Starting phenix.real_space_refine
on Thu Feb 13 16:46:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ni2_9375/02_2025/6ni2_9375.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ni2_9375/02_2025/6ni2_9375.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ni2_9375/02_2025/6ni2_9375.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ni2_9375/02_2025/6ni2_9375.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ni2_9375/02_2025/6ni2_9375.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ni2_9375/02_2025/6ni2_9375.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4506 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      21      5.16       5
     C    3402      2.51       5
     N     910      2.21       5
     O    1042      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5381
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 865
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 2, 'TRANS': 110}
    Chain: "B"
      Number of atoms: 2699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2699
          Classifications: {'peptide': 353}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 101
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 72
    Chain: "H"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 908
          Classifications: {'peptide': 117}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 800
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "V"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 109
          Classifications: {'peptide': 14}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 13}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 3.94, per 1000 atoms: 0.73
  Number of scatterers: 5381
  At special positions: 0
  Unit cell: (95.68, 91.52, 109.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P       6     15.00
     O    1042      8.00
     N     910      7.00
     C    3402      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.05

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 901.3 milliseconds
  

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1312

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 15 sheets defined
      2.8% alpha, 44.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'B' and resid 98 through 109
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'H' and resid 90 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 23
      removed outlier: 3.728A  pdb=" N   MET A  82 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER A  70 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38
    Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93
      removed outlier: 3.537A  pdb=" N   THR A 108 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 117
      removed outlier: 3.580A  pdb=" N   LYS B  10 " --> pdb=" O   ALA V 361 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.700A  pdb=" N   VAL B 164 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 168 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.907A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL B  53 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   GLN B  85 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL B  55 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   ASN B  83 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   CYS B  59 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE B  75 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.700A  pdb=" N   VAL B 164 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 168 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.907A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 188
      removed outlier: 3.680A  pdb=" N   HIS B 198 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 274 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR B 272 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL B 218 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LYS B 270 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL B 220 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   PHE B 268 " --> pdb=" O   VAL B 220 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 208
      removed outlier: 4.629A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.511A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LYS B 230 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ILE B 231 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLU B 257 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   ILE B 233 " --> pdb=" O   MET B 255 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   MET B 255 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   VAL B 235 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   CYS B 251 " --> pdb=" O   GLN B 237 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ALA B 239 " --> pdb=" O   TYR B 249 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   TYR B 249 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE B 241 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 208
      removed outlier: 4.629A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.511A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL B 343 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 10
      removed outlier: 3.557A  pdb=" N   SER H  24 " --> pdb=" O   SER H  10 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU H  21 " --> pdb=" O   MET H  86 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14
      removed outlier: 6.094A  pdb=" N   GLY H  13 " --> pdb=" O   THR H 120 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 13 through 14
      removed outlier: 6.094A  pdb=" N   GLY H  13 " --> pdb=" O   THR H 120 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   ARG H 103 " --> pdb=" O   LEU H 110 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   LEU H 110 " --> pdb=" O   ARG H 103 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.659A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.926A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)

    179 hydrogen bonds defined for protein.
    465 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.02

