Starting phenix.real_space_refine
on Wed Sep 17 03:19:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hud_0274/09_2025/6hud_0274.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hud_0274/09_2025/6hud_0274.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hud_0274/09_2025/6hud_0274.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hud_0274/09_2025/6hud_0274.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hud_0274/09_2025/6hud_0274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hud_0274/09_2025/6hud_0274.map"
  }
  resolution = 4.0
  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      15      5.16       5
     C    1795      2.51       5
     N     470      2.21       5
     O     625      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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2905
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 581
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.63, per 1000 atoms: 0.22
  Number of scatterers: 2905
  At special positions: 0
  Unit cell: (85.152, 71.847, 44.35, 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      15     16.00
     O     625      8.00
     N     470      7.00
     C    1795      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  91 " distance=2.02

  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: 0.23
  Conformation dependent library (CDL) restraints added in 71.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  700

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 54.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
      removed outlier: 6.345A  pdb=" N   MET A   3 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   MET B   3 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   MET D   3 " --> pdb=" O   LEU E   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 20
      removed outlier: 6.098A  pdb=" N   THR C  19 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 29
    Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 36
      removed outlier: 6.453A  pdb=" N   HIS A  32 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   GLN B  35 " --> pdb=" O   HIS A  32 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   VAL A  34 " --> pdb=" O   GLN B  35 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   HIS B  32 " --> pdb=" O   TYR C  33 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLN C  35 " --> pdb=" O   HIS B  32 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   VAL B  34 " --> pdb=" O   GLN C  35 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   HIS C  32 " --> pdb=" O   TYR D  33 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   GLN D  35 " --> pdb=" O   HIS C  32 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   VAL C  34 " --> pdb=" O   GLN D  35 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   HIS D  32 " --> pdb=" O   TYR E  33 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLN E  35 " --> pdb=" O   HIS D  32 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   VAL D  34 " --> pdb=" O   GLN E  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 73
      removed outlier: 5.946A  pdb=" N   ILE A  67 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   SER B  70 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   SER A  69 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ASN B  72 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   SER A  71 " --> pdb=" O   ASN B  72 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   ILE B  67 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   SER C  70 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   SER B  69 " --> pdb=" O   SER C  70 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ASN C  72 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   SER B  71 " --> pdb=" O   ASN C  72 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ILE C  67 " --> pdb=" O   ASP D  68 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER D  70 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   SER C  69 " --> pdb=" O   SER D  70 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASN D  72 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   SER C  71 " --> pdb=" O   ASN D  72 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILE D  67 " --> pdb=" O   ASP E  68 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   SER E  70 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   SER D  69 " --> pdb=" O   SER E  70 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   ASN E  72 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   SER D  71 " --> pdb=" O   ASN E  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 94
