Starting phenix.real_space_refine
on Fri Aug 22 13:48:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g9r_29874/08_2025/8g9r_29874.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g9r_29874/08_2025/8g9r_29874.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g9r_29874/08_2025/8g9r_29874.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g9r_29874/08_2025/8g9r_29874.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g9r_29874/08_2025/8g9r_29874.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g9r_29874/08_2025/8g9r_29874.map"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    2315      2.51       5
     N     585      2.21       5
     O     665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3570
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 714
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.61, per 1000 atoms: 0.17
  Number of scatterers: 3570
  At special positions: 0
  Unit cell: (76.54, 92.02, 43, 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       5     16.00
     O     665      8.00
     N     585      7.00
     C    2315      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 0.15
  Conformation dependent library (CDL) restraints added in 90.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  870

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 51.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16
      removed outlier: 6.631A  pdb=" N   LEU B  12 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   LYS D  15 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   VAL B  14 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU A  12 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   LYS B  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL A  14 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL C  14 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL E  14 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21
      removed outlier: 6.635A  pdb=" N   VAL B  20 " --> pdb=" O   ARG D  21 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL A  20 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 30 through 34
      removed outlier: 6.806A  pdb=" N   HIS A  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   ARG C  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   PHE A  33 " --> pdb=" O   ARG C  34 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   HIS C  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   ARG E  34 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   PHE C  33 " --> pdb=" O   ARG E  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 60 through 80
      removed outlier: 9.281A  pdb=" N   THR B  60 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 10.933A  pdb=" N   GLU D  63 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLU B  62 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   VAL D  65 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   PHE B  64 " --> pdb=" O   VAL D  65 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   GLY D  67 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 8.796A  pdb=" N   GLU B  66 " --> pdb=" O   GLY D  67 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   TYR D  69 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   ILE B  68 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
      removed outlier: 9.045A  pdb=" N   VAL D  71 " --> pdb=" O   ILE B  68 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LYS B  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   ILE D  73 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 9.145A  pdb=" N   GLU B  72 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   THR D  75 " --> pdb=" O   GLU B  72 " (cutoff:3.500A)
      removed outlier: 8.829A  pdb=" N   ASP B  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 10.844A  pdb=" N   SER D  77 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 9.399A  pdb=" N   LYS B  76 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 10.219A  pdb=" N   TRP D  79 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   TYR B  78 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 9.272A  pdb=" N   THR A  60 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 10.928A  pdb=" N   GLU B  63 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   GLU A  62 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 9.008A  pdb=" N   VAL B  65 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   PHE A  64 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 8.700A  pdb=" N   GLY B  67 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   GLU A  66 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   TYR B  69 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   ILE A  68 " --> pdb=" O   TYR B  69 " (cutoff:3.500A)
      removed outlier: 9.020A  pdb=" N   VAL B  71 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LYS A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   ILE B  73 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 9.117A  pdb=" N   GLU A  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   THR B  75 " --> pdb=" O   GLU A  72 " (cutoff:3.500A)
