Starting phenix.real_space_refine
on Fri Oct 10 14:43:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x9s_38183/10_2025/8x9s_38183.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x9s_38183/10_2025/8x9s_38183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x9s_38183/10_2025/8x9s_38183.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x9s_38183/10_2025/8x9s_38183.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x9s_38183/10_2025/8x9s_38183.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x9s_38183/10_2025/8x9s_38183.map"
  }
  resolution = 3.49
  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=   0.001 sd=   0.014
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      42      5.16       5
     C    4329      2.51       5
     N    1146      2.21       5
     O    1257      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6774
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2515
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 104
          Unresolved non-hydrogen dihedrals: 72
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "G"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 417
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "R"
      Number of atoms: 2039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2039
          Classifications: {'peptide': 268}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 6, 'TRANS': 261}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1782
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 73
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'DHT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.09, per 1000 atoms: 0.31
  Number of scatterers: 6774
  At special positions: 0
  Unit cell: (76.36, 103.04, 124.2, 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      42     16.00
     O    1257      8.00
     N    1146      7.00
     C    4329      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 632 " - pdb=" SG  CYS R 704 " 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: 0.62
  Conformation dependent library (CDL) restraints added in 504.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1684

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      43.3% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.901A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 33
    Processing helix  chain 'B' and resid 172 through 174
      No H-bonds generated for 'chain 'B' and resid 172 through 174'
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.168A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.556A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 566 through 591
    Processing helix  chain 'R' and resid 599 through 624
      removed outlier: 4.023A  pdb=" N   HIS R 603 " --> pdb=" O   ASN R 599 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG R 624 " --> pdb=" O   LEU R 620 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 629 through 662
      removed outlier: 3.562A  pdb=" N   GLN R 633 " --> pdb=" O   THR R 629 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 671 through 680
    Processing helix  chain 'R' and resid 681 through 694
      removed outlier: 4.048A  pdb=" N   PHE R 693 " --> pdb=" O   ILE R 689 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 713 through 743
      removed outlier: 3.747A  pdb=" N   ALA R 718 " --> pdb=" O   TRP R 714 " (cutoff:3.500A)
      Proline residue:  R 719  - end of helix
    Processing helix  chain 'R' and resid 754 through 770
      removed outlier: 4.026A  pdb=" N   THR R 758 " --> pdb=" O   ALA R 754 " (cutoff:3.500A)
      Proline residue:  R 767  - end of helix
      removed outlier: 3.707A  pdb=" N   GLY R 770 " --> pdb=" O   LEU R 766 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 774 through 781
      removed outlier: 3.865A  pdb=" N   LEU R 778 " --> pdb=" O   VAL R 774 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 787 through 795
      removed outlier: 3.786A  pdb=" N   ASN R 795 " --> pdb=" O   PHE R 791 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 797 through 807
    Processing helix  chain 'R' and resid 810 through 827
      removed outlier: 3.677A  pdb=" N   ARG R 814 " --> pdb=" O   ASN R 810 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA R 815 " --> pdb=" O   SER R 811 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR R 827 " --> pdb=" O   VAL R 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.676A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 59
      removed outlier: 4.147A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.592A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.738A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.308A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 4.073A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.697A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50
      removed outlier: 8.003A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.760A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.479A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.945A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 191
      removed outlier: 3.508A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232
      removed outlier: 4.487A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.612A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 210
      removed outlier: 3.849A  pdb=" N   THR A 210 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 221 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 210
      removed outlier: 3.849A  pdb=" N   THR A 210 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 221 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.945A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    906 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.82 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: 2195
