  62 " --> pdb=" O   ALA C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 91
      removed outlier: 3.610A  pdb=" N   LEU C  84 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 111
      removed outlier: 4.323A  pdb=" N   ILE C  97 " --> pdb=" O   MET C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 128
      removed outlier: 3.504A  pdb=" N   VAL C 115 " --> pdb=" O   GLY C 111 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL C 120 " --> pdb=" O   LEU C 116 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR C 128 " --> pdb=" O   VAL C 124 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 28 through 32
    Processing helix  chain 'h' and resid 87 through 91
      removed outlier: 3.749A  pdb=" N   THR h  91 " --> pdb=" O   ALA h  88 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 84 through 88
      removed outlier: 4.144A  pdb=" N   VAL l  88 " --> pdb=" O   ALA l  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.750A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 84 through 88
      removed outlier: 4.143A  pdb=" N   VAL L  88 " --> pdb=" O   ALA L  85 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'h' and resid 3 through 7
      removed outlier: 4.121A  pdb=" N   GLN h   3 " --> pdb=" O   SER h  25 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER h  25 " --> pdb=" O   GLN h   3 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU h  81 " --> pdb=" O   LEU h  20 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   CYS h  22 " --> pdb=" O   LEU h  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'h' and resid 10 through 12
      removed outlier: 7.099A  pdb=" N   MET h  34 " --> pdb=" O   TYR h  50 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   TYR h  50 " --> pdb=" O   MET h  34 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   TRP h  36 " --> pdb=" O   LEU h  48 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TYR h  50 " --> pdb=" O   ASP h  59 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP h  59 " --> pdb=" O   TYR h  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'h' and resid 10 through 12
    Processing sheet with id=AA4, first strand: chain 'l' and resid 4 through 7
      removed outlier: 3.574A  pdb=" N   PHE l  76 " --> pdb=" O   CYS l  23 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR l  77 " --> pdb=" O   SER l  70 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER l  70 " --> pdb=" O   THR l  77 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'l' and resid 10 through 12
      removed outlier: 3.695A  pdb=" N   LEU l  11 " --> pdb=" O   LYS l 108 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLU l 110 " --> pdb=" O   LEU l  11 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   MET l  94 " --> pdb=" O   SER l  39 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER l  39 " --> pdb=" O   MET l  94 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   PHE l  38 " --> pdb=" O   TYR l  54 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   TYR l  54 " --> pdb=" O   PHE l  38 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   TRP l  40 " --> pdb=" O   LEU l  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'l' and resid 10 through 12
      removed outlier: 3.695A  pdb=" N   LEU l  11 " --> pdb=" O   LYS l 108 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLU l 110 " --> pdb=" O   LEU l  11 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR l 102 " --> pdb=" O   GLN l  95 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
      removed outlier: 4.120A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU H  81 " --> pdb=" O   LEU H  20 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   CYS H  22 " --> pdb=" O   LEU H  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 7.100A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TYR H  50 " --> pdb=" O   ASP H  59 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP H  59 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.574A  pdb=" N   PHE L  76 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR L  77 " --> pdb=" O   SER L  70 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER L  70 " --> pdb=" O   THR L  77 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.696A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 108 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU L 110 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   MET L  94 " --> pdb=" O   SER L  39 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER L  39 " --> pdb=" O   MET L  94 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   PHE L  38 " --> pdb=" O   TYR L  54 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   TYR L  54 " --> pdb=" O   PHE L  38 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   TRP L  40 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.696A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 108 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU L 110 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   THR L 102 " --> pdb=" O   GLN L  95 " (cutoff:3.500A)

    403 hydrogen bonds defined for protein.
    1068 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: 1.95