      removed outlier: 8.822A  pdb=" N   ASP A  74 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 10.840A  pdb=" N   SER B  77 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 9.389A  pdb=" N   LYS A  76 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 10.215A  pdb=" N   TRP B  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   TYR A  78 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   GLU A  61 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   GLU C  62 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   GLU A  63 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   PHE C  64 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   ILE C  68 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   TYR A  69 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   ASP C  74 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   THR A  75 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LYS C  76 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   SER A  77 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   TYR C  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS C  80 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   GLU C  61 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   GLU E  62 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   GLU C  63 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE E  64 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   ILE E  68 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   TYR C  69 " --> pdb=" O   ILE E  68 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   ASP E  74 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   THR C  75 " --> pdb=" O   ASP E  74 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   LYS E  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   SER C  77 " --> pdb=" O   LYS E  76 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   TYR E  78 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS E  80 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 97
      removed outlier: 6.839A  pdb=" N   GLU B  92 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   PHE D  95 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL B  94 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   ALA D  97 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   THR B  96 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   GLU A  92 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   PHE B  95 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL A  94 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 8.423A  pdb=" N   ALA B  97 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   THR A  96 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL C  94 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA A  97 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL E  94 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA C  97 " --> pdb=" O   THR E  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.715A  pdb=" N   ARG B 104 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 8.651A  pdb=" N   ILE D 107 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   THR B 106 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   ALA D 109 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ALA B 108 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ARG A 104 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ILE B 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   THR A 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   ALA B 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   ALA A 108 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ALA A 109 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   LEU C 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   ALA C 109 " --> pdb=" O   ALA E 108 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   LEU E 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.186A  pdb=" N   TYR B 114 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   TYR A 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER A 115 " --> pdb=" O   TYR C 114 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER C 115 " --> pdb=" O   TYR E 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 122
      removed outlier: 7.021A  pdb=" N   THR B 119 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   VAL D 122 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   VAL B 121 " --> pdb=" O   VAL D 122 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   THR A 119 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 8.413A  pdb=" N   VAL B 122 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL A 121 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 120 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA C 120 " --> pdb=" O   THR E 119 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    168 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: 0.28

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1110
        1.34 -     1.46: 594
        1.46 -     1.57: 1941
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 3655
  Sorted by residual:
  bond pdb=" CA  ASN C  27 "
       pdb=" C   ASN C  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.525 -0.006 1.16e-02 7.43e+03 2.32e-01
  bond pdb=" CA  ASN A  27 "
       pdb=" C   ASN A  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.525 -0.005 1.16e-02 7.43e+03 2.15e-01
  bond pdb=" N   ILE C  73 "
       pdb=" CA  ILE C  73 "
    ideal  model  delta    sigma   weight residual
    1.457  1.463 -0.006 1.28e-02 6.10e+03 1.99e-01
  bond pdb=" N   LEU C  17 "
       pdb=" CA  LEU C  17 "
    ideal  model  delta    sigma   weight residual
    1.462  1.467 -0.006 1.31e-02 5.83e+03 1.94e-01
  bond pdb=" CA  ASN B  27 "
       pdb=" C   ASN B  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.525 -0.005 1.16e-02 7.43e+03 1.93e-01
  ... (remaining 3650 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.89: 4427
        0.89 -     1.78: 463
        1.78 -     2.67: 50
        2.67 -     3.55: 25
        3.55 -     4.44: 10
  Bond angle restraints: 4975
  Sorted by residual:
  angle pdb=" N   GLY C  67 "
        pdb=" CA  GLY C  67 "
        pdb=" C   GLY C  67 "
      ideal   model   delta    sigma   weight residual
     113.18  117.37   -4.19 2.37e+00 1.78e-01 3.13e+00