  Time building geometry restraints manager: 1.60 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: 1685
        1.34 -     1.46: 1215
        1.46 -     1.58: 2547
        1.58 -     1.70: 22
        1.70 -     1.82: 28
  Bond restraints: 5497
  Sorted by residual:
  bond pdb=" OG1 TPO V 360 "
       pdb=" P   TPO V 360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.605  0.112 2.00e-02 2.50e+03 3.16e+01
  bond pdb=" OG1 TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.625  0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" O1P TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.525  1.610 -0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" O2P TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.607 -0.079 2.00e-02 2.50e+03 1.57e+01
  bond pdb=" O2P TPO V 360 "
       pdb=" P   TPO V 360 "
    ideal  model  delta    sigma   weight residual
    1.528  1.605 -0.077 2.00e-02 2.50e+03 1.47e+01
  ... (remaining 5492 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.13: 7216
        3.13 -     6.26: 240
        6.26 -     9.40: 27
        9.40 -    12.53: 3
       12.53 -    15.66: 2
  Bond angle restraints: 7488
  Sorted by residual:
  angle pdb=" N   GLU B 156 "
        pdb=" CA  GLU B 156 "
        pdb=" C   GLU B 156 "
      ideal   model   delta    sigma   weight residual
     110.24  117.78   -7.54 1.41e+00 5.03e-01 2.86e+01
  angle pdb=" C   THR B  74 "
        pdb=" N   PHE B  75 "
        pdb=" CA  PHE B  75 "
      ideal   model   delta    sigma   weight residual
     122.29  130.49   -8.20 1.65e+00 3.67e-01 2.47e+01
  angle pdb=" C   GLN B 189 "
        pdb=" N   PHE B 190 "
        pdb=" CA  PHE B 190 "
      ideal   model   delta    sigma   weight residual
     122.07  112.79    9.28 2.01e+00 2.48e-01 2.13e+01
  angle pdb=" CA  LEU A  85 "
        pdb=" CB  LEU A  85 "
        pdb=" CG  LEU A  85 "
      ideal   model   delta    sigma   weight residual
     116.30  100.64   15.66 3.50e+00 8.16e-02 2.00e+01
  angle pdb=" N   PHE B  75 "
        pdb=" CA  PHE B  75 "
        pdb=" C   PHE B  75 "
      ideal   model   delta    sigma   weight residual
     109.23  102.62    6.61 1.55e+00 4.16e-01 1.82e+01
  ... (remaining 7483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.64: 3059
       13.64 -    27.29: 185
       27.29 -    40.93: 30
       40.93 -    54.58: 7
       54.58 -    68.22: 4
  Dihedral angle restraints: 3285
    sinusoidal: 1239
      harmonic: 2046
  Sorted by residual:
  dihedral pdb=" CA  ALA A  51 "
           pdb=" C   ALA A  51 "
           pdb=" N   THR A  52 "
           pdb=" CA  THR A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.84   35.16     0      5.00e+00 4.00e-02 4.95e+01
  dihedral pdb=" CA  TYR A  59 "
           pdb=" C   TYR A  59 "
           pdb=" N   ALA A  60 "
           pdb=" CA  ALA A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  SER A  50 "
           pdb=" C   SER A  50 "
           pdb=" N   ALA A  51 "
           pdb=" CA  ALA A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.98   25.02     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 3282 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 641
       0.077 -    0.154: 188
       0.154 -    0.231: 23
       0.231 -    0.308: 2
       0.308 -    0.385: 2
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CB  VAL B 164 "
            pdb=" CA  VAL B 164 "
            pdb=" CG1 VAL B 164 "
            pdb=" CG2 VAL B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.24   -0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" CA  GLU B 156 "
            pdb=" N   GLU B 156 "
            pdb=" C   GLU B 156 "
            pdb=" CB  GLU B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.13e+00
  chirality pdb=" CA  VAL B 164 "
            pdb=" N   VAL B 164 "
            pdb=" C   VAL B 164 "
            pdb=" CB  VAL B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.57e+00
  ... (remaining 853 not shown)