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1311
        1.30 -     1.43: 2339
        1.43 -     1.56: 4553
        1.56 -     1.69: 3
        1.69 -     1.82: 51
  Bond restraints: 8257
  Sorted by residual:
  bond pdb=" C   LEU C  65 "
       pdb=" N   MET C  66 "
    ideal  model  delta    sigma   weight residual
    1.335  1.226  0.109 1.38e-02 5.25e+03 6.22e+01
  bond pdb=" C   GLY h  26 "
       pdb=" N   PHE h  27 "
    ideal  model  delta    sigma   weight residual
    1.330  1.231  0.099 1.26e-02 6.30e+03 6.21e+01
  bond pdb=" C   GLY H  26 "
       pdb=" N   PHE H  27 "
    ideal  model  delta    sigma   weight residual
    1.330  1.231  0.099 1.26e-02 6.30e+03 6.18e+01
  bond pdb=" C   LEU C  68 "
       pdb=" N   ALA C  69 "
    ideal  model  delta    sigma   weight residual
    1.335  1.437 -0.102 1.31e-02 5.83e+03 6.05e+01
  bond pdb=" C   SER A 106 "
       pdb=" N   CYS A 107 "
    ideal  model  delta    sigma   weight residual
    1.334  1.427 -0.093 1.23e-02 6.61e+03 5.70e+01
  ... (remaining 8252 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 10459
        1.69 -     3.38: 628
        3.38 -     5.07: 132
        5.07 -     6.76: 26
        6.76 -     8.44: 6
  Bond angle restraints: 11251
  Sorted by residual:
  angle pdb=" O   LEU C  65 "
        pdb=" C   LEU C  65 "
        pdb=" N   MET C  66 "
      ideal   model   delta    sigma   weight residual
     122.15  115.26    6.89 1.14e+00 7.69e-01 3.65e+01
  angle pdb=" O   ASN C  67 "
        pdb=" C   ASN C  67 "
        pdb=" N   LEU C  68 "
      ideal   model   delta    sigma   weight residual
     122.12  115.90    6.22 1.06e+00 8.90e-01 3.44e+01
  angle pdb=" N   GLU A   8 "
        pdb=" CA  GLU A   8 "
        pdb=" C   GLU A   8 "
      ideal   model   delta    sigma   weight residual
     113.50  106.34    7.16 1.23e+00 6.61e-01 3.39e+01
  angle pdb=" O   SER D  74 "
        pdb=" C   SER D  74 "
        pdb=" N   ASN D  75 "
      ideal   model   delta    sigma   weight residual
     122.09  115.90    6.19 1.08e+00 8.57e-01 3.28e+01
  angle pdb=" CA  LEU C  65 "
        pdb=" C   LEU C  65 "
        pdb=" N   MET C  66 "
      ideal   model   delta    sigma   weight residual
     117.39  124.29   -6.90 1.24e+00 6.50e-01 3.10e+01
  ... (remaining 11246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 4182
       17.68 -    35.37: 513
       35.37 -    53.05: 133
       53.05 -    70.73: 18
       70.73 -    88.42: 2
  Dihedral angle restraints: 4848
    sinusoidal: 1904
      harmonic: 2944
  Sorted by residual:
  dihedral pdb=" CA  PRO D   5 "
           pdb=" C   PRO D   5 "
           pdb=" N   TYR D   6 "
           pdb=" CA  TYR D   6 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.59  -18.41     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  GLN h  39 "
           pdb=" C   GLN h  39 "
           pdb=" N   VAL h  40 "
           pdb=" CA  VAL h  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.69   16.31     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  GLN H  39 "
           pdb=" C   GLN H  39 "
           pdb=" N   VAL H  40 "
           pdb=" CA  VAL H  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.82   16.18     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 4845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 854
       0.041 -    0.083: 213
       0.083 -    0.124: 123
       0.124 -    0.165: 26
       0.165 -    0.207: 14
  Chirality restraints: 1230
  Sorted by residual:
  chirality pdb=" CA  GLN l  95 "
            pdb=" N   GLN l  95 "
            pdb=" C   GLN l  95 "
            pdb=" CB  GLN l  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  GLN L  95 "
            pdb=" N   GLN L  95 "
            pdb=" C   GLN L  95 "
            pdb=" CB  GLN L  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  LEU D  15 "
            pdb=" N   LEU D  15 "
            pdb=" C   LEU D  15 "
            pdb=" CB  LEU D  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.38e-01
  ... (remaining 1227 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR L  14 "   -0.074 5.00e-02 4.00e+02   1.08e-01 1.86e+01
        pdb=" N   PRO L  15 "    0.186 5.00e-02 4.00e+02
        pdb=" CA  PRO L  15 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO L  15 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 137 "    0.060 5.00e-02 4.00e+02   8.79e-02 1.24e+01
        pdb=" N   PRO A 138 "   -0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO A 138 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 138 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  56 "   -0.250 9.50e-02 1.11e+02   1.12e-01 7.70e+00
        pdb=" NE  ARG C  56 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  56 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  56 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  56 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.89: 3325
        2.89 -     3.39: 7856
        3.39 -     3.89: 12376
        3.89 -     4.40: 13430
        4.40 -     4.90: 22346
  Nonbonded interactions: 59333
  Sorted by model distance:
  nonbonded pdb=" O   ASN B  67 "
            pdb=" OG1 THR B  70 "
     model   vdw
     2.383 3.040
  nonbonded pdb=" O   ASP h 102 "
            pdb=" OG  SER h 103 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" O   ASP H 102 "
            pdb=" OG  SER H 103 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" OG1 THR h  49 "
            pdb=" O   ASP h  59 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" OG1 THR H  49 "
            pdb=" O   ASP H  59 "
     model   vdw
     2.397 3.040
  ... (remaining 59328 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 40 or resid 50 through 141))
  selection = (chain 'B' and (resid 3 through 40 or resid 50 through 141))
  selection = (chain 'C' and (resid 3 through 40 or resid 50 through 141))
  selection = chain 'D'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'h'
}
ncs_group {
  reference = chain 'L'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     19.830
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6713
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      :  0.007   0.109   8257  Z= 0.480
  Angle     :  0.928   8.445  11251  Z= 0.631
  Chirality :  0.052   0.207   1230
  Planarity :  0.008   0.112   1443
  Dihedral  : 16.052  88.418   2946
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.80 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 29.55 %
    Favored  : 68.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.27), residues: 1001
  helix:  0.89 (0.27), residues: 346
  sheet:  1.00 (0.42), residues: 162
  loop : -0.30 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 102 
 HIS   0.005   0.001   HIS A 104 
 PHE   0.029   0.002   PHE B 110 
 TYR   0.017   0.002   TYR B   6 
 ARG   0.004   0.001   ARG l  97 