      removed outlier: 8.851A  pdb=" N   THR A  77 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   GLY B  80 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   SER A  79 " --> pdb=" O   GLY B  80 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   LYS B  82 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LEU A  81 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   GLU B  84 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   THR A  83 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   GLU B  86 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ASP A  85 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ASP B  88 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ALA A  87 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   TYR B  90 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   TYR A  89 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   GLN B  92 " --> pdb=" O   TYR A  89 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   CYS A  91 " --> pdb=" O   GLN B  92 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   TYR B  94 " --> pdb=" O   CYS A  91 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   SER A  93 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 8.970A  pdb=" N   THR B  77 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 9.453A  pdb=" N   GLY C  80 " --> pdb=" O   THR B  77 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   SER B  79 " --> pdb=" O   GLY C  80 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   LYS C  82 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   LEU B  81 " --> pdb=" O   LYS C  82 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   GLU C  84 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   THR B  83 " --> pdb=" O   GLU C  84 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   GLU C  86 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP B  85 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ASP C  88 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ALA B  87 " --> pdb=" O   ASP C  88 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   TYR C  90 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   TYR B  89 " --> pdb=" O   TYR C  90 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   GLN C  92 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   CYS B  91 " --> pdb=" O   GLN C  92 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   TYR C  94 " --> pdb=" O   CYS B  91 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   SER B  93 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE D  78 " --> pdb=" O   THR C  77 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   SER C  79 " --> pdb=" O   ILE D  78 " (cutoff:3.500A)
      removed outlier: 8.886A  pdb=" N   THR D  77 " --> pdb=" O   ILE E  78 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   GLY E  80 " --> pdb=" O   THR D  77 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   SER D  79 " --> pdb=" O   GLY E  80 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LYS E  82 " --> pdb=" O   SER D  79 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LEU D  81 " --> pdb=" O   LYS E  82 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   GLU E  84 " --> pdb=" O   LEU D  81 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   THR D  83 " --> pdb=" O   GLU E  84 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   GLU E  86 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ASP D  85 " --> pdb=" O   GLU E  86 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ASP E  88 " --> pdb=" O   ASP D  85 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ALA D  87 " --> pdb=" O   ASP E  88 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   TYR E  90 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   TYR D  89 " --> pdb=" O   TYR E  90 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN E  92 " --> pdb=" O   TYR D  89 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   CYS D  91 " --> pdb=" O   GLN E  92 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   TYR E  94 " --> pdb=" O   CYS D  91 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   SER D  93 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99
      removed outlier: 6.526A  pdb=" N   ASN A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASN B  97 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASN C  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ASN D  97 " --> pdb=" O   ASN E  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 102 through 104
      removed outlier: 6.766A  pdb=" N   PHE C 102 " --> pdb=" O   GLY D 103 " (cutoff:3.500A)

    53 hydrogen bonds defined for protein.
    159 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: 0.24

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 930
        1.34 -     1.46: 798
        1.46 -     1.58: 1227
        1.58 -     1.70: 0
        1.70 -     1.81: 20
  Bond restraints: 2975
  Sorted by residual:
  bond pdb=" CB  VAL D  34 "
       pdb=" CG1 VAL D  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.95e+00
  bond pdb=" CB  VAL E  34 "
       pdb=" CG1 VAL E  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.94e+00
  bond pdb=" CB  VAL A  34 "
       pdb=" CG1 VAL A  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.93e+00
  bond pdb=" CG  LEU A  81 "
       pdb=" CD2 LEU A  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.93e+00
  bond pdb=" CG  LEU D  81 "
       pdb=" CD2 LEU D  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.92e+00
  ... (remaining 2970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 3655
        1.76 -     3.52: 327
        3.52 -     5.27: 43
        5.27 -     7.03: 5
        7.03 -     8.79: 10
  Bond angle restraints: 4040
  Sorted by residual:
  angle pdb=" C   GLN C  35 "
        pdb=" N   TRP C  36 "