  Planarity restraints: 951
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B   9 "    0.028 2.00e-02 2.50e+03   2.35e-02 9.65e+00
        pdb=" CG  PHE B   9 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE B   9 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE B   9 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B   9 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE B   9 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B   9 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 113 "    0.022 2.00e-02 2.50e+03   2.04e-02 8.32e+00
        pdb=" CG  TYR B 113 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 113 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 113 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 113 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 113 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 113 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 113 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  21 "    0.019 2.00e-02 2.50e+03   1.97e-02 7.76e+00
        pdb=" CG  TYR B  21 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  21 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  21 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  21 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  21 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  21 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR B  21 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 948 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1065
        2.78 -     3.31: 4502
        3.31 -     3.84: 8646
        3.84 -     4.37: 9354
        4.37 -     4.90: 16512
  Nonbonded interactions: 40079
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 204 "
            pdb=" OH  TYR B 208 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   ASP A  89 "
            pdb=" OH  TYR A  93 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG  SEP V 363 "
            pdb=" N   SEP V 364 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" O   ASP L  83 "
            pdb=" OH  TYR L  87 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OD1 ASP H  76 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.337 3.040
  ... (remaining 40074 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.100
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
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      :  0.010   0.121   5497  Z= 0.626
  Angle     :  1.327  15.660   7488  Z= 0.729
  Chirality :  0.070   0.385    856
  Planarity :  0.007   0.055    951
  Dihedral  :  9.614  68.220   1967
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.74 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.31), residues: 682
  helix: -0.31 (1.30), residues: 12
  sheet: -0.88 (0.30), residues: 271
  loop : -1.06 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.004   TRP A  36 
 HIS   0.012   0.004   HIS A  44 
 PHE   0.054   0.005   PHE B   9 
 TYR   0.051   0.005   TYR B 113 
 ARG   0.015   0.002   ARG H 101 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.6443 (tpt-90) cc_final: 0.6016 (tpp80)
REVERT: A   64 LYS cc_start: 0.8636 (ptpt) cc_final: 0.8060 (ptpp)
REVERT: A   67 PHE cc_start: 0.7543 (m-10) cc_final: 0.7182 (m-10)
REVERT: A   85 LEU cc_start: 0.7294 (mt) cc_final: 0.7091 (mt)
REVERT: B   42 LEU cc_start: 0.7307 (tp) cc_final: 0.6995 (pp)
REVERT: B   77 LYS cc_start: 0.8015 (tppt) cc_final: 0.7525 (mmtm)
REVERT: B  232 LYS cc_start: 0.6625 (mttt) cc_final: 0.5500 (tttt)
REVERT: H   48 LEU cc_start: 0.9402 (mt) cc_final: 0.9089 (tp)
REVERT: H   71 PHE cc_start: 0.8088 (m-10) cc_final: 0.6749 (m-10)
REVERT: L   25 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8169 (mtm-85)
REVERT: L   28 GLN cc_start: 0.8997 (tt0) cc_final: 0.8639 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2097
  time to fit residues: 39.4853
Evaluate side-chains
  75 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0000
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B  85 GLN
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.106715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.091360 restraints weight = 18999.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.093779 restraints weight = 11529.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.095500 restraints weight = 8039.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5497  Z= 0.275
  Angle     :  0.776  13.486   7488  Z= 0.400
  Chirality :  0.047   0.154    856
  Planarity :  0.005   0.058    951
  Dihedral  :  6.857  57.513    780
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.51 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.32), residues: 682
  helix:  0.41 (1.44), residues: 12
  sheet: -0.14 (0.31), residues: 274
  loop : -0.54 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  36 
 HIS   0.008   0.002   HIS B 219 
 PHE   0.014   0.003   PHE B 277 
 TYR   0.030   0.002   TYR H  57 
 ARG   0.008   0.001   ARG A  45 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.6590 (tpt-90) cc_final: 0.6163 (tpp80)
REVERT: A   22 CYS cc_start: 0.6770 (t) cc_final: 0.6540 (m)
REVERT: A   64 LYS cc_start: 0.8569 (ptpt) cc_final: 0.8310 (ptpp)
REVERT: A   75 LYS cc_start: 0.8506 (tttt) cc_final: 0.8253 (ttmt)
REVERT: A   82 MET cc_start: 0.8176 (mtp) cc_final: 0.7570 (mtp)
REVERT: B   77 LYS cc_start: 0.8231 (tppt) cc_final: 0.7753 (mmtm)
REVERT: B  185 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6955 (mt-10)
REVERT: H   40 VAL cc_start: 0.9139 (t) cc_final: 0.8891 (m)
REVERT: L   28 GLN cc_start: 0.8860 (tt0) cc_final: 0.8579 (mt0)
REVERT: L   82 GLU cc_start: 0.8463 (pm20) cc_final: 0.8165 (pp20)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2028
  time to fit residues: 27.0867
Evaluate side-chains
  79 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain H residue   76 ASP
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0370
   chunk 46 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    2.0064