*********************** 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
  308 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 292
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 LEU cc_start: 0.7070 (mt) cc_final: 0.6780 (mt)
REVERT: B   57 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7922 (mm-40)
REVERT: B   93 MET cc_start: 0.7641 (mtp) cc_final: 0.7216 (mtm)
REVERT: B  127 ARG cc_start: 0.3549 (tpt170) cc_final: 0.3161 (tmt170)
REVERT: A   30 LEU cc_start: 0.8373 (mp) cc_final: 0.8086 (mp)
REVERT: A  107 CYS cc_start: 0.8189 (t) cc_final: 0.7437 (t)
REVERT: A  108 LEU cc_start: 0.8185 (mt) cc_final: 0.7891 (mt)
REVERT: D   59 ILE cc_start: 0.8184 (mm) cc_final: 0.7840 (mm)
REVERT: D  107 CYS cc_start: 0.7752 (m) cc_final: 0.7085 (m)
REVERT: C  118 TYR cc_start: 0.7504 (t80) cc_final: 0.7056 (t80)
REVERT: h    7 SER cc_start: 0.6519 (m) cc_final: 0.6239 (t)
REVERT: h   50 TYR cc_start: 0.5457 (p90) cc_final: 0.4753 (p90)
REVERT: H   31 LYS cc_start: 0.7844 (mttt) cc_final: 0.7548 (mttt)
REVERT: H   50 TYR cc_start: 0.7102 (p90) cc_final: 0.6734 (p90)
REVERT: H   83 MET cc_start: 0.6271 (mtm) cc_final: 0.5911 (mtm)
  outliers start: 16
  outliers final: 3
  residues processed: 301
  average time/residue: 0.1920
  time to fit residues: 78.3309
Evaluate side-chains
  275 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 272
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain h residue  106 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0980
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 104 HIS
D  51 HIS
** D  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.151885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.132501 restraints weight = 17915.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.136344 restraints weight = 10261.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.138890 restraints weight = 6653.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8257  Z= 0.196
  Angle     :  0.667   8.527  11251  Z= 0.345
  Chirality :  0.043   0.241   1230
  Planarity :  0.006   0.059   1443
  Dihedral  :  4.765  52.302   1122
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.60 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 23.30 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.76 (0.27), residues: 1001
  helix:  1.42 (0.27), residues: 363
  sheet:  0.30 (0.37), residues: 204
  loop : -0.08 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 102 
 HIS   0.007   0.002   HIS D  51 
 PHE   0.018   0.002   PHE H  27 
 TYR   0.022   0.002   TYR A  88 
 ARG   0.004   0.001   ARG C  56 

*********************** 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
  349 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 296
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7929 (mm-40)
REVERT: B   62 TRP cc_start: 0.8096 (t-100) cc_final: 0.7881 (t-100)
REVERT: B   93 MET cc_start: 0.7837 (mtp) cc_final: 0.7355 (mtm)
REVERT: B  112 ARG cc_start: 0.7351 (tpp-160) cc_final: 0.7147 (mmt-90)
REVERT: A  107 CYS cc_start: 0.8075 (t) cc_final: 0.7503 (t)
REVERT: C   57 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7746 (mp10)
REVERT: C   83 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5984 (mp0)
REVERT: C  101 LEU cc_start: 0.8632 (mm) cc_final: 0.8430 (mm)
REVERT: h    7 SER cc_start: 0.6726 (m) cc_final: 0.6390 (t)
REVERT: h   19 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7855 (ptp-170)
REVERT: h   64 VAL cc_start: 0.7253 (m) cc_final: 0.6937 (p)
REVERT: h   83 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.5900 (mpp)
REVERT: H   31 LYS cc_start: 0.7873 (mttt) cc_final: 0.7631 (mttt)
REVERT: H   50 TYR cc_start: 0.7352 (p90) cc_final: 0.7151 (p90)
REVERT: H  108 SER cc_start: 0.8052 (p) cc_final: 0.7832 (p)
  outliers start: 53
  outliers final: 27
  residues processed: 317
  average time/residue: 0.1753
  time to fit residues: 75.8137
Evaluate side-chains
  300 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 270
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LYS
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue  141 SER
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain D residue   51 HIS
Chi-restraints excluded: chain D residue   67 ASN
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain h residue   83 MET
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain l residue   68 SER
Chi-restraints excluded: chain H residue   48 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   28 THR
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   75 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0770
   chunk 60 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
D  51 HIS
D  52 HIS
** D  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
l  50 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.149068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.129308 restraints weight = 17987.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.133150 restraints weight = 10430.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.135775 restraints weight = 6856.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8257  Z= 0.180
  Angle     :  0.640  11.133  11251  Z= 0.321
  Chirality :  0.042   0.191   1230
  Planarity :  0.005   0.056   1443
  Dihedral  :  4.453  49.381   1118
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.10 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 25.91 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.27), residues: 1001
  helix:  1.57 (0.27), residues: 363
  sheet:  0.12 (0.36), residues: 212
  loop : -0.08 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H 109 
 HIS   0.014   0.001   HIS D  51 
 PHE   0.018   0.002   PHE B  23 
 TYR   0.043   0.002   TYR A  88 
 ARG   0.005   0.000   ARG L  66 

