Starting phenix.real_space_refine
on Fri Aug 22 21:44:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i97_35259/08_2025/8i97_35259.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i97_35259/08_2025/8i97_35259.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i97_35259/08_2025/8i97_35259.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i97_35259/08_2025/8i97_35259.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i97_35259/08_2025/8i97_35259.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i97_35259/08_2025/8i97_35259.map"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.032
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      54      5.16       5
     C    5189      2.51       5
     N    1402      2.21       5
     O    1485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8130
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 2046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2046
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 14, 'TRANS': 261}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 133
          Unresolved non-hydrogen angles: 166
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "A"
      Number of atoms: 1565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1565
          Classifications: {'peptide': 210}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 4, 'TRANS': 205}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 59
    Chain: "B"
      Number of atoms: 2427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2427
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 174
          Unresolved non-hydrogen angles: 217
          Unresolved non-hydrogen dihedrals: 131
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 99
    Chain: "G"
      Number of atoms: 403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 403
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "H"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1689
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 51
  Time building chain proxies: 1.98, per 1000 atoms: 0.24
  Number of scatterers: 8130
  At special positions: 0
  Unit cell: (86.1111, 119.067, 122.257, 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      54     16.00
     O    1485      8.00
     N    1402      7.00
     C    5189      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS C 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 121 " - pdb=" SG  CYS C 355 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.03

  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: 0.60
  Conformation dependent library (CDL) restraints added in 442.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      37.3% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'C' and resid 20 through 50
      removed outlier: 3.834A  pdb=" N   SER C  26 " --> pdb=" O   PRO C  22 " (cutoff:3.500A)
      Proline residue:  C  39  - end of helix
    Processing helix  chain 'C' and resid 55 through 84
      removed outlier: 3.985A  pdb=" N   TRP C  60 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE C  61 " --> pdb=" O   ASN C  57 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   CYS C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
      Proline residue:  C  76  - end of helix
    Processing helix  chain 'C' and resid 91 through 126
      Proline residue:  C  99  - end of helix
      removed outlier: 5.105A  pdb=" N   VAL C 103 " --> pdb=" O   PRO C  99 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 133
      removed outlier: 3.537A  pdb=" N   ASN C 132 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 153
    Processing helix  chain 'C' and resid 154 through 160
    Processing helix  chain 'C' and resid 333 through 363
      removed outlier: 5.972A  pdb=" N   LEU C 347 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
      Proline residue:  C 348  - end of helix
    Processing helix  chain 'C' and resid 373 through 390
      removed outlier: 3.520A  pdb=" N   ARG C 377 " --> pdb=" O   SER C 373 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 390 through 403
      removed outlier: 3.819A  pdb=" N   LEU C 401 " --> pdb=" O   GLY C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 435
      removed outlier: 6.388A  pdb=" N   LEU C 413 " --> pdb=" O   LEU C 409 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   HIS C 418 " --> pdb=" O   MET C 414 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   VAL C 419 " --> pdb=" O   SER C 415 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER C 428 " --> pdb=" O   ALA C 424 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   CYS C 429 " --> pdb=" O   SER C 425 " (cutoff:3.500A)
      Proline residue:  C 432  - end of helix
    Processing helix  chain 'C' and resid 439 through 450
    Processing helix  chain 'A' and resid 8 through 31
      removed outlier: 3.630A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.674A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 4.135A  pdb=" N   ILE A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.680A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 332 through 351
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.502A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.568A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.957A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.936A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 162 through 164