        pdb=" CA  TRP C  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.51    7.85 1.60e+00 3.91e-01 2.41e+01
  angle pdb=" C   GLN D  35 "
        pdb=" N   TRP D  36 "
        pdb=" CA  TRP D  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.52    7.84 1.60e+00 3.91e-01 2.40e+01
  angle pdb=" C   GLN B  35 "
        pdb=" N   TRP B  36 "
        pdb=" CA  TRP B  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.55    7.81 1.60e+00 3.91e-01 2.38e+01
  angle pdb=" C   GLN A  35 "
        pdb=" N   TRP A  36 "
        pdb=" CA  TRP A  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.55    7.81 1.60e+00 3.91e-01 2.38e+01
  angle pdb=" C   GLN E  35 "
        pdb=" N   TRP E  36 "
        pdb=" CA  TRP E  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.59    7.77 1.60e+00 3.91e-01 2.36e+01
  ... (remaining 4035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.86: 1316
        6.86 -    13.72: 304
       13.72 -    20.58: 70
       20.58 -    27.44: 10
       27.44 -    34.30: 5
  Dihedral angle restraints: 1705
    sinusoidal: 605
      harmonic: 1100
  Sorted by residual:
  dihedral pdb=" CA  TYR D  33 "
           pdb=" C   TYR D  33 "
           pdb=" N   VAL D  34 "
           pdb=" CA  VAL D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  TYR A  33 "
           pdb=" C   TYR A  33 "
           pdb=" N   VAL A  34 "
           pdb=" CA  VAL A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  TYR C  33 "
           pdb=" C   TYR C  33 "
           pdb=" N   VAL C  34 "
           pdb=" CA  VAL C  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 1702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 275
       0.050 -    0.100: 110
       0.100 -    0.150: 35
       0.150 -    0.200: 10
       0.200 -    0.250: 5
  Chirality restraints: 435
  Sorted by residual:
  chirality pdb=" CG  LEU B  81 "
            pdb=" CB  LEU B  81 "
            pdb=" CD1 LEU B  81 "
            pdb=" CD2 LEU B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CG  LEU C  81 "
            pdb=" CB  LEU C  81 "
            pdb=" CD1 LEU C  81 "
            pdb=" CD2 LEU C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CG  LEU D  81 "
            pdb=" CB  LEU D  81 "
            pdb=" CD1 LEU D  81 "
            pdb=" CD2 LEU D  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 432 not shown)

  Planarity restraints: 515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D   6 "   -0.041 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO D   7 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO D   7 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D   7 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C   6 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.16e+00
        pdb=" N   PRO C   7 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO C   7 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C   7 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B   6 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.15e+00
        pdb=" N   PRO B   7 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B   7 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B   7 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 512 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 314
        2.75 -     3.29: 2579
        3.29 -     3.83: 4944
        3.83 -     4.36: 5090
        4.36 -     4.90: 9062
  Nonbonded interactions: 21989
  Sorted by model distance:
  nonbonded pdb=" O   SER C  69 "
            pdb=" OG  SER D  70 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   SER A  69 "
            pdb=" OG  SER B  70 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   SER D  69 "
            pdb=" OG  SER E  70 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" O   SER B  69 "
            pdb=" OG  SER C  70 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" ND1 HIS B  32 "
            pdb=" OG  SER B  71 "
     model   vdw
     2.389 3.120
  ... (remaining 21984 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 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:             2.090
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     3.450
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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   0.057   2980  Z= 0.332
  Angle     :  1.126   8.787   4050  Z= 0.649
  Chirality :  0.066   0.250    435
  Planarity :  0.008   0.062    515
  Dihedral  :  8.281  34.301    990
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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: -5.06 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.017   0.004   TYR C  94 
 PHE   0.016   0.005   PHE A 102 
 TRP   0.022   0.004   TRP B  36 
 HIS   0.007   0.003   HIS B   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00722 ( 2975)
  covalent geometry    : angle       1.12420 ( 4040)
  SS BOND              : bond        0.01062 (    5)
  SS BOND              : angle       1.83230 (   10)
  hydrogen bonds       : bond        0.15000 (   53)
  hydrogen bonds       : angle       7.97490 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 MET cc_start: 0.8032 (mmm) cc_final: 0.7819 (mmt)
REVERT: A   90 TYR cc_start: 0.8006 (m-80) cc_final: 0.5939 (p90)