*********************** 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
  318 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 272
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7949 (mm-40)
REVERT: B   62 TRP cc_start: 0.8084 (t-100) cc_final: 0.7835 (t-100)
REVERT: B   93 MET cc_start: 0.7796 (mtp) cc_final: 0.7293 (mtt)
REVERT: A   72 VAL cc_start: 0.8448 (t) cc_final: 0.8221 (p)
REVERT: D   61 CYS cc_start: 0.8772 (t) cc_final: 0.8360 (m)
REVERT: D  102 TRP cc_start: 0.8283 (t-100) cc_final: 0.8037 (t-100)
REVERT: C   57 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7829 (mp10)
REVERT: C   83 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6005 (mp0)
REVERT: C  118 TYR cc_start: 0.7239 (t80) cc_final: 0.6752 (t80)
REVERT: h    7 SER cc_start: 0.6779 (m) cc_final: 0.6475 (t)
REVERT: h   13 GLN cc_start: 0.7571 (tm-30) cc_final: 0.6879 (tm-30)
REVERT: h   64 VAL cc_start: 0.7285 (m) cc_final: 0.6983 (p)
REVERT: h   95 PHE cc_start: 0.6371 (m-80) cc_final: 0.6153 (m-80)
REVERT: l   29 LEU cc_start: 0.8328 (mt) cc_final: 0.7749 (mt)
REVERT: l   31 HIS cc_start: 0.6811 (t-90) cc_final: 0.6297 (t-90)
REVERT: l   33 ASN cc_start: 0.8268 (t0) cc_final: 0.7992 (t0)
REVERT: l   38 PHE cc_start: 0.7289 (t80) cc_final: 0.7087 (m-80)
REVERT: H   18 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7900 (mt)
REVERT: L   84 GLU cc_start: 0.7321 (pm20) cc_final: 0.6401 (pm20)
  outliers start: 46
  outliers final: 31
  residues processed: 294
  average time/residue: 0.1842
  time to fit residues: 73.8639
Evaluate side-chains
  299 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 265
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain D residue   51 HIS
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   67 ASN
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain C residue    6 TYR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   57 GLN
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain h residue   84 ASN
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   28 THR
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   90 VAL
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 89 optimal weight:    7.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
D  51 HIS
** D  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.145360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.125502 restraints weight = 17990.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.129312 restraints weight = 10311.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.131937 restraints weight = 6753.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8257  Z= 0.216
  Angle     :  0.659  13.608  11251  Z= 0.331
  Chirality :  0.042   0.211   1230
  Planarity :  0.005   0.059   1443
  Dihedral  :  4.523  49.971   1118
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.60 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 26.48 %
    Favored  : 67.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.74 (0.27), residues: 1001
  helix:  1.54 (0.27), residues: 357
  sheet:  0.30 (0.37), residues: 192
  loop : -0.20 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  47 
 HIS   0.009   0.001   HIS D  51 
 PHE   0.028   0.002   PHE D  24 
 TYR   0.052   0.002   TYR A  88 
 ARG   0.003   0.000   ARG L  59 

*********************** 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
  323 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 272
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7980 (mm-40)
REVERT: B   62 TRP cc_start: 0.8062 (t-100) cc_final: 0.7640 (t-100)
REVERT: B   93 MET cc_start: 0.7869 (mtp) cc_final: 0.7437 (mtm)
REVERT: B  112 ARG cc_start: 0.7432 (tpp-160) cc_final: 0.7224 (mmt-90)
REVERT: A    8 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7291 (tp30)
REVERT: A   53 THR cc_start: 0.7523 (p) cc_final: 0.7049 (t)
REVERT: A   55 LEU cc_start: 0.8657 (tp) cc_final: 0.8305 (tt)
REVERT: A  107 CYS cc_start: 0.7654 (t) cc_final: 0.7073 (t)
REVERT: A  108 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8233 (pp)
REVERT: D   61 CYS cc_start: 0.8663 (t) cc_final: 0.8155 (m)
REVERT: D  102 TRP cc_start: 0.8344 (t-100) cc_final: 0.8141 (t-100)
REVERT: C   83 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6096 (mp0)
REVERT: C   87 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.7239 (p)
REVERT: h    7 SER cc_start: 0.6783 (m) cc_final: 0.6443 (t)
REVERT: h   13 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7109 (tm-30)
REVERT: h   64 VAL cc_start: 0.7216 (m) cc_final: 0.6946 (p)
REVERT: h   95 PHE cc_start: 0.6374 (m-80) cc_final: 0.6151 (m-80)
REVERT: l   29 LEU cc_start: 0.8285 (mt) cc_final: 0.7833 (mt)
REVERT: l   31 HIS cc_start: 0.6831 (t-90) cc_final: 0.6286 (t-90)
REVERT: l   33 ASN cc_start: 0.8295 (t0) cc_final: 0.8032 (t0)
REVERT: H   50 TYR cc_start: 0.7368 (p90) cc_final: 0.7127 (p90)
REVERT: L   84 GLU cc_start: 0.7192 (pm20) cc_final: 0.6130 (pm20)
  outliers start: 51
  outliers final: 37
  residues processed: 293
  average time/residue: 0.1828
  time to fit residues: 73.4323
Evaluate side-chains
  306 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 265
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain D residue   51 HIS
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   67 ASN
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  107 CYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain h residue   84 ASN
Chi-restraints excluded: chain h residue  108 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain l residue   77 THR
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 89 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
D  51 HIS
H  35 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.145109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.125134 restraints weight = 17663.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.128818 restraints weight = 10396.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.131334 restraints weight = 6955.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8257  Z= 0.173
  Angle     :  0.637   9.325  11251  Z= 0.314
  Chirality :  0.041   0.190   1230
  Planarity :  0.005   0.059   1443
  Dihedral  :  4.442  50.193   1118
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.80 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 28.52 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.58 (0.27), residues: 1001
  helix:  1.47 (0.27), residues: 363
  sheet:  0.02 (0.35), residues: 210
  loop : -0.27 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP H  47 
 HIS   0.006   0.001   HIS D  51 
 PHE   0.023   0.002   PHE D  24 
 TYR   0.048   0.002   TYR A  88 
 ARG   0.006   0.000   ARG H  67 

