Starting phenix.real_space_refine
on Tue Mar  3 19:28:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7try_26103/03_2026/7try_26103.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7try_26103/03_2026/7try_26103.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7try_26103/03_2026/7try_26103.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7try_26103/03_2026/7try_26103.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7try_26103/03_2026/7try_26103.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7try_26103/03_2026/7try_26103.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    5281      2.51       5
     N    1491      2.21       5
     O    1529      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8340
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "P"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2031
          Classifications: {'peptide': 325}
          Incomplete info: {'truncation_to_alanine': 196}
          Link IDs: {'PTRANS': 9, 'TRANS': 315}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 746
          Unresolved non-hydrogen angles: 967
          Unresolved non-hydrogen dihedrals: 628
          Unresolved non-hydrogen chiralities: 78
          Planarities with less than four sites: {'ASN:plan1': 9, 'ASP:plan': 5, 'GLN:plan1': 9, 'TRP:plan': 4, 'ARG:plan': 11, 'GLU:plan': 14, 'TYR:plan': 11, 'HIS:plan': 5, 'PHE:plan': 16}
          Unresolved non-hydrogen planarities: 423
    Chain: "U"
      Number of atoms: 233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 233
          Classifications: {'peptide': 39}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 37}
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 50
    Chain: "A"
      Number of atoms: 1642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1642
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PTRANS': 5, 'TRANS': 216}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 249
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 12, 'ASN:plan1': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 125
    Chain: "B"
      Number of atoms: 2385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2385
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 61}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 215
          Unresolved non-hydrogen angles: 265
          Unresolved non-hydrogen dihedrals: 165
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 17, 'GLN:plan1': 6, 'ARG:plan': 6, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 141
    Chain: "G"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 372
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "H"
      Number of atoms: 1677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1677
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'GLU:plan': 7, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 63
  Time building chain proxies: 2.03, per 1000 atoms: 0.24
  Number of scatterers: 8340
  At special positions: 0
  Unit cell: (105.545, 137.94, 145.255, 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      39     16.00
     O    1529      8.00
     N    1491      7.00
     C    5281      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS P  64 " - pdb=" SG  CYS P  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P 184 " - pdb=" SG  CYS P 254 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04

  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: 0.78
  Conformation dependent library (CDL) restraints added in 260.7 milliseconds
  

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2286

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 15 sheets defined
      40.3% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'P' and resid 109 through 141
      removed outlier: 3.790A  pdb=" N   TYR P 113 " --> pdb=" O   TYR P 109 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 146 through 169
    Processing helix  chain 'P' and resid 173 through 179
    Processing helix  chain 'P' and resid 181 through 215
    Processing helix  chain 'P' and resid 215 through 222
      removed outlier: 3.843A  pdb=" N   GLU P 220 " --> pdb=" O   THR P 216 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 223 through 233
      removed outlier: 3.708A  pdb=" N   PHE P 227 " --> pdb=" O   ARG P 223 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE P 229 " --> pdb=" O   CYS P 225 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 234 through 250
      removed outlier: 3.957A  pdb=" N   ILE P 238 " --> pdb=" O   ILE P 234 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 265 through 298
      Proline residue:  P 271  - end of helix
      removed outlier: 3.505A  pdb=" N   LEU P 274 " --> pdb=" O   GLY P 270 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR P 298 " --> pdb=" O   LEU P 294 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 300 through 319
      Proline residue:  P 317  - end of helix
    Processing helix  chain 'P' and resid 321 through 326
      removed outlier: 4.002A  pdb=" N   PHE P 326 " --> pdb=" O   THR P 322 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 333 through 361
      removed outlier: 4.422A  pdb=" N   GLY P 352 " --> pdb=" O   GLN P 348 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   PHE P 353 " --> pdb=" O   SER P 349 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 363 through 383
    Processing helix  chain 'U' and resid 5 through 7
      No H-bonds generated for 'chain 'U' and resid 5 through 7'
    Processing helix  chain 'U' and resid 8 through 40
    Processing helix  chain 'A' and resid 13 through 38
    Processing helix  chain 'A' and resid 47 through 50
    Processing helix  chain 'A' and resid 51 through 61
      removed outlier: 3.955A  pdb=" N   ILE A  61 " --> pdb=" O   LYS A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.865A  pdb=" N   ILE A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLU A 221 " --> pdb=" O   HIS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 4.131A  pdb=" N   ASP A 236 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 260
    Processing helix  chain 'A' and resid 275 through 286
      removed outlier: 3.819A  pdb=" N   LEU A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 4.032A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE B  37 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 3.962A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.569A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'P' and resid 62 through 63
      removed outlier: 3.631A  pdb=" N   TYR P  80 " --> pdb=" O   ASN P  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 67 through 68
    Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 195
      removed outlier: 6.434A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 10.708A  pdb=" N   SER A 225 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   LYS A  41 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 8.463A  pdb=" N   MET A 227 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU A  43 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LEU A 229 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU A  45 " --> pdb=" O   LEU A 229 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   ALA A 231 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 52
      removed outlier: 7.031A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.839A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.070A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.548A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.010A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.730A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.150A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.790A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148
      removed outlier: 7.032A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASN H 194 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 146 through 148
      removed outlier: 4.102A  pdb=" N   GLN H 231 " --> pdb=" O   THR H 238 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   THR H 238 " --> pdb=" O   GLN H 231 " (cutoff:3.500A)

    490 hydrogen bonds defined for protein.