  angle pdb=" N   GLY B  67 "
        pdb=" CA  GLY B  67 "
        pdb=" C   GLY B  67 "
      ideal   model   delta    sigma   weight residual
     113.18  117.37   -4.19 2.37e+00 1.78e-01 3.12e+00
  angle pdb=" N   GLY D  67 "
        pdb=" CA  GLY D  67 "
        pdb=" C   GLY D  67 "
      ideal   model   delta    sigma   weight residual
     113.18  117.35   -4.17 2.37e+00 1.78e-01 3.10e+00
  angle pdb=" N   GLY E  67 "
        pdb=" CA  GLY E  67 "
        pdb=" C   GLY E  67 "
      ideal   model   delta    sigma   weight residual
     113.18  117.33   -4.15 2.37e+00 1.78e-01 3.07e+00
  angle pdb=" N   GLY A  67 "
        pdb=" CA  GLY A  67 "
        pdb=" C   GLY A  67 "
      ideal   model   delta    sigma   weight residual
     113.18  117.33   -4.15 2.37e+00 1.78e-01 3.07e+00
  ... (remaining 4970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 1880
       16.91 -    33.82: 195
       33.82 -    50.73: 70
       50.73 -    67.64: 5
       67.64 -    84.55: 10
  Dihedral angle restraints: 2160
    sinusoidal: 820
      harmonic: 1340
  Sorted by residual:
  dihedral pdb=" CG  ARG E  21 "
           pdb=" CD  ARG E  21 "
           pdb=" NE  ARG E  21 "
           pdb=" CZ  ARG E  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.63   42.37     2      1.50e+01 4.44e-03 9.69e+00
  dihedral pdb=" CG  ARG D  21 "
           pdb=" CD  ARG D  21 "
           pdb=" NE  ARG D  21 "
           pdb=" CZ  ARG D  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.65   42.35     2      1.50e+01 4.44e-03 9.68e+00
  dihedral pdb=" CG  ARG A  21 "
           pdb=" CD  ARG A  21 "
           pdb=" NE  ARG A  21 "
           pdb=" CZ  ARG A  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.66   42.34     2      1.50e+01 4.44e-03 9.68e+00
  ... (remaining 2157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 294
       0.025 -    0.050: 171
       0.050 -    0.075: 45
       0.075 -    0.100: 21
       0.100 -    0.125: 59
  Chirality restraints: 590
  Sorted by residual:
  chirality pdb=" CA  VAL C  14 "
            pdb=" N   VAL C  14 "
            pdb=" C   VAL C  14 "
            pdb=" CB  VAL C  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  VAL D 121 "
            pdb=" N   VAL D 121 "
            pdb=" C   VAL D 121 "
            pdb=" CB  VAL D 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  ILE E  68 "
            pdb=" N   ILE E  68 "
            pdb=" C   ILE E  68 "
            pdb=" CB  ILE E  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 587 not shown)

  Planarity restraints: 610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 101 "   -0.045 5.00e-02 4.00e+02   6.88e-02 7.57e+00
        pdb=" N   PRO D 102 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO D 102 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO D 102 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 101 "   -0.045 5.00e-02 4.00e+02   6.86e-02 7.52e+00
        pdb=" N   PRO A 102 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 101 "   -0.045 5.00e-02 4.00e+02   6.85e-02 7.51e+00
        pdb=" N   PRO E 102 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E 102 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO E 102 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 607 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 1743
        3.01 -     3.49: 2937
        3.49 -     3.96: 4492
        3.96 -     4.43: 4746
        4.43 -     4.90: 9525
  Nonbonded interactions: 23443
  Sorted by model distance:
  nonbonded pdb=" O   ASP A  99 "
            pdb=" O   SER C 100 "
     model   vdw
     2.542 3.040
  nonbonded pdb=" N   ASP E  18 "
            pdb=" OD1 ASP E  18 "
     model   vdw
     2.556 3.120
  nonbonded pdb=" N   ASP A  18 "
            pdb=" OD1 ASP A  18 "
     model   vdw
     2.557 3.120
  nonbonded pdb=" N   ASP D  18 "
            pdb=" OD1 ASP D  18 "
     model   vdw
     2.557 3.120
  nonbonded pdb=" N   ASP B  18 "
            pdb=" OD1 ASP B  18 "
     model   vdw
     2.557 3.120
  ... (remaining 23438 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.880
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0613
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   3655  Z= 0.128
  Angle     :  0.594   4.442   4975  Z= 0.339
  Chirality :  0.049   0.125    590
  Planarity :  0.008   0.069    610
  Dihedral  : 16.845  84.550   1290
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.08 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.38 (0.30), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.23), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  21 
 TYR   0.009   0.001   TYR E 114 
 PHE   0.008   0.001   PHE D  95 
 TRP   0.003   0.001   TRP B  79 
 HIS   0.002   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3655)
  covalent geometry    : angle       0.59357 ( 4975)
  hydrogen bonds       : bond        0.44028 (   56)
  hydrogen bonds       : angle       6.51991 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: D   79 TRP cc_start: 0.4176 (m-10) cc_final: 0.2471 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0989
  time to fit residues: 3.5400
Evaluate side-chains
  18 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5129 r_free = 0.5129 target = 0.234893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.203800 restraints weight = 4862.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.4917 rms_B_bonded: 4.69
r_work (final): 0.4917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1472
moved from start:          0.5524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3655  Z= 0.168
  Angle     :  0.700   5.650   4975  Z= 0.382
  Chirality :  0.054   0.159    590
  Planarity :  0.006   0.052    610