*********************** 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
  315 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 272
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7909 (mm-40)
REVERT: B   93 MET cc_start: 0.7811 (mtp) cc_final: 0.7405 (mtm)
REVERT: A  107 CYS cc_start: 0.7671 (t) cc_final: 0.7075 (t)
REVERT: A  108 LEU cc_start: 0.8383 (pp) cc_final: 0.8158 (pp)
REVERT: D   61 CYS cc_start: 0.8620 (t) cc_final: 0.8088 (m)
REVERT: D   97 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7702 (tt)
REVERT: D  102 TRP cc_start: 0.8317 (t-100) cc_final: 0.8095 (t-100)
REVERT: C   64 GLU cc_start: 0.7151 (tt0) cc_final: 0.6887 (mt-10)
REVERT: C   72 VAL cc_start: 0.8987 (t) cc_final: 0.8732 (p)
REVERT: C   83 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6143 (mp0)
REVERT: h    7 SER cc_start: 0.6771 (m) cc_final: 0.6383 (t)
REVERT: h   13 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7091 (tm-30)
REVERT: h   64 VAL cc_start: 0.7208 (m) cc_final: 0.6946 (p)
REVERT: h   95 PHE cc_start: 0.6335 (m-80) cc_final: 0.6105 (m-80)
REVERT: l   31 HIS cc_start: 0.6796 (t-90) cc_final: 0.6344 (t-90)
REVERT: l   33 ASN cc_start: 0.8359 (t0) cc_final: 0.8129 (t0)
REVERT: l   38 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7044 (m-10)
REVERT: H   18 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7873 (mt)
REVERT: H   59 ASP cc_start: 0.7881 (t0) cc_final: 0.7634 (t0)
REVERT: L   59 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7916 (mtp180)
REVERT: L   84 GLU cc_start: 0.7231 (pm20) cc_final: 0.6117 (pm20)
  outliers start: 43
  outliers final: 31
  residues processed: 290
  average time/residue: 0.1751
  time to fit residues: 69.1967
Evaluate side-chains
  302 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 267
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   67 ASN
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  107 CYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   83 GLU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  121 SER
Chi-restraints excluded: chain h residue  108 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   38 PHE
Chi-restraints excluded: chain l residue   57 SER
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain L residue   90 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0370
   chunk 19 optimal weight:    0.5980
   chunk 33 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    1.3062

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

Flipped N/Q/H residues before XYZ refinement:
h  57 ASN
H  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.141673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.121360 restraints weight = 17730.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.124962 restraints weight = 10426.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.127336 restraints weight = 7032.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   8257  Z= 0.224
  Angle     :  0.650   8.849  11251  Z= 0.327
  Chirality :  0.043   0.179   1230
  Planarity :  0.005   0.060   1443
  Dihedral  :  4.532  52.917   1118
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.80 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 29.89 %
    Favored  : 64.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.51 (0.27), residues: 1001
  helix:  1.43 (0.27), residues: 364
  sheet: -0.09 (0.36), residues: 210
  loop : -0.29 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP H  47 
 HIS   0.006   0.001   HIS C 104 
 PHE   0.021   0.002   PHE C  23 
 TYR   0.045   0.002   TYR A  88 
 ARG   0.007   0.001   ARG L  24 

*********************** 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
  325 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 275
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 GLU cc_start: 0.8264 (mp0) cc_final: 0.8028 (mp0)
REVERT: B   57 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7955 (mm-40)
REVERT: B   62 TRP cc_start: 0.8233 (t-100) cc_final: 0.7935 (t-100)
REVERT: B   93 MET cc_start: 0.7819 (mtp) cc_final: 0.7415 (mtm)
REVERT: A    8 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7002 (tp30)
REVERT: A    9 PHE cc_start: 0.7323 (m-80) cc_final: 0.6926 (m-10)
REVERT: A   51 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6980 (m90)
REVERT: A  107 CYS cc_start: 0.7814 (t) cc_final: 0.6831 (t)
REVERT: A  108 LEU cc_start: 0.8419 (pp) cc_final: 0.8087 (pp)
REVERT: A  127 ARG cc_start: 0.3648 (OUTLIER) cc_final: 0.2211 (tmt170)
REVERT: D   61 CYS cc_start: 0.8607 (t) cc_final: 0.8067 (m)
REVERT: C   64 GLU cc_start: 0.7172 (tt0) cc_final: 0.6896 (mt-10)
REVERT: C   72 VAL cc_start: 0.9085 (t) cc_final: 0.8867 (p)
REVERT: h   13 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7070 (tm-30)
REVERT: h   34 MET cc_start: 0.5936 (mtp) cc_final: 0.5609 (mtp)
REVERT: h   64 VAL cc_start: 0.7200 (m) cc_final: 0.6951 (p)
REVERT: h   95 PHE cc_start: 0.6309 (m-80) cc_final: 0.6058 (m-80)
REVERT: l   31 HIS cc_start: 0.6938 (t-90) cc_final: 0.6446 (t-90)
REVERT: l   33 ASN cc_start: 0.8435 (t0) cc_final: 0.8196 (t0)
REVERT: l   38 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7326 (m-10)
REVERT: H   18 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7786 (mt)
REVERT: H   59 ASP cc_start: 0.7923 (t0) cc_final: 0.7666 (t0)
  outliers start: 50
  outliers final: 34
  residues processed: 294
  average time/residue: 0.1768
  time to fit residues: 70.8116
Evaluate side-chains
  308 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 269
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain D residue   28 ARG
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  121 SER
Chi-restraints excluded: chain h residue  108 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   38 PHE
Chi-restraints excluded: chain l residue   57 SER
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain l residue   77 THR
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain L residue   90 VAL
Chi-restraints excluded: chain L residue   99 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 62 optimal weight:    8.9990
   chunk 82 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.143888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.123568 restraints weight = 17628.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.127244 restraints weight = 10279.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.129753 restraints weight = 6851.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8257  Z= 0.169
  Angle     :  0.656   9.697  11251  Z= 0.320
  Chirality :  0.043   0.267   1230
  Planarity :  0.005   0.060   1443
  Dihedral  :  4.463  53.446   1118
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.70 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 32.05 %
    Favored  : 63.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.46 (0.27), residues: 1001
  helix:  1.29 (0.27), residues: 371
  sheet: -0.03 (0.36), residues: 210
  loop : -0.30 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  47 
 HIS   0.006   0.001   HIS C 104 
 PHE   0.024   0.002   PHE C  23 
 TYR   0.047   0.001   TYR A  88 
 ARG   0.006   0.000   ARG A  56 