REVERT: B  102 PHE cc_start: 0.7613 (m-10) cc_final: 0.7358 (m-10)
REVERT: C   85 ASP cc_start: 0.7969 (m-30) cc_final: 0.7680 (m-30)
REVERT: D   85 ASP cc_start: 0.8232 (m-30) cc_final: 0.7984 (m-30)
REVERT: E   88 ASP cc_start: 0.7333 (m-30) cc_final: 0.6543 (m-30)
REVERT: E   90 TYR cc_start: 0.8343 (m-80) cc_final: 0.8092 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0415
  time to fit residues: 5.4757
Evaluate side-chains
  61 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   1 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 = 0.4180 r_free = 0.4180 target = 0.165801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.123569 restraints weight = 7689.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.125901 restraints weight = 5243.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.127697 restraints weight = 4032.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.128808 restraints weight = 3288.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.129143 restraints weight = 2844.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2980  Z= 0.182
  Angle     :  0.713   7.791   4050  Z= 0.394
  Chirality :  0.048   0.158    435
  Planarity :  0.005   0.041    515
  Dihedral  :  6.639  20.893    400
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  9.39 %
    Favored  : 90.30 %
  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: -5.01 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.81 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR C  37 
 PHE   0.012   0.002   PHE A   2 
 TRP   0.014   0.002   TRP E 100 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 2975)
  covalent geometry    : angle       0.71352 ( 4040)
  SS BOND              : bond        0.00126 (    5)
  SS BOND              : angle       0.39684 (   10)
  hydrogen bonds       : bond        0.03309 (   53)
  hydrogen bonds       : angle       5.94893 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8577 (m-80) cc_final: 0.6195 (p90)
REVERT: A  102 PHE cc_start: 0.8418 (m-10) cc_final: 0.8187 (m-10)
REVERT: B   12 GLU cc_start: 0.7712 (mp0) cc_final: 0.7467 (mp0)
REVERT: D   12 GLU cc_start: 0.7873 (mp0) cc_final: 0.7429 (mp0)
REVERT: E   16 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8188 (mmtm)
REVERT: E   84 GLU cc_start: 0.7947 (mp0) cc_final: 0.7689 (mp0)
REVERT: E   86 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: E   88 ASP cc_start: 0.8237 (m-30) cc_final: 0.7711 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0503
  time to fit residues: 4.5823
Evaluate side-chains
  58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   16 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.4170 r_free = 0.4170 target = 0.162572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.120740 restraints weight = 7776.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.122893 restraints weight = 5355.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.124558 restraints weight = 4115.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.125693 restraints weight = 3368.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.126566 restraints weight = 2904.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.4036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2980  Z= 0.199
  Angle     :  0.684   6.662   4050  Z= 0.385
  Chirality :  0.048   0.150    435
  Planarity :  0.005   0.040    515
  Dihedral  :  6.548  19.359    400
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 11.21 %
    Favored  : 87.88 %
  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: -4.99 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.002   TYR E  90 
 PHE   0.011   0.002   PHE C   2 
 TRP   0.015   0.002   TRP D 100 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 2975)
  covalent geometry    : angle       0.68388 ( 4040)
  SS BOND              : bond        0.00338 (    5)
  SS BOND              : angle       0.86676 (   10)
  hydrogen bonds       : bond        0.03466 (   53)
  hydrogen bonds       : angle       5.88504 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8595 (m-80) cc_final: 0.6241 (p90)
REVERT: A  102 PHE cc_start: 0.8385 (m-10) cc_final: 0.7894 (m-10)
REVERT: B    3 MET cc_start: 0.8161 (mmt) cc_final: 0.7392 (mmp)
REVERT: B   12 GLU cc_start: 0.7939 (mp0) cc_final: 0.7452 (mp0)
REVERT: C    3 MET cc_start: 0.8085 (mmp) cc_final: 0.7761 (mmp)
REVERT: C   12 GLU cc_start: 0.8293 (mp0) cc_final: 0.7814 (mp0)
REVERT: D   12 GLU cc_start: 0.7960 (mp0) cc_final: 0.7696 (mp0)
REVERT: D   16 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8071 (mmmm)
REVERT: E   16 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8243 (mmtp)
REVERT: E   86 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7520 (tm-30)
REVERT: E   88 ASP cc_start: 0.8038 (m-30) cc_final: 0.7303 (m-30)
REVERT: E   90 TYR cc_start: 0.9081 (m-80) cc_final: 0.8754 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 62
  average time/residue: 0.0501
  time to fit residues: 3.9430
Evaluate side-chains
  59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain E residue   16 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