  Dihedral  :  5.994  17.558    490
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 16.15 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.99 (0.32), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.25), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  34 
 TYR   0.040   0.003   TYR A 105 
 PHE   0.024   0.003   PHE D  33 
 TRP   0.022   0.003   TRP E  79 
 HIS   0.008   0.003   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3655)
  covalent geometry    : angle       0.69971 ( 4975)
  hydrogen bonds       : bond        0.03460 (   56)
  hydrogen bonds       : angle       6.06890 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 27
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   13 MET cc_start: 0.2376 (mmt) cc_final: 0.1106 (ptp)
REVERT: A   26 ILE cc_start: -0.1854 (OUTLIER) cc_final: -0.2396 (pt)
REVERT: A   35 LYS cc_start: -0.0869 (ttmt) cc_final: -0.1304 (mttp)
REVERT: D   35 LYS cc_start: -0.0010 (ttmt) cc_final: -0.0539 (mttp)
REVERT: E   26 ILE cc_start: -0.2240 (OUTLIER) cc_final: -0.2509 (pt)
  outliers start: 20
  outliers final: 9
  residues processed: 47
  average time/residue: 0.1435
  time to fit residues: 7.5375
Evaluate side-chains
  29 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 18
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain D residue   88 HIS
Chi-restraints excluded: chain D residue   96 THR
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue   96 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 38 optimal weight:    0.0270
   chunk 25 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
C  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5246 r_free = 0.5246 target = 0.273410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.219678 restraints weight = 5253.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.4911 rms_B_bonded: 5.43
r_work (final): 0.4911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1616
moved from start:          0.6423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3655  Z= 0.092
  Angle     :  0.499   4.717   4975  Z= 0.271
  Chirality :  0.047   0.133    590
  Planarity :  0.005   0.038    610
  Dihedral  :  4.910  20.216    490
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 15.38 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.64 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  21 
 TYR   0.009   0.001   TYR E 105 
 PHE   0.011   0.001   PHE C  95 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.003   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 3655)
  covalent geometry    : angle       0.49926 ( 4975)
  hydrogen bonds       : bond        0.03023 (   56)
  hydrogen bonds       : angle       4.89879 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 20
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   35 LYS cc_start: -0.1094 (ttmt) cc_final: -0.1522 (mttt)
REVERT: D   35 LYS cc_start: -0.0009 (ttmt) cc_final: -0.0423 (mttp)
REVERT: E   35 LYS cc_start: -0.1009 (mmtt) cc_final: -0.1575 (mmtt)
  outliers start: 14
  outliers final: 10
  residues processed: 32
  average time/residue: 0.1122
  time to fit residues: 4.1314
Evaluate side-chains
  30 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 20
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain D residue   96 THR
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   96 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 27 optimal weight:   30.0000
   chunk 35 optimal weight:    0.3980
   chunk 44 optimal weight:    9.9990
   chunk 9 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0670
   chunk 20 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    2.8322

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

Flipped N/Q/H residues before XYZ refinement:
C  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.257655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.5015 r_free = 0.5015 target = 0.213321 restraints weight = 4848.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.4999 rms_B_bonded: 5.42
r_work (final): 0.4999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1989
moved from start:          1.0260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3655  Z= 0.211
  Angle     :  0.753   6.367   4975  Z= 0.415
  Chirality :  0.052   0.165    590
  Planarity :  0.006   0.042    610
  Dihedral  :  6.695  20.385    490
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.21 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.23 (0.32), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.46 (0.25), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  21 
 TYR   0.021   0.003   TYR C 114 
 PHE   0.014   0.003   PHE E  95 
 TRP   0.025   0.004   TRP E  79 
 HIS   0.005   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 3655)
  covalent geometry    : angle       0.75252 ( 4975)
  hydrogen bonds       : bond        0.02767 (   56)
  hydrogen bonds       : angle       6.15212 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  103 ARG cc_start: 0.6503 (mtt180) cc_final: 0.6220 (mtt180)
REVERT: C  112 SER cc_start: 0.6050 (OUTLIER) cc_final: 0.5792 (p)
REVERT: D   88 HIS cc_start: 0.4020 (OUTLIER) cc_final: 0.3775 (p-80)
REVERT: E  104 ARG cc_start: 0.3286 (OUTLIER) cc_final: 0.1688 (ttp-170)
  outliers start: 10
  outliers final: 5
  residues processed: 37
  average time/residue: 0.1085
  time to fit residues: 4.6088
Evaluate side-chains
  29 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain D residue   88 HIS
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  104 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0270
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.7240