*********************** 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
  317 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 282
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 GLU cc_start: 0.8261 (mp0) cc_final: 0.8017 (mp0)
REVERT: B   57 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7904 (mm-40)
REVERT: B   62 TRP cc_start: 0.8181 (t-100) cc_final: 0.7832 (t-100)
REVERT: B   93 MET cc_start: 0.7725 (mtp) cc_final: 0.7308 (mtm)
REVERT: B   99 GLN cc_start: 0.8666 (mt0) cc_final: 0.8181 (tt0)
REVERT: A    8 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6947 (tp30)
REVERT: A    9 PHE cc_start: 0.7343 (m-80) cc_final: 0.7042 (m-10)
REVERT: A   23 PHE cc_start: 0.3915 (OUTLIER) cc_final: 0.2860 (m-80)
REVERT: A  105 ILE cc_start: 0.8949 (tt) cc_final: 0.8587 (tp)
REVERT: A  127 ARG cc_start: 0.3640 (OUTLIER) cc_final: 0.2166 (tmt170)
REVERT: D   61 CYS cc_start: 0.8572 (t) cc_final: 0.8041 (m)
REVERT: D   97 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7903 (tt)
REVERT: C   64 GLU cc_start: 0.7312 (tt0) cc_final: 0.6987 (mt-10)
REVERT: C   72 VAL cc_start: 0.9043 (t) cc_final: 0.8815 (p)
REVERT: C   93 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7795 (ptp)
REVERT: h    7 SER cc_start: 0.6972 (t) cc_final: 0.6735 (t)
REVERT: h   13 GLN cc_start: 0.7639 (tm-30) cc_final: 0.6987 (tm-30)
REVERT: h   64 VAL cc_start: 0.7194 (m) cc_final: 0.6952 (p)
REVERT: h   95 PHE cc_start: 0.6302 (m-80) cc_final: 0.6094 (m-80)
REVERT: l   31 HIS cc_start: 0.6900 (t-90) cc_final: 0.6442 (t-90)
REVERT: l   33 ASN cc_start: 0.8463 (t0) cc_final: 0.8246 (t0)
REVERT: l   38 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7139 (m-10)
REVERT: H   18 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7775 (mt)
REVERT: H   59 ASP cc_start: 0.7943 (t0) cc_final: 0.7672 (t0)
REVERT: L   74 THR cc_start: 0.8073 (p) cc_final: 0.7749 (p)
REVERT: L   84 GLU cc_start: 0.7457 (pm20) cc_final: 0.6250 (pm20)
  outliers start: 35
  outliers final: 26
  residues processed: 296
  average time/residue: 0.1753
  time to fit residues: 71.5436
Evaluate side-chains
  303 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 270
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain h residue  108 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   38 PHE
Chi-restraints excluded: chain l residue   42 LEU
Chi-restraints excluded: chain l residue   57 SER
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain l residue   77 THR
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain L residue   90 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
h  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.142582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.122270 restraints weight = 17677.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.125939 restraints weight = 10348.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.128433 restraints weight = 6928.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.4720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8257  Z= 0.184
  Angle     :  0.670   9.577  11251  Z= 0.327
  Chirality :  0.043   0.186   1230
  Planarity :  0.005   0.060   1443
  Dihedral  :  4.492  54.609   1118
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.50 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 31.48 %
    Favored  : 63.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.48 (0.27), residues: 1001
  helix:  1.14 (0.27), residues: 372
  sheet:  0.17 (0.37), residues: 194
  loop : -0.22 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP H  47 
 HIS   0.006   0.001   HIS C 104 
 PHE   0.023   0.002   PHE C  23 
 TYR   0.054   0.002   TYR A  88 
 ARG   0.006   0.000   ARG A  56 