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

Flipped N/Q/H residues before XYZ refinement:
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** 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 = 0.3882 r_free = 0.3882 target = 0.104524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.089466 restraints weight = 19552.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.091838 restraints weight = 11716.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.093501 restraints weight = 8135.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5497  Z= 0.289
  Angle     :  0.703   7.696   7488  Z= 0.366
  Chirality :  0.046   0.154    856
  Planarity :  0.005   0.054    951
  Dihedral  :  6.727  58.313    780
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 12.81 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.32), residues: 682
  helix:  1.09 (1.50), residues: 12
  sheet:  0.11 (0.31), residues: 283
  loop : -0.51 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  36 
 HIS   0.007   0.002   HIS A  44 
 PHE   0.014   0.002   PHE A  67 
 TYR   0.027   0.002   TYR H  83 
 ARG   0.006   0.001   ARG L  25 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.7521 (m-10) cc_final: 0.7199 (m-10)
REVERT: A   82 MET cc_start: 0.8052 (mtp) cc_final: 0.7339 (mtp)
REVERT: B  225 ASN cc_start: 0.8253 (m110) cc_final: 0.8012 (p0)
REVERT: H   32 VAL cc_start: 0.7802 (p) cc_final: 0.7526 (t)
REVERT: H   55 SER cc_start: 0.8763 (t) cc_final: 0.8527 (m)
REVERT: L   28 GLN cc_start: 0.8907 (tt0) cc_final: 0.8643 (mt0)
REVERT: L   88 TYR cc_start: 0.8412 (m-10) cc_final: 0.8141 (m-10)
  outliers start: 27
  outliers final: 20
  residues processed: 95
  average time/residue: 0.1626
  time to fit residues: 20.7797
Evaluate side-chains
  88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue   80 PHE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   76 ASP
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.108634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.093707 restraints weight = 19726.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.095993 restraints weight = 12125.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.097555 restraints weight = 8498.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5497  Z= 0.281
  Angle     :  0.675   8.284   7488  Z= 0.350
  Chirality :  0.045   0.145    856
  Planarity :  0.005   0.044    951
  Dihedral  :  6.598  58.813    780
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 13.86 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.31), residues: 682
  helix:  1.55 (1.56), residues: 12
  sheet:  0.42 (0.32), residues: 259
  loop : -0.72 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  36 
 HIS   0.006   0.001   HIS A  44 
 PHE   0.011   0.002   PHE B 277 
 TYR   0.022   0.002   TYR H  83 
 ARG   0.004   0.001   ARG A  45 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.7521 (m-10) cc_final: 0.7153 (m-10)
REVERT: A   82 MET cc_start: 0.7749 (mtp) cc_final: 0.7353 (mtp)
REVERT: H   32 VAL cc_start: 0.7672 (p) cc_final: 0.7461 (t)
REVERT: H   55 SER cc_start: 0.8792 (t) cc_final: 0.8533 (m)
REVERT: L   28 GLN cc_start: 0.8968 (tt0) cc_final: 0.8717 (mt0)
  outliers start: 29
  outliers final: 21
  residues processed: 91
  average time/residue: 0.1632
  time to fit residues: 19.7591
Evaluate side-chains
  88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue   80 PHE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** 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 = 0.3921 r_free = 0.3921 target = 0.110741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.095764 restraints weight = 19293.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.098065 restraints weight = 11753.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.099767 restraints weight = 8143.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5497  Z= 0.194