    1377 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: 1.15

  Time building geometry restraints manager: 0.96 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: 2773
        1.34 -     1.47: 2143
        1.47 -     1.59: 3537
        1.59 -     1.71: 0
        1.71 -     1.83: 53
  Bond restraints: 8506
  Sorted by residual:
  bond pdb=" C   PHE P 236 "
       pdb=" N   PRO P 237 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.25e-02 6.40e+03 2.50e+00
  bond pdb=" C   ASP H  74 "
       pdb=" N   PRO H  75 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.25e-02 6.40e+03 2.41e+00
  bond pdb=" C   ILE P 234 "
       pdb=" N   PRO P 235 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.018 1.25e-02 6.40e+03 1.98e+00
  bond pdb=" CB  ASN B 237 "
       pdb=" CG  ASN B 237 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 2.50e-02 1.60e+03 1.61e+00
  bond pdb=" C   ALA H  40 "
       pdb=" N   PRO H  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.016 1.36e-02 5.41e+03 1.46e+00
  ... (remaining 8501 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 11286
        2.05 -     4.10: 310
        4.10 -     6.15: 31
        6.15 -     8.20: 11
        8.20 -    10.25: 1
  Bond angle restraints: 11639
  Sorted by residual:
  angle pdb=" N   GLY P 270 "
        pdb=" CA  GLY P 270 "
        pdb=" C   GLY P 270 "
      ideal   model   delta    sigma   weight residual
     112.34  119.59   -7.25 2.04e+00 2.40e-01 1.26e+01
  angle pdb=" N   ILE P 234 "
        pdb=" CA  ILE P 234 "
        pdb=" C   ILE P 234 "
      ideal   model   delta    sigma   weight residual
     112.35  116.56   -4.21 1.20e+00 6.94e-01 1.23e+01
  angle pdb=" C   ARG H 191 "
        pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
      ideal   model   delta    sigma   weight residual
     121.54  127.72   -6.18 1.91e+00 2.74e-01 1.05e+01
  angle pdb=" N   MET B 262 "
        pdb=" CA  MET B 262 "
        pdb=" C   MET B 262 "
      ideal   model   delta    sigma   weight residual
     108.55  113.72   -5.17 1.62e+00 3.81e-01 1.02e+01
  angle pdb=" C   PHE P 327 "
        pdb=" N   VAL P 328 "
        pdb=" CA  VAL P 328 "
      ideal   model   delta    sigma   weight residual
     121.70  127.14   -5.44 1.80e+00 3.09e-01 9.14e+00
  ... (remaining 11634 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.89: 4606
        9.89 -    19.79: 291
       19.79 -    29.68: 32
       29.68 -    39.57: 16
       39.57 -    49.47: 7
  Dihedral angle restraints: 4952
    sinusoidal: 1433
      harmonic: 3519
  Sorted by residual:
  dihedral pdb=" CA  CYS P 254 "
           pdb=" C   CYS P 254 "
           pdb=" N   TRP P 255 "
           pdb=" CA  TRP P 255 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.20  -22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  HIS H  35 "
           pdb=" C   HIS H  35 "
           pdb=" N   TRP H  36 "
           pdb=" CA  TRP H  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.35   19.65     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  PHE H  32 "
           pdb=" C   PHE H  32 "
           pdb=" N   GLY H  33 "
           pdb=" CA  GLY H  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.63   19.37     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 4949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 961
       0.045 -    0.089: 297
       0.089 -    0.134: 89
       0.134 -    0.179: 27
       0.179 -    0.223: 5
  Chirality restraints: 1379
  Sorted by residual:
  chirality pdb=" CA  ILE H 100 "
            pdb=" N   ILE H 100 "
            pdb=" C   ILE H 100 "
            pdb=" CB  ILE H 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  PHE P 236 "
            pdb=" N   PHE P 236 "
            pdb=" C   PHE P 236 "
            pdb=" CB  PHE P 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.90e-01
  chirality pdb=" CG  LEU H 174 "
            pdb=" CB  LEU H 174 "
            pdb=" CD1 LEU H 174 "
            pdb=" CD2 LEU H 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.43e-01
  ... (remaining 1376 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU P 276 "   -0.015 2.00e-02 2.50e+03   2.94e-02 8.67e+00
        pdb=" C   LEU P 276 "    0.051 2.00e-02 2.50e+03
        pdb=" O   LEU P 276 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU P 277 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE P 159 "   -0.014 2.00e-02 2.50e+03   2.11e-02 7.76e+00
        pdb=" CG  PHE P 159 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE P 159 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE P 159 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE P 159 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE P 159 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE P 159 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG P 288 "   -0.014 2.00e-02 2.50e+03   2.76e-02 7.59e+00