        1.34 -     1.46: 1353
        1.46 -     1.58: 3310
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6917
  Sorted by residual:
  bond pdb=" CB  PRO R 767 "
       pdb=" CG  PRO R 767 "
    ideal  model  delta    sigma   weight residual
    1.492  1.642 -0.150 5.00e-02 4.00e+02 8.95e+00
  bond pdb=" CA  LEU R 794 "
       pdb=" C   LEU R 794 "
    ideal  model  delta    sigma   weight residual
    1.522  1.506  0.016 9.30e-03 1.16e+04 3.02e+00
  bond pdb=" CA  ALA R 565 "
       pdb=" C   ALA R 565 "
    ideal  model  delta    sigma   weight residual
    1.526  1.505  0.021 1.39e-02 5.18e+03 2.24e+00
  bond pdb=" CA  VAL R 564 "
       pdb=" C   VAL R 564 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.017 1.27e-02 6.20e+03 1.88e+00
  bond pdb=" C10 DHT R 901 "
       pdb=" C9  DHT R 901 "
    ideal  model  delta    sigma   weight residual
    1.551  1.524  0.027 2.00e-02 2.50e+03 1.87e+00
  ... (remaining 6912 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 9326
        2.39 -     4.79: 89
        4.79 -     7.18: 9
        7.18 -     9.57: 0
        9.57 -    11.96: 2
  Bond angle restraints: 9426
  Sorted by residual:
  angle pdb=" CA  PRO R 767 "
        pdb=" N   PRO R 767 "
        pdb=" CD  PRO R 767 "
      ideal   model   delta    sigma   weight residual
     112.00  100.04   11.96 1.40e+00 5.10e-01 7.30e+01
  angle pdb=" N   LYS A 305 "
        pdb=" CA  LYS A 305 "
        pdb=" C   LYS A 305 "
      ideal   model   delta    sigma   weight residual
     114.62  109.91    4.71 1.14e+00 7.69e-01 1.70e+01
  angle pdb=" CB  MET A 386 "
        pdb=" CG  MET A 386 "
        pdb=" SD  MET A 386 "
      ideal   model   delta    sigma   weight residual
     112.70  122.70  -10.00 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" N   PRO R 767 "
        pdb=" CD  PRO R 767 "
        pdb=" CG  PRO R 767 "
      ideal   model   delta    sigma   weight residual
     103.20   98.59    4.61 1.50e+00 4.44e-01 9.46e+00
  angle pdb=" CA  LYS A 305 "
        pdb=" C   LYS A 305 "
        pdb=" N   SER A 306 "
      ideal   model   delta    sigma   weight residual
     119.71  116.33    3.38 1.17e+00 7.31e-01 8.33e+00
  ... (remaining 9421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.51: 3538
       19.51 -    39.01: 419
       39.01 -    58.52: 118
       58.52 -    78.03: 9
       78.03 -    97.53: 12
  Dihedral angle restraints: 4096
    sinusoidal: 1500
      harmonic: 2596
  Sorted by residual:
  dihedral pdb=" CB  CYS R 632 "
           pdb=" SG  CYS R 632 "
           pdb=" SG  CYS R 704 "
           pdb=" CB  CYS R 704 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.26  -45.74     1      1.00e+01 1.00e-02 2.90e+01
  dihedral pdb=" CA  ILE B  81 "
           pdb=" C   ILE B  81 "
           pdb=" N   TRP B  82 "
           pdb=" CA  TRP B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  PRO R 767 "
           pdb=" C   PRO R 767 "
           pdb=" N   ILE R 768 "
           pdb=" CA  ILE R 768 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.56   17.44     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 4093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 943
       0.055 -    0.109: 147
       0.109 -    0.164: 17
       0.164 -    0.218: 2
       0.218 -    0.273: 1
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" C10 DHT R 901 "
            pdb=" C1  DHT R 901 "
            pdb=" C5  DHT R 901 "
            pdb=" C9  DHT R 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.97   -2.70   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C13 DHT R 901 "
            pdb=" C12 DHT R 901 "
            pdb=" C14 DHT R 901 "
            pdb=" C17 DHT R 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.87   -2.67   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C17 DHT R 901 "
            pdb=" C13 DHT R 901 "
            pdb=" C16 DHT R 901 "
            pdb=" O17 DHT R 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.63   -0.17 2.00e-01 2.50e+01 6.98e-01
  ... (remaining 1107 not shown)

  Planarity restraints: 1192
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  DHT R 901 "    0.030 2.00e-02 2.50e+03   5.69e-02 3.24e+01
        pdb=" C3  DHT R 901 "   -0.098 2.00e-02 2.50e+03
        pdb=" C4  DHT R 901 "    0.030 2.00e-02 2.50e+03
        pdb=" O3  DHT R 901 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 766 "   -0.076 5.00e-02 4.00e+02   1.07e-01 1.82e+01
        pdb=" N   PRO R 767 "    0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO R 767 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO R 767 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "   -0.008 2.00e-02 2.50e+03   1.21e-02 3.63e+00
        pdb=" CG  TRP B  82 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1189 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1680
        2.79 -     3.32: 6488
        3.32 -     3.84: 10720
        3.84 -     4.37: 11031
        4.37 -     4.90: 19855
  Nonbonded interactions: 49774
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   CYS B  25 "
            pdb=" NZ  LYS G  29 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   THR B  34 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER R 593 "
            pdb=" NZ  LYS R 820 "
     model   vdw
     2.322 3.120
  ... (remaining 49769 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.590
  Find NCS groups from input model:        0.030
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.150   6918  Z= 0.130
  Angle     :  0.569  11.964   9428  Z= 0.309