  Angle     :  0.627   7.206   7488  Z= 0.321
  Chirality :  0.044   0.138    856
  Planarity :  0.004   0.040    951
  Dihedral  :  6.289  56.798    780
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 16.14 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.32), residues: 682
  helix:  1.80 (1.64), residues: 12
  sheet:  0.38 (0.30), residues: 286
  loop : -0.50 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B 198 
 PHE   0.010   0.002   PHE A  29 
 TYR   0.018   0.002   TYR H  83 
 ARG   0.003   0.000   ARG L  25 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7881 (mtp) cc_final: 0.7417 (mtp)
REVERT: H   32 VAL cc_start: 0.7649 (p) cc_final: 0.7417 (t)
REVERT: H   55 SER cc_start: 0.8800 (t) cc_final: 0.8565 (m)
  outliers start: 24
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1509
  time to fit residues: 18.9660
Evaluate side-chains
  86 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 25 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.109623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.094693 restraints weight = 19484.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.096998 restraints weight = 11900.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.098697 restraints weight = 8265.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5497  Z= 0.250
  Angle     :  0.656   7.000   7488  Z= 0.336
  Chirality :  0.046   0.236    856
  Planarity :  0.004   0.039    951
  Dihedral  :  6.320  58.631    780
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 18.07 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.32), residues: 682
  helix:  1.93 (1.65), residues: 12
  sheet:  0.49 (0.31), residues: 278
  loop : -0.60 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  36 
 HIS   0.004   0.001   HIS A  44 
 PHE   0.009   0.002   PHE B 277 
 TYR   0.017   0.002   TYR H  83 
 ARG   0.003   0.000   ARG L  25 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  240 ASP cc_start: 0.7693 (p0) cc_final: 0.7347 (m-30)
REVERT: H   32 VAL cc_start: 0.7518 (p) cc_final: 0.7296 (t)
REVERT: H   55 SER cc_start: 0.8844 (t) cc_final: 0.8622 (m)
  outliers start: 24
  outliers final: 22
  residues processed: 83
  average time/residue: 0.1594
  time to fit residues: 17.6470
Evaluate side-chains
  88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 36 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** 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 = 0.3928 r_free = 0.3928 target = 0.109962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.095207 restraints weight = 19681.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.097511 restraints weight = 12065.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.099136 restraints weight = 8451.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5497  Z= 0.169
  Angle     :  0.611   6.877   7488  Z= 0.310
  Chirality :  0.045   0.234    856
  Planarity :  0.004   0.038    951
  Dihedral  :  5.955  55.225    780
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.42 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.33), residues: 682
  helix:  1.99 (1.66), residues: 12
  sheet:  0.52 (0.31), residues: 290
  loop : -0.44 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  36 
 HIS   0.002   0.001   HIS B 198 
 PHE   0.016   0.002   PHE A  67 
 TYR   0.017   0.002   TYR B 249 
 ARG   0.003   0.000   ARG L  25 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8453 (tttt) cc_final: 0.8085 (tptt)
REVERT: B  240 ASP cc_start: 0.7382 (p0) cc_final: 0.7055 (m-30)
REVERT: H   32 VAL cc_start: 0.7499 (p) cc_final: 0.7283 (t)
  outliers start: 22
  outliers final: 21
  residues processed: 83
  average time/residue: 0.1673
  time to fit residues: 18.4545
Evaluate side-chains
  82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 10 optimal weight:    0.1980
   chunk 62 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    5.6388