        pdb=" C   ARG P 288 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ARG P 288 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE P 289 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1680
        2.79 -     3.32: 7543
        3.32 -     3.84: 13538
        3.84 -     4.37: 14606
        4.37 -     4.90: 26214
  Nonbonded interactions: 63581
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" NZ  LYS A 215 "
            pdb=" OD1 ASN B 230 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" NH2 ARG P 376 "
            pdb=" O   HIS B 311 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" O   ILE B 123 "
            pdb=" OG  SER B 136 "
     model   vdw
     2.362 3.040
  ... (remaining 63576 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.150
  Find NCS groups from input model:        0.050
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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      :  0.004   0.047   8510  Z= 0.213
  Angle     :  0.805  10.254  11647  Z= 0.487
  Chirality :  0.050   0.223   1379
  Planarity :  0.006   0.042   1511
  Dihedral  :  7.340  42.297   2654
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.03 (0.23), residues: 1185
  helix:  1.35 (0.22), residues: 420
  sheet:  0.61 (0.29), residues: 270
  loop :  0.29 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 202 
 TYR   0.019   0.002   TYR A 356 
 PHE   0.048   0.003   PHE P 159 
 TRP   0.022   0.002   TRP B 169 
 HIS   0.014   0.003   HIS P 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8506)
  covalent geometry    : angle       0.80274 (11639)
  SS BOND              : bond        0.00488 (    4)
  SS BOND              : angle       2.19021 (    8)
  hydrogen bonds       : bond        0.12922 (  486)
  hydrogen bonds       : angle       6.17424 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 366
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  305 TYR cc_start: 0.5770 (m-10) cc_final: 0.4705 (t80)
REVERT: P  312 THR cc_start: 0.9161 (m) cc_final: 0.8860 (t)
REVERT: B   52 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7467 (ptp-110)
REVERT: B  146 LEU cc_start: 0.8681 (tp) cc_final: 0.8170 (mp)
REVERT: B  188 MET cc_start: 0.7922 (mmm) cc_final: 0.7551 (mmm)
REVERT: B  241 PHE cc_start: 0.8381 (p90) cc_final: 0.8053 (p90)
REVERT: G   22 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7044 (mt-10)
REVERT: H   81 LEU cc_start: 0.8327 (tp) cc_final: 0.8060 (tp)
REVERT: H  174 LEU cc_start: 0.8449 (tp) cc_final: 0.7562 (tp)
REVERT: H  178 LEU cc_start: 0.8722 (tp) cc_final: 0.8409 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 366
  average time/residue: 0.0969
  time to fit residues: 47.1930
Evaluate side-chains
  198 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.0370
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.0040
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    1.2030

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

Flipped N/Q/H residues before XYZ refinement:
P 124 HIS
P 152 HIS
P 170 GLN
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 HIS
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 352 ASN
B  32 GLN
B  91 HIS
B 183 HIS
H 142 GLN
H 231 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.094668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.079200 restraints weight = 30665.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.081812 restraints weight = 14200.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.083490 restraints weight = 8454.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.084595 restraints weight = 5947.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.085293 restraints weight = 4653.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8510  Z= 0.142
  Angle     :  0.608  10.045  11647  Z= 0.322
  Chirality :  0.044   0.192   1379
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.235  30.222   1284
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 16.27 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole:  1.85 (0.24), residues: 1185
  helix:  2.59 (0.23), residues: 434
  sheet:  0.79 (0.31), residues: 259
  loop :  0.30 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 306 
 TYR   0.017   0.002   TYR H 190 
 PHE   0.017   0.002   PHE A  55 
 TRP   0.016   0.002   TRP P 201 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8506)
  covalent geometry    : angle       0.60196 (11639)
  SS BOND              : bond        0.00999 (    4)
  SS BOND              : angle       3.37996 (    8)
  hydrogen bonds       : bond        0.03644 (  486)