*********************** 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
  318 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 276
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7911 (mm-40)
REVERT: B   62 TRP cc_start: 0.8110 (t-100) cc_final: 0.7884 (t-100)
REVERT: B   93 MET cc_start: 0.7732 (mtp) cc_final: 0.7494 (mtp)
REVERT: B  112 ARG cc_start: 0.7466 (tpp-160) cc_final: 0.7225 (mmt-90)
REVERT: A    9 PHE cc_start: 0.7377 (m-80) cc_final: 0.6973 (m-10)
REVERT: A   23 PHE cc_start: 0.4077 (OUTLIER) cc_final: 0.3028 (m-80)
REVERT: A   93 MET cc_start: 0.8038 (ttm) cc_final: 0.7731 (ttm)
REVERT: A  127 ARG cc_start: 0.3636 (OUTLIER) cc_final: 0.2148 (tmt170)
REVERT: D   61 CYS cc_start: 0.8604 (t) cc_final: 0.8029 (m)
REVERT: D   97 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7897 (tt)
REVERT: D  102 TRP cc_start: 0.8322 (t-100) cc_final: 0.7951 (t60)
REVERT: C   64 GLU cc_start: 0.7301 (tt0) cc_final: 0.6919 (mt-10)
REVERT: C   72 VAL cc_start: 0.9073 (t) cc_final: 0.8853 (p)
REVERT: C   93 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7854 (ptp)
REVERT: h    7 SER cc_start: 0.7110 (t) cc_final: 0.6861 (t)
REVERT: h   13 GLN cc_start: 0.7622 (tm-30) cc_final: 0.6934 (tm-30)
REVERT: h   64 VAL cc_start: 0.7152 (m) cc_final: 0.6909 (p)
REVERT: h   95 PHE cc_start: 0.6289 (m-80) cc_final: 0.6081 (m-80)
REVERT: l   38 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7126 (m-10)
REVERT: H   18 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7502 (mt)
REVERT: H   59 ASP cc_start: 0.7981 (t0) cc_final: 0.7706 (t0)
REVERT: L   24 ARG cc_start: 0.6018 (tpp-160) cc_final: 0.5774 (tpp-160)
REVERT: L   84 GLU cc_start: 0.7467 (pm20) cc_final: 0.6236 (pm20)
  outliers start: 42
  outliers final: 33
  residues processed: 292
  average time/residue: 0.1723
  time to fit residues: 69.2220
Evaluate side-chains
  319 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 280
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   93 MET
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  121 SER
Chi-restraints excluded: chain h residue   40 VAL
Chi-restraints excluded: chain h residue  108 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   38 PHE
Chi-restraints excluded: chain l residue   42 LEU
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain l residue   77 THR
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain L residue   90 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 7 optimal weight:    0.3980
   chunk 58 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
h  57 ASN
L  36 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.138179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.117704 restraints weight = 18081.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.121350 restraints weight = 10504.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.123837 restraints weight = 7031.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8257  Z= 0.246
  Angle     :  0.728  11.465  11251  Z= 0.365
  Chirality :  0.046   0.208   1230
  Planarity :  0.005   0.061   1443
  Dihedral  :  4.871  59.114   1118
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.70 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 30.91 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.27 (0.27), residues: 1001
  helix:  1.08 (0.27), residues: 371
  sheet: -0.04 (0.37), residues: 194
  loop : -0.39 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP H  47 
 HIS   0.009   0.001   HIS A  51 
 PHE   0.033   0.002   PHE H  68 
 TYR   0.062   0.002   TYR A  88 
 ARG   0.006   0.001   ARG A  56 

*********************** 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
  340 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 298
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8021 (mm-40)
REVERT: B   62 TRP cc_start: 0.8222 (t-100) cc_final: 0.7936 (t-100)
REVERT: B   99 GLN cc_start: 0.8665 (mt0) cc_final: 0.8294 (tt0)
REVERT: B  127 ARG cc_start: 0.3176 (tpt170) cc_final: 0.2774 (tmt170)
REVERT: A    8 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7173 (tp30)
REVERT: A   23 PHE cc_start: 0.4486 (OUTLIER) cc_final: 0.3521 (m-80)
REVERT: A   53 THR cc_start: 0.7892 (p) cc_final: 0.7226 (t)
REVERT: A   57 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8110 (mm-40)
REVERT: A   93 MET cc_start: 0.8044 (ttm) cc_final: 0.7782 (ttm)
REVERT: A  105 ILE cc_start: 0.8947 (tp) cc_final: 0.8642 (tp)
REVERT: A  127 ARG cc_start: 0.3790 (OUTLIER) cc_final: 0.2277 (tmt170)
REVERT: D   61 CYS cc_start: 0.8625 (t) cc_final: 0.8069 (m)
REVERT: D   97 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8025 (tt)
REVERT: C   60 LEU cc_start: 0.8503 (mt) cc_final: 0.8123 (mt)
REVERT: C   64 GLU cc_start: 0.7351 (tt0) cc_final: 0.6936 (mt-10)
REVERT: C   87 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7476 (t)
REVERT: h   95 PHE cc_start: 0.6405 (m-80) cc_final: 0.6118 (m-80)
REVERT: l   33 ASN cc_start: 0.8589 (t0) cc_final: 0.8294 (p0)
REVERT: l   38 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7224 (m-10)
REVERT: H   59 ASP cc_start: 0.8055 (t0) cc_final: 0.7763 (t0)
REVERT: L   24 ARG cc_start: 0.6173 (tpp-160) cc_final: 0.5972 (tpp-160)
  outliers start: 42
  outliers final: 31
  residues processed: 316
  average time/residue: 0.1808
  time to fit residues: 78.4657
Evaluate side-chains
  333 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 296
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain D residue   28 ARG
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  121 SER
Chi-restraints excluded: chain h residue   40 VAL
Chi-restraints excluded: chain h residue  108 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   38 PHE
Chi-restraints excluded: chain l residue   42 LEU
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain L residue   33 ASN
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain L residue   90 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0870
   chunk 91 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 23 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6562