      removed outlier: 3.538A  pdb=" N   GLU C 162 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE C 164 " --> pdb=" O   ARG C 171 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ARG C 171 " --> pdb=" O   PHE C 164 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192
      removed outlier: 6.381A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.545A  pdb=" N   ASP A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.018A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.898A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.676A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.635A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.591A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.563A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.240A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.240A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA H  92 " --> pdb=" O   LEU H 117 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141
      removed outlier: 3.652A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148
      removed outlier: 6.466A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1239 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: 1.30

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1486
        1.33 -     1.45: 2164
        1.45 -     1.57: 4585
        1.57 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 8306
  Sorted by residual:
  bond pdb=" N   GLN C 372 "
       pdb=" CA  GLN C 372 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.23e-02 6.61e+03 1.09e+01
  bond pdb=" N   PHE C 107 "
       pdb=" CA  PHE C 107 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.33e-02 5.65e+03 9.60e+00
  bond pdb=" N   MET C 153 "
       pdb=" CA  MET C 153 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.32e-02 5.74e+03 6.97e+00
  bond pdb=" C   PHE C 111 "
       pdb=" O   PHE C 111 "
    ideal  model  delta    sigma   weight residual
    1.236  1.205  0.031 1.29e-02 6.01e+03 5.65e+00
  bond pdb=" N   LEU A  13 "
       pdb=" CA  LEU A  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.30e-02 5.92e+03 4.63e+00
  ... (remaining 8301 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 10992
        1.56 -     3.12: 266
        3.12 -     4.68: 40
        4.68 -     6.24: 17
        6.24 -     7.81: 3
  Bond angle restraints: 11318
  Sorted by residual:
  angle pdb=" N   GLU A   9 "
        pdb=" CA  GLU A   9 "
        pdb=" C   GLU A   9 "
      ideal   model   delta    sigma   weight residual
     113.20  107.49    5.71 1.21e+00 6.83e-01 2.22e+01
  angle pdb=" N   ARG A  10 "
        pdb=" CA  ARG A  10 "
        pdb=" C   ARG A  10 "
      ideal   model   delta    sigma   weight residual
     111.82  106.54    5.28 1.16e+00 7.43e-01 2.07e+01
  angle pdb=" N   LEU A  13 "
        pdb=" CA  LEU A  13 "
        pdb=" C   LEU A  13 "
      ideal   model   delta    sigma   weight residual
     112.23  107.67    4.56 1.26e+00 6.30e-01 1.31e+01
  angle pdb=" C   ARG C 340 "
        pdb=" CA  ARG C 340 "
        pdb=" CB  ARG C 340 "
      ideal   model   delta    sigma   weight residual
     110.96  106.21    4.75 1.54e+00 4.22e-01 9.53e+00
  angle pdb=" CA  PHE C 107 "
        pdb=" C   PHE C 107 "
        pdb=" O   PHE C 107 "
      ideal   model   delta    sigma   weight residual
     119.31  115.51    3.80 1.24e+00 6.50e-01 9.38e+00
  ... (remaining 11313 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 4429
       17.06 -    34.12: 343
       34.12 -    51.18: 66
       51.18 -    68.25: 12
       68.25 -    85.31: 1
  Dihedral angle restraints: 4851
    sinusoidal: 1643
      harmonic: 3208
  Sorted by residual:
  dihedral pdb=" CA  PRO C  99 "
           pdb=" C   PRO C  99 "
           pdb=" N   SER C 100 "
           pdb=" CA  SER C 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.53   20.47     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CB  CYS C 121 "
           pdb=" SG  CYS C 121 "
           pdb=" SG  CYS C 355 "
           pdb=" CB  CYS C 355 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.68  -33.68     1      1.00e+01 1.00e-02 1.61e+01
  dihedral pdb=" C   PHE C 107 "
           pdb=" N   PHE C 107 "
           pdb=" CA  PHE C 107 "
           pdb=" CB  PHE C 107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.42    9.82     0      2.50e+00 1.60e-01 1.54e+01
  ... (remaining 4848 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1112
       0.060 -    0.121: 194
       0.121 -    0.181: 12
       0.181 -    0.242: 3
       0.242 -    0.302: 1
  Chirality restraints: 1322
  Sorted by residual:
  chirality pdb=" CA  PHE C 107 "
            pdb=" N   PHE C 107 "
            pdb=" C   PHE C 107 "
            pdb=" CB  PHE C 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  ARG C 340 "
            pdb=" N   ARG C 340 "
            pdb=" C   ARG C 340 "
            pdb=" CB  ARG C 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  VAL A 202 "
            pdb=" CA  VAL A 202 "
            pdb=" CG1 VAL A 202 "
            pdb=" CG2 VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1319 not shown)