  hydrogen bonds       : angle       4.53136 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  151 ILE cc_start: 0.8682 (mt) cc_final: 0.7976 (tp)
REVERT: P  159 PHE cc_start: 0.8854 (m-10) cc_final: 0.8516 (m-10)
REVERT: P  305 TYR cc_start: 0.5880 (m-10) cc_final: 0.4757 (t80)
REVERT: P  312 THR cc_start: 0.9300 (m) cc_final: 0.8946 (t)
REVERT: A   24 MET cc_start: 0.8110 (tmm) cc_final: 0.7768 (tmm)
REVERT: A  274 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7937 (p0)
REVERT: A  312 MET cc_start: 0.7912 (tmm) cc_final: 0.7656 (tmm)
REVERT: B   52 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7640 (ptp-110)
REVERT: B  146 LEU cc_start: 0.8607 (tp) cc_final: 0.8155 (mp)
REVERT: B  241 PHE cc_start: 0.9029 (p90) cc_final: 0.8373 (p90)
REVERT: B  289 TYR cc_start: 0.8318 (m-80) cc_final: 0.8032 (m-80)
REVERT: H  229 CYS cc_start: 0.4791 (p) cc_final: 0.4561 (p)
  outliers start: 31
  outliers final: 20
  residues processed: 231
  average time/residue: 0.0732
  time to fit residues: 24.4356
Evaluate side-chains
  203 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  286 ILE
Chi-restraints excluded: chain P residue  328 VAL
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   32 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 57 optimal weight:   30.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 237 GLN
** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 142 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.087138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.071591 restraints weight = 30651.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073930 restraints weight = 14119.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.075461 restraints weight = 8508.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.076485 restraints weight = 6053.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.077055 restraints weight = 4792.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   8510  Z= 0.266
  Angle     :  0.645   7.134  11647  Z= 0.345
  Chirality :  0.046   0.219   1379
  Planarity :  0.004   0.041   1511
  Dihedral  :  4.377  23.504   1284
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 17.90 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.78 (0.24), residues: 1185
  helix:  2.67 (0.23), residues: 424
  sheet:  0.56 (0.31), residues: 267
  loop :  0.29 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 314 
 TYR   0.023   0.002   TYR H 190 
 PHE   0.017   0.002   PHE H  32 
 TRP   0.025   0.003   TRP B 332 
 HIS   0.006   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 8506)
  covalent geometry    : angle       0.64349 (11639)
  SS BOND              : bond        0.01174 (    4)
  SS BOND              : angle       1.66930 (    8)
  hydrogen bonds       : bond        0.03722 (  486)
  hydrogen bonds       : angle       4.61419 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 183
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  305 TYR cc_start: 0.6322 (m-10) cc_final: 0.5048 (t80)
REVERT: P  312 THR cc_start: 0.9383 (m) cc_final: 0.9033 (t)
REVERT: A   24 MET cc_start: 0.8121 (tmm) cc_final: 0.7771 (tmm)
REVERT: A   41 LYS cc_start: 0.7854 (mppt) cc_final: 0.7605 (mppt)
REVERT: A  312 MET cc_start: 0.7929 (tmm) cc_final: 0.7510 (tmm)
REVERT: B   52 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7773 (ptp-110)
REVERT: B   82 TRP cc_start: 0.9103 (m100) cc_final: 0.8804 (m100)
REVERT: B   85 TYR cc_start: 0.8955 (m-10) cc_final: 0.8036 (m-10)
REVERT: G   11 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8648 (tp-100)
REVERT: H   20 LEU cc_start: 0.8482 (mt) cc_final: 0.8254 (mt)
REVERT: H  111 TRP cc_start: 0.8423 (m-10) cc_final: 0.8137 (m-10)
REVERT: H  229 CYS cc_start: 0.5591 (p) cc_final: 0.5371 (p)
  outliers start: 39
  outliers final: 28
  residues processed: 212
  average time/residue: 0.0839
  time to fit residues: 24.8376
Evaluate side-chains
  190 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  111 LEU
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  283 LEU
Chi-restraints excluded: chain P residue  322 THR
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   chunk 54 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 57 optimal weight:   30.0000
   chunk 20 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0170
   chunk 65 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0050
   overall best weight:    0.4432

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

Flipped N/Q/H residues before XYZ refinement:
P 154 ASN