E  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.159221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.117536 restraints weight = 7859.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.119623 restraints weight = 5420.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.121151 restraints weight = 4171.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.122057 restraints weight = 3425.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.122969 restraints weight = 2988.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.4718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   2980  Z= 0.264
  Angle     :  0.723   5.649   4050  Z= 0.412
  Chirality :  0.049   0.150    435
  Planarity :  0.005   0.044    515
  Dihedral  :  6.711  20.180    400
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.12 %
    Favored  : 86.36 %
  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: -5.05 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.002   TYR B  37 
 PHE   0.017   0.002   PHE C   2 
 TRP   0.017   0.003   TRP E 100 
 HIS   0.005   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 2975)
  covalent geometry    : angle       0.72128 ( 4040)
  SS BOND              : bond        0.01085 (    5)
  SS BOND              : angle       1.14520 (   10)
  hydrogen bonds       : bond        0.03539 (   53)
  hydrogen bonds       : angle       6.36070 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8562 (m-80) cc_final: 0.6261 (p90)
REVERT: A  102 PHE cc_start: 0.8416 (m-10) cc_final: 0.8069 (m-10)
REVERT: B   12 GLU cc_start: 0.7963 (mp0) cc_final: 0.7407 (mp0)
REVERT: C    3 MET cc_start: 0.8013 (mmp) cc_final: 0.7683 (mmp)
REVERT: C   12 GLU cc_start: 0.8279 (mp0) cc_final: 0.7948 (mp0)
REVERT: D   12 GLU cc_start: 0.8101 (mp0) cc_final: 0.7877 (mp0)
REVERT: D   16 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8098 (mmmm)
REVERT: E   16 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8203 (mmtm)
REVERT: E   86 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7551 (tm-30)
REVERT: E   88 ASP cc_start: 0.8164 (m-30) cc_final: 0.7597 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 64
  average time/residue: 0.0533
  time to fit residues: 4.3014
Evaluate side-chains
  59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain E residue   16 LYS
Chi-restraints excluded: chain E residue   83 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.4158 r_free = 0.4158 target = 0.165077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.121423 restraints weight = 7718.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.123588 restraints weight = 5347.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.124859 restraints weight = 4088.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.126127 restraints weight = 3405.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.126855 restraints weight = 2919.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2980  Z= 0.176
  Angle     :  0.655   7.218   4050  Z= 0.363
  Chirality :  0.047   0.134    435
  Planarity :  0.004   0.040    515
  Dihedral  :  6.285  19.923    400
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 13.94 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.98 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.002   TYR D  90 
 PHE   0.010   0.001   PHE C   2 
 TRP   0.016   0.002   TRP E 100 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 2975)
  covalent geometry    : angle       0.65384 ( 4040)
  SS BOND              : bond        0.00215 (    5)
  SS BOND              : angle       1.00378 (   10)
  hydrogen bonds       : bond        0.02836 (   53)
  hydrogen bonds       : angle       5.90323 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8147 (m-80) cc_final: 0.6058 (p90)
REVERT: B   12 GLU cc_start: 0.8016 (mp0) cc_final: 0.7579 (mp0)
REVERT: E   88 ASP cc_start: 0.7807 (m-30) cc_final: 0.7328 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0526
  time to fit residues: 3.9389
Evaluate side-chains
  56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   83 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.167517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.123883 restraints weight = 7739.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.126041 restraints weight = 5336.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.127528 restraints weight = 4099.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.128658 restraints weight = 3384.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.129501 restraints weight = 2926.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.5161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2980  Z= 0.129
  Angle     :  0.610   5.958   4050  Z= 0.334
  Chirality :  0.045   0.130    435
  Planarity :  0.004   0.035    515
  Dihedral  :  5.955  18.730    400
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.94 %
    Favored  : 83.94 %
  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: -4.92 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.75 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.001   TYR E  90 
 PHE   0.016   0.001   PHE D 102 
 TRP   0.015   0.001   TRP E 100 
 HIS   0.005   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2975)
  covalent geometry    : angle       0.60891 ( 4040)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       0.82643 (   10)
  hydrogen bonds       : bond        0.02190 (   53)