  Planarity restraints: 1442
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  20 "    0.041 5.00e-02 4.00e+02   6.26e-02 6.26e+00
        pdb=" N   PRO C  21 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO C  21 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C  21 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO G  49 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  10 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   ARG A  10 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG A  10 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A  11 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1439 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1984
        2.79 -     3.32: 7592
        3.32 -     3.84: 13451
        3.84 -     4.37: 15509
        4.37 -     4.90: 27873
  Nonbonded interactions: 66409
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 220 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   ARG H  67 "
            pdb=" OG1 THR H  84 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR A 291 "
            pdb=" OD1 ASP A 299 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.304 3.040
  ... (remaining 66404 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:             2.800
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.570
  Find NCS groups from input model:        0.040
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
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      :  0.005   0.050   8310  Z= 0.216
  Angle     :  0.613   7.805  11326  Z= 0.340
  Chirality :  0.046   0.302   1322
  Planarity :  0.004   0.063   1442
  Dihedral  : 12.744  85.308   2769
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.76 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.00 (0.27), residues: 1095
  helix:  1.40 (0.28), residues: 377
  sheet: -0.53 (0.32), residues: 290
  loop : -0.79 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 161 
 TYR   0.015   0.002   TYR B 105 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.011   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 8306)
  covalent geometry    : angle       0.61296 (11318)
  SS BOND              : bond        0.00418 (    4)
  SS BOND              : angle       0.95553 (    8)
  hydrogen bonds       : bond        0.18663 (  429)
  hydrogen bonds       : angle       7.62453 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C  372 GLN cc_start: 0.7290 (tt0) cc_final: 0.6974 (tt0)
REVERT: A  254 ILE cc_start: 0.8561 (tp) cc_final: 0.8118 (tp)
REVERT: H  101 TYR cc_start: 0.7875 (m-80) cc_final: 0.7597 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 119
  average time/residue: 0.0841
  time to fit residues: 13.9042
Evaluate side-chains
  106 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 427 ASN
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 256 ASN
A 295 ASN
B  88 ASN
B 259 GLN
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.195597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.158655 restraints weight = 8899.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.79
r_work: 0.3656 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8310  Z= 0.195
  Angle     :  0.608   6.843  11326  Z= 0.322
  Chirality :  0.045   0.197   1322
  Planarity :  0.004   0.049   1442
  Dihedral  :  4.590  49.559   1185
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  8.20 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.10 (0.26), residues: 1095
  helix:  1.35 (0.28), residues: 379
  sheet: -0.60 (0.31), residues: 276
  loop : -0.87 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 161 
 TYR   0.013   0.002   TYR H 190 
 PHE   0.011   0.002   PHE C 442 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.007   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 8306)
  covalent geometry    : angle       0.60745 (11318)
  SS BOND              : bond        0.00500 (    4)
  SS BOND              : angle       1.24503 (    8)
  hydrogen bonds       : bond        0.04500 (  429)
  hydrogen bonds       : angle       5.45479 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.306 
Fit side-chains
REVERT: C   61 PHE cc_start: 0.7652 (m-10) cc_final: 0.7434 (m-10)
REVERT: C  372 GLN cc_start: 0.7461 (tt0) cc_final: 0.7095 (tt0)
REVERT: A  254 ILE cc_start: 0.8723 (tp) cc_final: 0.8207 (tp)
  outliers start: 11
  outliers final: 10
  residues processed: 119
  average time/residue: 0.0772
  time to fit residues: 13.0152
Evaluate side-chains
  116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 53 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0980
   chunk 4 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 106 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.198200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.161588 restraints weight = 8823.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.82
r_work: 0.3688 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3557 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8310  Z= 0.132
  Angle     :  0.550   8.161  11326  Z= 0.287
  Chirality :  0.043   0.205   1322
  Planarity :  0.004   0.050   1442
  Dihedral  :  4.365  50.348   1185
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.47 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 (0.26), residues: 1095