  Chirality :  0.039   0.273   1110
  Planarity :  0.004   0.107   1192
  Dihedral  : 18.163  97.531   2409
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 33.71 %
    Favored  : 65.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.29), residues: 880
  helix:  1.92 (0.28), residues: 343
  sheet:  0.29 (0.46), residues: 141
  loop : -2.23 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.007   0.001   TYR A 318 
 PHE   0.009   0.001   PHE B 222 
 TRP   0.031   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6917)
  covalent geometry    : angle       0.56931 ( 9426)
  SS BOND              : bond        0.00691 (    1)
  SS BOND              : angle       0.35365 (    2)
  hydrogen bonds       : bond        0.15731 (  309)
  hydrogen bonds       : angle       5.46207 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.9089 (t70) cc_final: 0.8886 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0814
  time to fit residues: 8.3338
Evaluate side-chains
  64 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.070847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.060547 restraints weight = 21643.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 3.09
r_work: 0.2574 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.0917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   6918  Z= 0.114
  Angle     :  0.509   6.187   9428  Z= 0.266
  Chirality :  0.039   0.130   1110
  Planarity :  0.003   0.039   1192
  Dihedral  :  3.691  14.480   1003
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 28.73 %
    Favored  : 67.14 %
  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: -0.09 (0.29), residues: 880
  helix:  1.87 (0.29), residues: 351
  sheet:  0.43 (0.48), residues: 140
  loop : -2.21 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 373 
 TYR   0.008   0.001   TYR A 358 
 PHE   0.008   0.001   PHE A 340 
 TRP   0.022   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6917)
  covalent geometry    : angle       0.50914 ( 9426)
  SS BOND              : bond        0.00817 (    1)
  SS BOND              : angle       0.31904 (    2)
  hydrogen bonds       : bond        0.03791 (  309)
  hydrogen bonds       : angle       4.21976 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: R  601 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8494 (mtm-85)
  outliers start: 29
  outliers final: 17
  residues processed: 90
  average time/residue: 0.0813
  time to fit residues: 10.0564
Evaluate side-chains
  78 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 72 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
A 390 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.071049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.060669 restraints weight = 21622.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2659 rms_B_bonded: 3.09
r_work: 0.2569 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   6918  Z= 0.107
  Angle     :  0.493   6.706   9428  Z= 0.256
  Chirality :  0.038   0.130   1110
  Planarity :  0.003   0.038   1192
  Dihedral  :  3.458  14.515   1003
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 29.59 %
    Favored  : 66.86 %
  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: -0.05 (0.29), residues: 880
  helix:  1.88 (0.28), residues: 352
  sheet:  0.41 (0.47), residues: 140
  loop : -2.14 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.007   0.001   TYR A 358 
 PHE   0.008   0.001   PHE B 222 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6917)
  covalent geometry    : angle       0.49299 ( 9426)
  SS BOND              : bond        0.00809 (    1)
  SS BOND              : angle       0.45927 (    2)
  hydrogen bonds       : bond        0.03677 (  309)
  hydrogen bonds       : angle       4.01314 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.271 
Fit side-chains
REVERT: R  601 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8287 (mtm-85)
  outliers start: 25
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0761
  time to fit residues: 9.1242
Evaluate side-chains
  79 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  358 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    0.2980
   chunk 31 optimal weight:    3.9990
   chunk 70 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 10 optimal weight:    0.1980
   chunk 78 optimal weight:    0.0470
   chunk 65 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    0.4078

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
A 390 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.073338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.062989 restraints weight = 21228.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 3.09
r_work: 0.2626 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   6918  Z= 0.089
  Angle     :  0.480   7.059   9428  Z= 0.248
  Chirality :  0.038   0.129   1110
  Planarity :  0.003   0.037   1192
  Dihedral  :  3.333  16.943   1003
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 31.01 %
    Favored  : 66.15 %
  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:  0.09 (0.29), residues: 880
  helix:  2.01 (0.29), residues: 353
  sheet:  0.51 (0.47), residues: 139
  loop : -2.11 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.007   0.001   TYR A 358 
 PHE   0.010   0.001   PHE A 340 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 6917)
  covalent geometry    : angle       0.48049 ( 9426)
  SS BOND              : bond        0.00627 (    1)
  SS BOND              : angle       0.22700 (    2)
  hydrogen bonds       : bond        0.03157 (  309)
  hydrogen bonds       : angle       3.85414 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.197 
Fit side-chains