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

Flipped N/Q/H residues before XYZ refinement:
** l  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.140242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.119996 restraints weight = 17489.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.123586 restraints weight = 10230.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.126078 restraints weight = 6897.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.5285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8257  Z= 0.183
  Angle     :  0.731  13.074  11251  Z= 0.358
  Chirality :  0.048   0.405   1230
  Planarity :  0.005   0.058   1443
  Dihedral  :  4.663  58.381   1118
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.40 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 32.39 %
    Favored  : 63.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.39 (0.27), residues: 1001
  helix:  1.03 (0.27), residues: 370
  sheet:  0.38 (0.39), residues: 182
  loop : -0.36 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP H  47 
 HIS   0.006   0.001   HIS C 104 
 PHE   0.065   0.002   PHE H  68 
 TYR   0.056   0.002   TYR A  88 
 ARG   0.006   0.000   ARG C  56 

********************** 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
  331 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 298
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7735 (ttpp)
REVERT: B   57 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7898 (mm-40)
REVERT: B   62 TRP cc_start: 0.8091 (t-100) cc_final: 0.7830 (t-100)
REVERT: B   99 GLN cc_start: 0.8628 (mt0) cc_final: 0.8217 (tt0)
REVERT: B  112 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7066 (tpp-160)
REVERT: B  127 ARG cc_start: 0.3506 (tpt170) cc_final: 0.3033 (tmt170)
REVERT: A    8 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6922 (tp30)
REVERT: A    9 PHE cc_start: 0.7258 (m-80) cc_final: 0.6759 (m-10)
REVERT: A   23 PHE cc_start: 0.4451 (OUTLIER) cc_final: 0.3623 (m-80)
REVERT: A   53 THR cc_start: 0.7680 (p) cc_final: 0.7305 (t)
REVERT: A   93 MET cc_start: 0.8048 (ttm) cc_final: 0.7807 (ttm)
REVERT: A  105 ILE cc_start: 0.8938 (tp) cc_final: 0.8635 (tp)
REVERT: A  127 ARG cc_start: 0.3675 (OUTLIER) cc_final: 0.2132 (tmt170)
REVERT: D   61 CYS cc_start: 0.8578 (t) cc_final: 0.8033 (m)
REVERT: D   97 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7910 (tt)
REVERT: D  101 LEU cc_start: 0.8815 (mm) cc_final: 0.8530 (mp)
REVERT: D  102 TRP cc_start: 0.8567 (t60) cc_final: 0.8094 (t60)
REVERT: C   60 LEU cc_start: 0.8428 (mt) cc_final: 0.8052 (mt)
REVERT: C   64 GLU cc_start: 0.7329 (tt0) cc_final: 0.6908 (mt-10)
REVERT: h   13 GLN cc_start: 0.7474 (tm-30) cc_final: 0.6819 (tm-30)
REVERT: h   95 PHE cc_start: 0.6379 (m-80) cc_final: 0.6036 (m-80)
REVERT: h  111 GLN cc_start: 0.6613 (mm-40) cc_final: 0.6259 (tm-30)
REVERT: l   33 ASN cc_start: 0.8637 (t0) cc_final: 0.8347 (p0)
REVERT: l   38 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7168 (m-10)
REVERT: H   34 MET cc_start: 0.7178 (mmm) cc_final: 0.6960 (mmp)
REVERT: H   59 ASP cc_start: 0.8047 (t0) cc_final: 0.7742 (t0)
REVERT: L   24 ARG cc_start: 0.5958 (tpp-160) cc_final: 0.5755 (tpp-160)
REVERT: L   59 ARG cc_start: 0.8238 (mtt180) cc_final: 0.8030 (mtp180)
REVERT: L   84 GLU cc_start: 0.7566 (pm20) cc_final: 0.6226 (pm20)
  outliers start: 33
  outliers final: 28
  residues processed: 312
  average time/residue: 0.1806
  time to fit residues: 76.6073
Evaluate side-chains
  326 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 293
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain A residue    7 LYS
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  121 SER
Chi-restraints excluded: chain h residue   40 VAL
Chi-restraints excluded: chain h residue  108 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue    9 LEU
Chi-restraints excluded: chain l residue   38 PHE
Chi-restraints excluded: chain l residue   42 LEU
Chi-restraints excluded: chain l residue   67 PHE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain L residue   67 PHE
Chi-restraints excluded: chain L residue   72 SER
Chi-restraints excluded: chain L residue   90 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
h  57 ASN
** l  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.137710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.117338 restraints weight = 17624.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.121041 restraints weight = 10256.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.123491 restraints weight = 6834.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.5441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8257  Z= 0.204
  Angle     :  0.736  14.027  11251  Z= 0.365
  Chirality :  0.046   0.385   1230
  Planarity :  0.005   0.060   1443
  Dihedral  :  4.747  59.444   1118
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.80 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 32.05 %
    Favored  : 63.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.35 (0.27), residues: 1001
  helix:  1.05 (0.27), residues: 370
  sheet:  0.25 (0.39), residues: 182
  loop : -0.38 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP H  47 
 HIS   0.007   0.001   HIS C 104 
 PHE   0.063   0.002   PHE H  68 
 TYR   0.058   0.002   TYR A  88 
 ARG   0.007   0.001   ARG C  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2832.30 seconds
wall clock time: 49 minutes 45.18 seconds (2985.18 seconds total)