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.091014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.075624 restraints weight = 30462.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.078130 restraints weight = 13866.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.079783 restraints weight = 8229.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.080834 restraints weight = 5748.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.081541 restraints weight = 4503.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8510  Z= 0.110
  Angle     :  0.563   8.585  11647  Z= 0.288
  Chirality :  0.043   0.208   1379
  Planarity :  0.003   0.043   1511
  Dihedral  :  3.973  24.645   1284
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 20.86 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  2.00 (0.25), residues: 1185
  helix:  2.93 (0.23), residues: 427
  sheet:  0.59 (0.33), residues: 252
  loop :  0.39 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 213 
 TYR   0.017   0.002   TYR H 190 
 PHE   0.016   0.001   PHE A  55 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8506)
  covalent geometry    : angle       0.56182 (11639)
  SS BOND              : bond        0.00574 (    4)
  SS BOND              : angle       1.56762 (    8)
  hydrogen bonds       : bond        0.03172 (  486)
  hydrogen bonds       : angle       4.17192 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 195
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  305 TYR cc_start: 0.6300 (m-10) cc_final: 0.5125 (t80)
REVERT: P  312 THR cc_start: 0.9347 (m) cc_final: 0.9016 (t)
REVERT: A   24 MET cc_start: 0.8086 (tmm) cc_final: 0.7881 (tmm)
REVERT: A   41 LYS cc_start: 0.7781 (mppt) cc_final: 0.7485 (mppt)
REVERT: B   52 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7623 (ptp-110)
REVERT: B   85 TYR cc_start: 0.8856 (m-10) cc_final: 0.7819 (m-10)
REVERT: G   11 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8792 (tp-100)
REVERT: H  202 ARG cc_start: 0.8447 (ptp-170) cc_final: 0.8182 (mtm110)
REVERT: H  229 CYS cc_start: 0.5622 (p) cc_final: 0.5353 (p)
  outliers start: 31
  outliers final: 16
  residues processed: 214
  average time/residue: 0.0749
  time to fit residues: 23.0905
Evaluate side-chains
  191 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  275 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 57 optimal weight:   30.0000
   chunk 37 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   chunk 29 optimal weight:   20.0000
   chunk 63 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
P 154 ASN
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.090620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.075286 restraints weight = 30265.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.077730 restraints weight = 13750.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.079327 restraints weight = 8183.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.080400 restraints weight = 5742.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.081085 restraints weight = 4503.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.4879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8510  Z= 0.113
  Angle     :  0.559   9.583  11647  Z= 0.286
  Chirality :  0.043   0.261   1379
  Planarity :  0.004   0.046   1511
  Dihedral  :  3.917  24.281   1284
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 22.04 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.99 (0.25), residues: 1185
  helix:  2.93 (0.24), residues: 427
  sheet:  0.58 (0.33), residues: 254
  loop :  0.38 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 314 
 TYR   0.016   0.001   TYR A 356 
 PHE   0.024   0.001   PHE H 212 
 TRP   0.038   0.002   TRP B 332 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8506)
  covalent geometry    : angle       0.55662 (11639)
  SS BOND              : bond        0.00708 (    4)
  SS BOND              : angle       1.91527 (    8)
  hydrogen bonds       : bond        0.03044 (  486)
  hydrogen bonds       : angle       4.12342 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  305 TYR cc_start: 0.6396 (m-10) cc_final: 0.6191 (m-80)
REVERT: P  312 THR cc_start: 0.9355 (m) cc_final: 0.9023 (t)
REVERT: A   24 MET cc_start: 0.8108 (tmm) cc_final: 0.7856 (tmm)
REVERT: A   41 LYS cc_start: 0.7745 (mppt) cc_final: 0.7476 (mppt)
REVERT: B   52 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7664 (ptp-110)
REVERT: B   85 TYR cc_start: 0.8910 (m-10) cc_final: 0.7790 (m-10)
REVERT: G   18 GLN cc_start: 0.8251 (tp40) cc_final: 0.7874 (tm-30)
REVERT: H  111 TRP cc_start: 0.8442 (m-10) cc_final: 0.7755 (m-10)
REVERT: H  192 MET cc_start: 0.7008 (ppp) cc_final: 0.6762 (ppp)
REVERT: H  229 CYS cc_start: 0.5711 (p) cc_final: 0.5428 (p)
  outliers start: 26
  outliers final: 18
  residues processed: 201
  average time/residue: 0.0758
  time to fit residues: 22.0157