REVERT: B  225 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8452 (t-170)
REVERT: B  275 SER cc_start: 0.9317 (m) cc_final: 0.9108 (m)
REVERT: R  601 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8620 (mtm-85)
  outliers start: 20
  outliers final: 10
  residues processed: 87
  average time/residue: 0.0704
  time to fit residues: 8.7330
Evaluate side-chains
  76 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0370
   chunk 16 optimal weight:    0.0370
   chunk 84 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    1.0140

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.072485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.062081 restraints weight = 21829.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.2683 rms_B_bonded: 3.12
r_work: 0.2594 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   6918  Z= 0.102
  Angle     :  0.495   9.203   9428  Z= 0.252
  Chirality :  0.038   0.129   1110
  Planarity :  0.003   0.036   1192
  Dihedral  :  3.362  13.992   1003
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 30.87 %
    Favored  : 65.43 %
  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:  0.07 (0.29), residues: 880
  helix:  1.98 (0.28), residues: 353
  sheet:  0.50 (0.46), residues: 141
  loop : -2.11 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.007   0.001   TYR A 358 
 PHE   0.010   0.001   PHE A 290 
 TRP   0.023   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 6917)
  covalent geometry    : angle       0.49462 ( 9426)
  SS BOND              : bond        0.00629 (    1)
  SS BOND              : angle       0.25382 (    2)
  hydrogen bonds       : bond        0.03329 (  309)
  hydrogen bonds       : angle       3.81545 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 65
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B  275 SER cc_start: 0.9362 (m) cc_final: 0.9160 (m)
REVERT: R  601 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8346 (mtm-85)
  outliers start: 26
  outliers final: 19
  residues processed: 86
  average time/residue: 0.0735
  time to fit residues: 9.0524
Evaluate side-chains
  84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 142 HIS
B 340 ASN
R 806 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.066837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.056396 restraints weight = 22162.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.2563 rms_B_bonded: 3.15
r_work: 0.2471 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6918  Z= 0.200
  Angle     :  0.571   8.876   9428  Z= 0.293
  Chirality :  0.040   0.136   1110
  Planarity :  0.003   0.035   1192
  Dihedral  :  3.859  15.863   1003
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 30.30 %
    Favored  : 65.01 %
  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: -0.19 (0.28), residues: 880
  helix:  1.63 (0.28), residues: 352
  sheet:  0.45 (0.44), residues: 149
  loop : -2.19 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 304 
 TYR   0.013   0.001   TYR R 602 
 PHE   0.011   0.001   PHE B 235 
 TRP   0.026   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 6917)
  covalent geometry    : angle       0.57079 ( 9426)
  SS BOND              : bond        0.01089 (    1)
  SS BOND              : angle       1.04116 (    2)
  hydrogen bonds       : bond        0.04488 (  309)
  hydrogen bonds       : angle       4.10193 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.309 
Fit side-chains
REVERT: R  601 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8858 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8357 (t80)
  outliers start: 33
  outliers final: 26
  residues processed: 85
  average time/residue: 0.0726
  time to fit residues: 8.7624
Evaluate side-chains
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 58
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0970
   chunk 79 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 640 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.071425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.061043 restraints weight = 21453.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.2668 rms_B_bonded: 3.08
r_work: 0.2579 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   6918  Z= 0.096
  Angle     :  0.516   9.513   9428  Z= 0.260
  Chirality :  0.038   0.125   1110
  Planarity :  0.003   0.035   1192
  Dihedral  :  3.470  14.418   1003
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 31.72 %
    Favored  : 64.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.29), residues: 880
  helix:  1.75 (0.28), residues: 359
  sheet:  0.36 (0.44), residues: 151
  loop : -2.09 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.008   0.001   TYR A 358 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6917)
  covalent geometry    : angle       0.51646 ( 9426)
  SS BOND              : bond        0.00792 (    1)
  SS BOND              : angle       0.44369 (    2)
  hydrogen bonds       : bond        0.03375 (  309)
  hydrogen bonds       : angle       3.79628 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B  189 SER cc_start: 0.8932 (m) cc_final: 0.8347 (p)
REVERT: R  601 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8646 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8009 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 86
  average time/residue: 0.0780
  time to fit residues: 9.5488
Evaluate side-chains
  84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
R 640 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.069871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.059489 restraints weight = 21957.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.2637 rms_B_bonded: 3.12