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5315 r_free = 0.5315 target = 0.257857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5024 r_free = 0.5024 target = 0.214523 restraints weight = 4887.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.5012 rms_B_bonded: 5.37
r_work: 0.4908 rms_B_bonded: 5.36 restraints_weight: 2.0000
r_work (final): 0.4908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2307
moved from start:          1.0769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3655  Z= 0.124
  Angle     :  0.565   5.126   4975  Z= 0.305
  Chirality :  0.048   0.158    590
  Planarity :  0.005   0.043    610
  Dihedral  :  5.626  21.314    490
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.46 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.13 (0.33), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.25), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  21 
 TYR   0.012   0.002   TYR E 114 
 PHE   0.013   0.002   PHE C  95 
 TRP   0.013   0.002   TRP E  79 
 HIS   0.002   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3655)
  covalent geometry    : angle       0.56543 ( 4975)
  hydrogen bonds       : bond        0.02127 (   56)
  hydrogen bonds       : angle       5.13209 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.128 
Fit side-chains
REVERT: C   26 ILE cc_start: -0.2624 (OUTLIER) cc_final: -0.2836 (mt)
REVERT: E  111 LEU cc_start: -0.1272 (OUTLIER) cc_final: -0.1486 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 36
  average time/residue: 0.0728
  time to fit residues: 3.2212
Evaluate side-chains
  34 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 23
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  111 LEU
Chi-restraints excluded: chain E residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 34 optimal weight:    0.1980
   chunk 5 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   overall best weight:    2.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.253110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.5037 r_free = 0.5037 target = 0.213275 restraints weight = 4925.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.4983 rms_B_bonded: 5.14
r_work (final): 0.4983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2511
moved from start:          1.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3655  Z= 0.182
  Angle     :  0.681   7.245   4975  Z= 0.376
  Chirality :  0.050   0.165    590
  Planarity :  0.005   0.041    610
  Dihedral  :  6.294  23.586    490
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.74 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.29 (0.33), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.25), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 104 
 TYR   0.017   0.002   TYR C 114 
 PHE   0.017   0.003   PHE C  95 
 TRP   0.019   0.003   TRP E  79 
 HIS   0.010   0.002   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3655)
  covalent geometry    : angle       0.68066 ( 4975)
  hydrogen bonds       : bond        0.02704 (   56)
  hydrogen bonds       : angle       5.47728 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.110 
Fit side-chains
REVERT: E   89 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.3542 (tp30)
REVERT: E  104 ARG cc_start: 0.3876 (OUTLIER) cc_final: 0.2038 (ttp80)
REVERT: E  112 SER cc_start: 0.5850 (t) cc_final: 0.5644 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0772
  time to fit residues: 3.8923
Evaluate side-chains
  39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  104 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:   30.0000
   chunk 41 optimal weight:    0.0770
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 13 optimal weight:    9.9990
   overall best weight:    0.6740

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5328 r_free = 0.5328 target = 0.257762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.213807 restraints weight = 4932.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.5005 rms_B_bonded: 5.27
r_work (final): 0.5005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2209
moved from start:          1.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3655  Z= 0.095
  Angle     :  0.558  14.467   4975  Z= 0.284
  Chirality :  0.047   0.191    590
  Planarity :  0.004   0.033    610
  Dihedral  :  5.248  20.349    490
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.23 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.97 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  21 
 TYR   0.009   0.001   TYR C  78 
 PHE   0.014   0.002   PHE C  95 
 TRP   0.003   0.001   TRP E  79 
 HIS   0.002   0.000   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 3655)
  covalent geometry    : angle       0.55830 ( 4975)
  hydrogen bonds       : bond        0.01654 (   56)
  hydrogen bonds       : angle       4.98238 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A   13 MET cc_start: 0.2300 (mmm) cc_final: 0.0493 (mtm)
REVERT: A  103 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6847 (mtt90)
REVERT: E  104 ARG cc_start: 0.3840 (OUTLIER) cc_final: 0.2279 (ttp80)
  outliers start: 10
  outliers final: 8
  residues processed: 38
  average time/residue: 0.0982
  time to fit residues: 4.3671
Evaluate side-chains
  37 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  104 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0570
   chunk 7 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0670
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.8240

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5294 r_free = 0.5294 target = 0.252280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.210644 restraints weight = 4976.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.5024 rms_B_bonded: 5.39
r_work (final): 0.5024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2434