  hydrogen bonds       : angle       5.32536 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8048 (m-80) cc_final: 0.5920 (p90)
REVERT: B   12 GLU cc_start: 0.8074 (mp0) cc_final: 0.7619 (mp0)
REVERT: D   12 GLU cc_start: 0.8007 (mp0) cc_final: 0.7760 (mp0)
REVERT: E   86 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7115 (tm-30)
REVERT: E   88 ASP cc_start: 0.7742 (m-30) cc_final: 0.7409 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0548
  time to fit residues: 4.2169
Evaluate side-chains
  59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   83 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 = 0.4260 r_free = 0.4260 target = 0.179842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.135936 restraints weight = 7861.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.137377 restraints weight = 5733.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.137957 restraints weight = 4743.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.138298 restraints weight = 4253.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.138596 restraints weight = 3907.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.5232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2980  Z= 0.120
  Angle     :  0.624   8.051   4050  Z= 0.332
  Chirality :  0.045   0.127    435
  Planarity :  0.004   0.033    515
  Dihedral  :  5.752  17.994    400
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.24 %
    Favored  : 83.94 %
  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: -4.89 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR A  37 
 PHE   0.010   0.001   PHE D 102 
 TRP   0.011   0.001   TRP E 100 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 2975)
  covalent geometry    : angle       0.62361 ( 4040)
  SS BOND              : bond        0.00194 (    5)
  SS BOND              : angle       0.71267 (   10)
  hydrogen bonds       : bond        0.01946 (   53)
  hydrogen bonds       : angle       5.14114 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8015 (m-80) cc_final: 0.5796 (p90)
REVERT: B   12 GLU cc_start: 0.8083 (mp0) cc_final: 0.7633 (mp0)
REVERT: B   88 ASP cc_start: 0.8316 (m-30) cc_final: 0.8052 (p0)
REVERT: D   12 GLU cc_start: 0.8058 (mp0) cc_final: 0.7824 (mp0)
REVERT: D   90 TYR cc_start: 0.8963 (m-10) cc_final: 0.8762 (m-10)
REVERT: E   86 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7211 (tm-30)
REVERT: E   88 ASP cc_start: 0.7758 (m-30) cc_final: 0.7445 (m-30)
  outliers start: 6
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0435
  time to fit residues: 3.3612
Evaluate side-chains
  57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   83 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0770
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    1.3142

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.165710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.122235 restraints weight = 7909.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.124186 restraints weight = 5422.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.125905 restraints weight = 4177.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.126915 restraints weight = 3407.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.127771 restraints weight = 2952.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.5426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2980  Z= 0.170
  Angle     :  0.664   7.483   4050  Z= 0.360
  Chirality :  0.046   0.135    435
  Planarity :  0.004   0.034    515
  Dihedral  :  5.875  18.162    400
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.45 %
    Favored  : 82.42 %
  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: -4.96 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR B  37 
 PHE   0.012   0.001   PHE A 102 
 TRP   0.010   0.001   TRP E 100 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 2975)
  covalent geometry    : angle       0.66309 ( 4040)
  SS BOND              : bond        0.00223 (    5)
  SS BOND              : angle       0.82426 (   10)
  hydrogen bonds       : bond        0.02634 (   53)
  hydrogen bonds       : angle       5.40179 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8180 (m-80) cc_final: 0.5998 (p90)
REVERT: B   12 GLU cc_start: 0.8045 (mp0) cc_final: 0.7628 (mp0)
REVERT: C  101 VAL cc_start: 0.8116 (m) cc_final: 0.7903 (p)
REVERT: D   90 TYR cc_start: 0.8860 (m-10) cc_final: 0.8628 (m-80)
REVERT: E   86 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7139 (tm-30)
REVERT: E   88 ASP cc_start: 0.7739 (m-30) cc_final: 0.7409 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0377
  time to fit residues: 2.6561
Evaluate side-chains
  53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   83 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 15 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.164223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.120522 restraints weight = 7985.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.122625 restraints weight = 5467.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.124016 restraints weight = 4170.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.124959 restraints weight = 3439.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.125911 restraints weight = 2990.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   2980  Z= 0.226