r_work: 0.2548 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6918  Z= 0.118
  Angle     :  0.521   8.035   9428  Z= 0.265
  Chirality :  0.039   0.127   1110
  Planarity :  0.003   0.034   1192
  Dihedral  :  3.496  14.471   1003
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 31.58 %
    Favored  : 64.30 %
  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: -0.02 (0.29), residues: 880
  helix:  1.87 (0.28), residues: 353
  sheet:  0.42 (0.44), residues: 151
  loop : -2.16 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.007   0.001   TYR A 358 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6917)
  covalent geometry    : angle       0.52108 ( 9426)
  SS BOND              : bond        0.00733 (    1)
  SS BOND              : angle       0.38252 (    2)
  hydrogen bonds       : bond        0.03574 (  309)
  hydrogen bonds       : angle       3.79661 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  391 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8053 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 86
  average time/residue: 0.0751
  time to fit residues: 9.3623
Evaluate side-chains
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
R 640 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.069867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.059381 restraints weight = 21912.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.2625 rms_B_bonded: 3.19
r_work: 0.2534 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6918  Z= 0.126
  Angle     :  0.542  10.981   9428  Z= 0.272
  Chirality :  0.039   0.127   1110
  Planarity :  0.003   0.034   1192
  Dihedral  :  3.552  14.659   1003
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 31.72 %
    Favored  : 64.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.29), residues: 880
  helix:  1.80 (0.28), residues: 353
  sheet:  0.50 (0.44), residues: 150
  loop : -2.18 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.007   0.001   TYR A 358 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6917)
  covalent geometry    : angle       0.54223 ( 9426)
  SS BOND              : bond        0.00779 (    1)
  SS BOND              : angle       0.44518 (    2)
  hydrogen bonds       : bond        0.03690 (  309)
  hydrogen bonds       : angle       3.82662 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 61
  time to evaluate  : 0.272 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.9098 (m-80) cc_final: 0.8866 (m-80)
REVERT: A  391 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8136 (t80)
  outliers start: 27
  outliers final: 23
  residues processed: 82
  average time/residue: 0.0763
  time to fit residues: 8.8619
Evaluate side-chains
  85 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 18 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0020
   chunk 46 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.3996

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 640 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.070258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.059825 restraints weight = 21919.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2628 rms_B_bonded: 3.12
r_work: 0.2538 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6918  Z= 0.120
  Angle     :  0.541  10.563   9428  Z= 0.272
  Chirality :  0.039   0.127   1110
  Planarity :  0.003   0.034   1192
  Dihedral  :  3.551  14.646   1003
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 31.15 %
    Favored  : 64.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.29), residues: 880
  helix:  1.80 (0.28), residues: 353
  sheet:  0.49 (0.44), residues: 150
  loop : -2.18 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.008   0.001   TYR A 358 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6917)
  covalent geometry    : angle       0.54068 ( 9426)
  SS BOND              : bond        0.00784 (    1)
  SS BOND              : angle       0.43393 (    2)
  hydrogen bonds       : bond        0.03662 (  309)
  hydrogen bonds       : angle       3.82417 (  906)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 61
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  391 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8089 (t80)
  outliers start: 29
  outliers final: 24
  residues processed: 83
  average time/residue: 0.0749
  time to fit residues: 8.8955
Evaluate side-chains
  85 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 640 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.071023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.060650 restraints weight = 21561.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.2668 rms_B_bonded: 3.09
r_work: 0.2579 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   6918  Z= 0.096
  Angle     :  0.528  10.177   9428  Z= 0.265
  Chirality :  0.038   0.128   1110
  Planarity :  0.003   0.034   1192
  Dihedral  :  3.453  13.953   1003
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 32.15 %
    Favored  : 64.86 %
  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: -0.02 (0.29), residues: 880
  helix:  1.87 (0.28), residues: 353
  sheet:  0.38 (0.44), residues: 151
  loop : -2.16 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 601 
 TYR   0.008   0.001   TYR A 358 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 6917)
  covalent geometry    : angle       0.52802 ( 9426)
  SS BOND              : bond        0.00662 (    1)
  SS BOND              : angle       0.11545 (    2)
  hydrogen bonds       : bond        0.03370 (  309)
  hydrogen bonds       : angle       3.75761 (  906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1394.17 seconds
wall clock time: 24 minutes 49.14 seconds (1489.14 seconds total)