moved from start:          1.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3655  Z= 0.136
  Angle     :  0.606   9.408   4975  Z= 0.324
  Chirality :  0.049   0.166    590
  Planarity :  0.005   0.066    610
  Dihedral  :  5.733  21.096    490
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.74 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 103 
 TYR   0.024   0.002   TYR D 105 
 PHE   0.017   0.002   PHE C  95 
 TRP   0.012   0.002   TRP E  79 
 HIS   0.002   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3655)
  covalent geometry    : angle       0.60585 ( 4975)
  hydrogen bonds       : bond        0.02193 (   56)
  hydrogen bonds       : angle       5.07878 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  103 ARG cc_start: 0.7326 (mtt180) cc_final: 0.6825 (mtt90)
REVERT: C  103 ARG cc_start: 0.6972 (mtt180) cc_final: 0.6508 (mtt90)
REVERT: E  104 ARG cc_start: 0.3853 (OUTLIER) cc_final: 0.2155 (mpt-90)
  outliers start: 8
  outliers final: 7
  residues processed: 37
  average time/residue: 0.0902
  time to fit residues: 3.9393
Evaluate side-chains
  38 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  104 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:   30.0000
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5321 r_free = 0.5321 target = 0.255444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5052 r_free = 0.5052 target = 0.212991 restraints weight = 4833.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.5009 rms_B_bonded: 5.15
r_work (final): 0.5009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2652
moved from start:          1.4348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3655  Z= 0.141
  Angle     :  0.601   7.957   4975  Z= 0.325
  Chirality :  0.049   0.156    590
  Planarity :  0.005   0.059    610
  Dihedral  :  5.870  21.701    490
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.74 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.08 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 103 
 TYR   0.013   0.002   TYR A 105 
 PHE   0.015   0.002   PHE C  95 
 TRP   0.013   0.002   TRP E  79 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3655)
  covalent geometry    : angle       0.60117 ( 4975)
  hydrogen bonds       : bond        0.02036 (   56)
  hydrogen bonds       : angle       5.14424 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.140 
Fit side-chains
REVERT: E  104 ARG cc_start: 0.4288 (OUTLIER) cc_final: 0.2450 (mtt180)
  outliers start: 9
  outliers final: 8
  residues processed: 37
  average time/residue: 0.0886
  time to fit residues: 3.9528
Evaluate side-chains
  39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  104 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:   30.0000
   chunk 40 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    2.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5290 r_free = 0.5290 target = 0.249122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5028 r_free = 0.5028 target = 0.210341 restraints weight = 5097.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.4998 rms_B_bonded: 5.15
r_work (final): 0.4998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3102
moved from start:          1.5373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3655  Z= 0.192
  Angle     :  0.719   8.122   4975  Z= 0.394
  Chirality :  0.051   0.183    590
  Planarity :  0.006   0.068    610
  Dihedral  :  6.702  25.353    490
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.00 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.31 (0.33), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.25), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 103 
 TYR   0.017   0.002   TYR C 105 
 PHE   0.028   0.003   PHE B  87 
 TRP   0.020   0.004   TRP E  79 
 HIS   0.009   0.002   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3655)
  covalent geometry    : angle       0.71859 ( 4975)
  hydrogen bonds       : bond        0.02950 (   56)
  hydrogen bonds       : angle       5.52784 (  168)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  103 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7287 (mtt90)
REVERT: E   89 GLU cc_start: 0.5371 (tm-30) cc_final: 0.4106 (tp30)
REVERT: E  104 ARG cc_start: 0.4772 (OUTLIER) cc_final: 0.2696 (mtt180)
  outliers start: 9
  outliers final: 6
  residues processed: 43
  average time/residue: 0.1185
  time to fit residues: 5.8820
Evaluate side-chains
  40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  104 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5339 r_free = 0.5339 target = 0.258073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5080 r_free = 0.5080 target = 0.216567 restraints weight = 4810.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.5029 rms_B_bonded: 5.08
r_work (final): 0.5029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2730
moved from start:          1.5165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3655  Z= 0.098
  Angle     :  0.539   7.604   4975  Z= 0.290
  Chirality :  0.047   0.134    590
  Planarity :  0.006   0.063    610
  Dihedral  :  5.529  21.247    490
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 21.28 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.03 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 103 
 TYR   0.011   0.001   TYR C 105 
 PHE   0.016   0.002   PHE C  95 
 TRP   0.002   0.001   TRP E  79 
 HIS   0.002   0.000   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 3655)
  covalent geometry    : angle       0.53855 ( 4975)
  hydrogen bonds       : bond        0.01768 (   56)
  hydrogen bonds       : angle       5.00929 (  168)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 939.71 seconds
wall clock time: 16 minutes 50.24 seconds (1010.24 seconds total)