  Angle     :  0.712   7.685   4050  Z= 0.392
  Chirality :  0.048   0.145    435
  Planarity :  0.004   0.036    515
  Dihedral  :  6.165  19.195    400
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.45 %
    Favored  : 82.42 %
  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: -5.03 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.002   TYR B  37 
 PHE   0.014   0.002   PHE A   2 
 TRP   0.010   0.002   TRP A 100 
 HIS   0.005   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 2975)
  covalent geometry    : angle       0.71161 ( 4040)
  SS BOND              : bond        0.00251 (    5)
  SS BOND              : angle       0.88299 (   10)
  hydrogen bonds       : bond        0.03202 (   53)
  hydrogen bonds       : angle       5.70927 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8431 (m-80) cc_final: 0.6211 (p90)
REVERT: B   12 GLU cc_start: 0.8032 (mp0) cc_final: 0.7546 (mp0)
REVERT: C  101 VAL cc_start: 0.8166 (m) cc_final: 0.7930 (p)
REVERT: D   12 GLU cc_start: 0.7971 (mp0) cc_final: 0.7718 (mp0)
REVERT: E   86 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: E   88 ASP cc_start: 0.7772 (m-30) cc_final: 0.7421 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0339
  time to fit residues: 2.4276
Evaluate side-chains
  50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   83 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 19 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0980
   chunk 16 optimal weight:    0.6980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.166776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.121903 restraints weight = 7866.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.123978 restraints weight = 5455.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.125397 restraints weight = 4190.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.126582 restraints weight = 3465.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.127417 restraints weight = 2963.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2980  Z= 0.174
  Angle     :  0.672   7.863   4050  Z= 0.363
  Chirality :  0.046   0.133    435
  Planarity :  0.004   0.035    515
  Dihedral  :  5.989  18.706    400
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.45 %
    Favored  : 83.03 %
  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: -4.97 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.017   0.002   TYR D  90 
 PHE   0.011   0.001   PHE C   2 
 TRP   0.012   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 2975)
  covalent geometry    : angle       0.67180 ( 4040)
  SS BOND              : bond        0.00208 (    5)
  SS BOND              : angle       0.70468 (   10)
  hydrogen bonds       : bond        0.02683 (   53)
  hydrogen bonds       : angle       5.50029 (  159)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8114 (m-80) cc_final: 0.6103 (p90)
REVERT: B   12 GLU cc_start: 0.8050 (mp0) cc_final: 0.7593 (mp0)
REVERT: C    3 MET cc_start: 0.8065 (mmp) cc_final: 0.7748 (tpt)
REVERT: C   84 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8184 (mm-30)
REVERT: C  101 VAL cc_start: 0.8153 (m) cc_final: 0.7895 (p)
REVERT: D   12 GLU cc_start: 0.7973 (mp0) cc_final: 0.7737 (mp0)
REVERT: E   86 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6932 (tm-30)
REVERT: E   88 ASP cc_start: 0.7742 (m-30) cc_final: 0.7388 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0385
  time to fit residues: 2.6906
Evaluate side-chains
  50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   84 GLU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   83 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.162288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.119098 restraints weight = 7786.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.121100 restraints weight = 5448.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.122468 restraints weight = 4209.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.123498 restraints weight = 3487.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.124089 restraints weight = 3059.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.5776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2980  Z= 0.258
  Angle     :  0.759   7.829   4050  Z= 0.420
  Chirality :  0.049   0.153    435
  Planarity :  0.005   0.039    515
  Dihedral  :  6.364  19.738    400
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.33 %
    Favored  : 87.67 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.06 %
    Favored  : 81.82 %
  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: -5.02 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.025   0.003   TYR D  90 
 PHE   0.016   0.002   PHE A   2 
 TRP   0.012   0.002   TRP A 100 
 HIS   0.006   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 2975)
  covalent geometry    : angle       0.75907 ( 4040)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.90272 (   10)
  hydrogen bonds       : bond        0.03601 (   53)
  hydrogen bonds       : angle       6.02905 (  159)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 655.37 seconds
wall clock time: 12 minutes 10.35 seconds (730.35 seconds total)