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

Flipped N/Q/H residues before XYZ refinement:
A  13 GLN
A  81 GLN
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.102664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.088512 restraints weight = 20117.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.090638 restraints weight = 12557.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.092167 restraints weight = 8858.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.5408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.090   5497  Z= 0.656
  Angle     :  0.960  11.125   7488  Z= 0.499
  Chirality :  0.053   0.222    856
  Planarity :  0.006   0.045    951
  Dihedral  :  7.387  62.840    780
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 20.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 17.37 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.31), residues: 682
  helix:  0.80 (1.42), residues: 12
  sheet:  0.06 (0.31), residues: 278
  loop : -1.31 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP L  36 
 HIS   0.009   0.002   HIS A  44 
 PHE   0.022   0.004   PHE H  71 
 TYR   0.028   0.003   TYR H  83 
 ARG   0.008   0.001   ARG H  22 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: B  215 SER cc_start: 0.9045 (m) cc_final: 0.8690 (p)
REVERT: B  240 ASP cc_start: 0.7325 (p0) cc_final: 0.6840 (m-30)
REVERT: B  267 THR cc_start: 0.8200 (m) cc_final: 0.7996 (m)
REVERT: B  326 LYS cc_start: 0.7469 (tttt) cc_final: 0.7033 (tttt)
REVERT: L   71 ASP cc_start: 0.7332 (m-30) cc_final: 0.6871 (p0)
  outliers start: 30
  outliers final: 26
  residues processed: 89
  average time/residue: 0.1494
  time to fit residues: 17.9988
Evaluate side-chains
  90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue   80 PHE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  255 MET
Chi-restraints excluded: chain B residue  268 PHE
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B 181 GLN
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.108033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.093332 restraints weight = 19457.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.095675 restraints weight = 11807.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.097371 restraints weight = 8126.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.5396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5497  Z= 0.248
  Angle     :  0.692   9.423   7488  Z= 0.353
  Chirality :  0.046   0.225    856
  Planarity :  0.004   0.038    951
  Dihedral  :  6.692  59.149    780
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.65 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.32), residues: 682
  helix:  1.85 (1.62), residues: 12
  sheet:  0.40 (0.32), residues: 265
  loop : -1.14 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  36 
 HIS   0.003   0.001   HIS A  44 
 PHE   0.013   0.002   PHE H  71 
 TYR   0.017   0.002   TYR H  83 
 ARG   0.003   0.001   ARG H  41 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8439 (tttt) cc_final: 0.8068 (tptt)
REVERT: B  215 SER cc_start: 0.9041 (m) cc_final: 0.8686 (p)
REVERT: L   71 ASP cc_start: 0.7120 (m-30) cc_final: 0.6713 (p0)
  outliers start: 22
  outliers final: 21
  residues processed: 81
  average time/residue: 0.1596
  time to fit residues: 17.2103
Evaluate side-chains
  84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 29 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 HIS ** 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 = 0.3897 r_free = 0.3897 target = 0.107650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.092978 restraints weight = 19591.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.095180 restraints weight = 12216.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.096719 restraints weight = 8633.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.5571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5497  Z= 0.234
  Angle     :  0.720   9.844   7488  Z= 0.362
  Chirality :  0.046   0.268    856
  Planarity :  0.004   0.040    951
  Dihedral  :  6.481  58.468    780
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.35 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.33), residues: 682
  helix:  2.00 (1.65), residues: 12
  sheet:  0.36 (0.33), residues: 261
  loop : -0.91 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  36 
 HIS   0.003   0.001   HIS A  44 
 PHE   0.024   0.002   PHE H  71 
 TYR   0.017   0.002   TYR B 249 
 ARG   0.004   0.001   ARG H  41 

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.8468 (tttt) cc_final: 0.8126 (tptt)
REVERT: B  215 SER cc_start: 0.9008 (m) cc_final: 0.8678 (p)
  outliers start: 20
  outliers final: 20
  residues processed: 75
  average time/residue: 0.1617
  time to fit residues: 16.1752
Evaluate side-chains
  82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  251 CYS
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 353 HIS ** 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 = 0.3896 r_free = 0.3896 target = 0.107756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.093061 restraints weight = 19850.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.095287 restraints weight = 12306.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.096879 restraints weight = 8674.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.5616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5497  Z= 0.246
  Angle     :  0.705   8.105   7488  Z= 0.356
  Chirality :  0.046   0.276    856
  Planarity :  0.004   0.039    951
  Dihedral  :  6.381  58.669    780
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.53 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.15 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.33), residues: 682
  helix:  2.08 (1.68), residues: 12
  sheet:  0.35 (0.33), residues: 261
  loop : -0.89 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  36 
 HIS   0.003   0.001   HIS A  44 
 PHE   0.011   0.002   PHE H  71 
 TYR   0.015   0.002   TYR L  88 
 ARG   0.003   0.001   ARG H  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1919.00 seconds
wall clock time: 35 minutes 16.45 seconds (2116.45 seconds total)