  helix:  1.44 (0.28), residues: 379
  sheet: -0.50 (0.32), residues: 267
  loop : -0.81 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 161 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.012   0.001   PHE H  29 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.004   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8306)
  covalent geometry    : angle       0.54932 (11318)
  SS BOND              : bond        0.00397 (    4)
  SS BOND              : angle       1.12444 (    8)
  hydrogen bonds       : bond        0.03862 (  429)
  hydrogen bonds       : angle       5.09778 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.311 
Fit side-chains
  outliers start: 11
  outliers final: 8
  residues processed: 114
  average time/residue: 0.0795
  time to fit residues: 12.7529
Evaluate side-chains
  114 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  141 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 15 optimal weight:    0.2980
   chunk 72 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 76 optimal weight:    0.2980
   chunk 41 optimal weight:    0.2980
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0770
   chunk 36 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0050
   overall best weight:    0.1952

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

Flipped N/Q/H residues before XYZ refinement:
A 295 ASN
B  32 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.200661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.164326 restraints weight = 8880.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.10
r_work: 0.3741 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3601 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8310  Z= 0.102
  Angle     :  0.518   7.317  11326  Z= 0.265
  Chirality :  0.042   0.161   1322
  Planarity :  0.003   0.051   1442
  Dihedral  :  3.878  18.263   1183
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.24 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.24 (0.26), residues: 1095
  helix:  1.66 (0.28), residues: 379
  sheet: -0.46 (0.31), residues: 280
  loop : -0.68 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 340 
 TYR   0.011   0.001   TYR H 190 
 PHE   0.013   0.001   PHE H  29 
 TRP   0.011   0.001   TRP B 297 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8306)
  covalent geometry    : angle       0.51717 (11318)
  SS BOND              : bond        0.00392 (    4)
  SS BOND              : angle       0.99848 (    8)
  hydrogen bonds       : bond        0.03261 (  429)
  hydrogen bonds       : angle       4.73027 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.290 
Fit side-chains
REVERT: C  151 PHE cc_start: 0.8077 (t80) cc_final: 0.7810 (t80)
REVERT: A  254 ILE cc_start: 0.8791 (tp) cc_final: 0.8193 (tp)
REVERT: H  116 THR cc_start: 0.8125 (t) cc_final: 0.7824 (p)
  outliers start: 10
  outliers final: 7
  residues processed: 118
  average time/residue: 0.0754
  time to fit residues: 12.7147
Evaluate side-chains
  117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain H residue   64 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 98 optimal weight:    0.4980
   chunk 106 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
B  32 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.197436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.158338 restraints weight = 8891.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 2.12
r_work: 0.3624 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8310  Z= 0.171
  Angle     :  0.566   7.162  11326  Z= 0.293
  Chirality :  0.044   0.145   1322
  Planarity :  0.004   0.050   1442
  Dihedral  :  4.086  23.735   1183
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.49 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.08 (0.26), residues: 1095
  helix:  1.53 (0.28), residues: 379
  sheet: -0.48 (0.31), residues: 274
  loop : -0.83 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.023   0.001   PHE C 442 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8306)
  covalent geometry    : angle       0.56502 (11318)
  SS BOND              : bond        0.00409 (    4)
  SS BOND              : angle       1.17513 (    8)
  hydrogen bonds       : bond        0.03602 (  429)
  hydrogen bonds       : angle       4.81985 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.263 
Fit side-chains
REVERT: C  151 PHE cc_start: 0.8092 (t80) cc_final: 0.7798 (t80)
REVERT: B  234 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8697 (m-80)
REVERT: H  116 THR cc_start: 0.8137 (t) cc_final: 0.7825 (p)
  outliers start: 15
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0725
  time to fit residues: 12.5387
Evaluate side-chains
  122 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 ARG
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  141 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 11 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.197537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.159225 restraints weight = 8843.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 2.07
r_work: 0.3659 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8310  Z= 0.153
  Angle     :  0.555   7.098  11326  Z= 0.287
  Chirality :  0.043   0.141   1322
  Planarity :  0.004   0.051   1442
  Dihedral  :  4.100  25.167   1183
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.24 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 (0.26), residues: 1095
  helix:  1.56 (0.28), residues: 378
  sheet: -0.52 (0.31), residues: 274
  loop : -0.85 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.009   0.001   PHE H  29 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8306)
  covalent geometry    : angle       0.55443 (11318)
  SS BOND              : bond        0.00403 (    4)
  SS BOND              : angle       1.11311 (    8)
  hydrogen bonds       : bond        0.03482 (  429)
  hydrogen bonds       : angle       4.81041 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.301 
Fit side-chains
REVERT: B  111 TYR cc_start: 0.9020 (m-80) cc_final: 0.8766 (m-80)
REVERT: B  234 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8734 (m-80)
REVERT: B  338 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8703 (mm)
REVERT: H  116 THR cc_start: 0.8252 (t) cc_final: 0.7959 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 128
  average time/residue: 0.0728
  time to fit residues: 13.3713
Evaluate side-chains
  127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  141 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0010
   chunk 52 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 59 optimal weight:    0.3980
   chunk 101 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.194784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.157535 restraints weight = 8932.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 1.83
r_work: 0.3663 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8310  Z= 0.167
  Angle     :  0.563   8.224  11326  Z= 0.291
  Chirality :  0.044   0.144   1322
  Planarity :  0.004   0.051   1442
  Dihedral  :  4.160  25.965   1183
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.37 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 (0.26), residues: 1095
  helix:  1.57 (0.28), residues: 378
  sheet: -0.66 (0.31), residues: 287
  loop : -0.81 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 340 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.009   0.001   PHE A 190 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8306)
  covalent geometry    : angle       0.56282 (11318)
  SS BOND              : bond        0.00387 (    4)
  SS BOND              : angle       1.06358 (    8)
  hydrogen bonds       : bond        0.03520 (  429)
  hydrogen bonds       : angle       4.84290 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.308 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8728 (m-80)
REVERT: B  338 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8692 (mm)
REVERT: H  116 THR cc_start: 0.8193 (t) cc_final: 0.7925 (p)
  outliers start: 21
  outliers final: 16
  residues processed: 125
  average time/residue: 0.0790
  time to fit residues: 14.2069
Evaluate side-chains
  127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  141 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 50 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 67 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.196956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.158555 restraints weight = 8864.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 2.07
r_work: 0.3652 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8310  Z= 0.160
  Angle     :  0.564  10.264  11326  Z= 0.290
  Chirality :  0.044   0.288   1322
  Planarity :  0.004   0.051   1442
  Dihedral  :  4.170  26.593   1183
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.49 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.01 (0.26), residues: 1095
  helix:  1.55 (0.28), residues: 380
  sheet: -0.68 (0.31), residues: 287
  loop : -0.82 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 340 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.009   0.001   PHE H  29 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8306)
  covalent geometry    : angle       0.56383 (11318)
  SS BOND              : bond        0.00391 (    4)
  SS BOND              : angle       1.02409 (    8)
  hydrogen bonds       : bond        0.03480 (  429)
  hydrogen bonds       : angle       4.84391 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.279 
Fit side-chains
REVERT: C  340 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6475 (pmt-80)
REVERT: B  111 TYR cc_start: 0.9015 (m-80) cc_final: 0.8760 (m-80)
REVERT: B  234 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8735 (m-80)
REVERT: B  338 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8700 (mm)
REVERT: H  116 THR cc_start: 0.8184 (t) cc_final: 0.7920 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 125
  average time/residue: 0.0812
  time to fit residues: 14.5109
Evaluate side-chains
  128 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  340 ARG
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  141 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 10 optimal weight:    0.0170
   chunk 61 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 68 optimal weight:    0.2980
   chunk 108 optimal weight:    0.4980
   chunk 89 optimal weight:    0.5980
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.2736

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.200104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.162322 restraints weight = 8888.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.02
r_work: 0.3689 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8310  Z= 0.112
  Angle     :  0.533  11.612  11326  Z= 0.272
  Chirality :  0.043   0.260   1322
  Planarity :  0.004   0.051   1442
  Dihedral  :  3.996  24.724   1183
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.38 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.15 (0.27), residues: 1095
  helix:  1.69 (0.28), residues: 380
  sheet: -0.62 (0.31), residues: 287
  loop : -0.75 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 340 
 TYR   0.010   0.001   TYR H 190 
 PHE   0.013   0.001   PHE H  29 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8306)
  covalent geometry    : angle       0.53247 (11318)
  SS BOND              : bond        0.00397 (    4)
  SS BOND              : angle       0.89120 (    8)
  hydrogen bonds       : bond        0.03217 (  429)
  hydrogen bonds       : angle       4.70273 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.392 
Fit side-chains
REVERT: C  340 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6361 (pmt-80)
REVERT: B  111 TYR cc_start: 0.8896 (m-80) cc_final: 0.8610 (m-80)
REVERT: B  234 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8770 (m-80)
REVERT: B  338 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8580 (mm)
REVERT: H  116 THR cc_start: 0.8025 (t) cc_final: 0.7816 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 116
  average time/residue: 0.0901
  time to fit residues: 14.8363
Evaluate side-chains
  121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 ARG
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  115 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0000
   chunk 42 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.196604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.158866 restraints weight = 8902.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 1.84
r_work: 0.3647 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3510 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8310  Z= 0.177
  Angle     :  0.579  11.942  11326  Z= 0.296
  Chirality :  0.044   0.260   1322
  Planarity :  0.004   0.051   1442
  Dihedral  :  4.163  24.748   1183
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.38 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.00 (0.26), residues: 1095
  helix:  1.55 (0.28), residues: 380
  sheet: -0.70 (0.30), residues: 287
  loop : -0.83 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 340 
 TYR   0.013   0.002   TYR H 190 
 PHE   0.009   0.001   PHE B 241 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 8306)
  covalent geometry    : angle       0.57892 (11318)
  SS BOND              : bond        0.00419 (    4)
  SS BOND              : angle       1.06590 (    8)
  hydrogen bonds       : bond        0.03507 (  429)
  hydrogen bonds       : angle       4.80922 ( 1239)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.296 
Fit side-chains
REVERT: C  340 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6394 (pmt-80)
REVERT: B  111 TYR cc_start: 0.9025 (m-80) cc_final: 0.8772 (m-80)
REVERT: B  211 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.8237 (m100)
REVERT: B  234 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8754 (m-80)
REVERT: H  116 THR cc_start: 0.8196 (t) cc_final: 0.7949 (p)
  outliers start: 19
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0824
  time to fit residues: 13.9822
Evaluate side-chains
  122 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 ARG
Chi-restraints excluded: chain C residue  398 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  295 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  115 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 78 optimal weight:    0.2980
   chunk 69 optimal weight:    0.2980
   chunk 58 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 ASN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.196951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.159160 restraints weight = 8932.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.85
r_work: 0.3655 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8310  Z= 0.164
  Angle     :  0.571  12.060  11326  Z= 0.292
  Chirality :  0.044   0.251   1322
  Planarity :  0.004   0.051   1442
  Dihedral  :  4.159  24.583   1183
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.50 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 (0.26), residues: 1095
  helix:  1.56 (0.28), residues: 380
  sheet: -0.74 (0.30), residues: 287
  loop : -0.83 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 340 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.009   0.001   PHE H  29 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8306)
  covalent geometry    : angle       0.57014 (11318)
  SS BOND              : bond        0.00398 (    4)
  SS BOND              : angle       1.01178 (    8)
  hydrogen bonds       : bond        0.03457 (  429)
  hydrogen bonds       : angle       4.81288 ( 1239)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2314.43 seconds
wall clock time: 40 minutes 19.08 seconds (2419.08 seconds total)