Evaluate side-chains
  194 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  322 THR
Chi-restraints excluded: chain P residue  328 VAL
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 57 optimal weight:   30.0000
   chunk 64 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.083982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.068183 restraints weight = 30976.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.070386 restraints weight = 14308.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.071835 restraints weight = 8749.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.072764 restraints weight = 6318.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.073376 restraints weight = 5096.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.5733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   8510  Z= 0.346
  Angle     :  0.694  11.871  11647  Z= 0.372
  Chirality :  0.047   0.295   1379
  Planarity :  0.005   0.048   1511
  Dihedral  :  4.507  22.628   1284
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 20.71 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.40 (0.25), residues: 1185
  helix:  2.34 (0.24), residues: 432
  sheet:  0.17 (0.32), residues: 258
  loop :  0.18 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  68 
 TYR   0.017   0.003   TYR H  59 
 PHE   0.031   0.003   PHE H 212 
 TRP   0.048   0.003   TRP P 232 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00725 ( 8506)
  covalent geometry    : angle       0.69218 (11639)
  SS BOND              : bond        0.00377 (    4)
  SS BOND              : angle       2.15484 (    8)
  hydrogen bonds       : bond        0.03896 (  486)
  hydrogen bonds       : angle       4.67789 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 173
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  312 THR cc_start: 0.9388 (m) cc_final: 0.9106 (t)
REVERT: A   41 LYS cc_start: 0.8038 (mppt) cc_final: 0.7698 (mppt)
REVERT: B   85 TYR cc_start: 0.9039 (m-10) cc_final: 0.8396 (m-10)
REVERT: B  188 MET cc_start: 0.8699 (mmm) cc_final: 0.8490 (mmm)
REVERT: G   11 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8804 (tp-100)
REVERT: G   15 LEU cc_start: 0.9245 (mt) cc_final: 0.8740 (mt)
REVERT: G   18 GLN cc_start: 0.8339 (tp40) cc_final: 0.8102 (tm-30)
REVERT: G   22 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7580 (mt-10)
REVERT: H   97 VAL cc_start: 0.9291 (t) cc_final: 0.8246 (t)
REVERT: H  159 CYS cc_start: 0.3612 (t) cc_final: 0.3383 (t)
REVERT: H  229 CYS cc_start: 0.5670 (p) cc_final: 0.5012 (p)
  outliers start: 35
  outliers final: 25
  residues processed: 194
  average time/residue: 0.0667
  time to fit residues: 18.8086
Evaluate side-chains
  182 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  283 LEU
Chi-restraints excluded: chain P residue  322 THR
Chi-restraints excluded: chain P residue  328 VAL
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  223 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   chunk 114 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9990
   chunk 40 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   chunk 12 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
P 149 ASN
P 154 ASN
** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 352 ASN
B 183 HIS
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.086790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.070929 restraints weight = 31461.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.073277 restraints weight = 14404.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.074818 restraints weight = 8769.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.075800 restraints weight = 6321.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.076412 restraints weight = 5096.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.6079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8510  Z= 0.256
  Angle     :  0.662  12.026  11647  Z= 0.345
  Chirality :  0.046   0.320   1379
  Planarity :  0.004   0.044   1511
  Dihedral  :  4.531  21.378   1284
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 21.89 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.31 (0.25), residues: 1185
  helix:  2.37 (0.24), residues: 430
  sheet:  0.18 (0.32), residues: 265
  loop : -0.02 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H 202 
 TYR   0.022   0.002   TYR H 228 
 PHE   0.018   0.002   PHE H  32 
 TRP   0.035   0.002   TRP P 232 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 8506)
  covalent geometry    : angle       0.65938 (11639)
  SS BOND              : bond        0.00435 (    4)
  SS BOND              : angle       2.35112 (    8)
  hydrogen bonds       : bond        0.03714 (  486)
  hydrogen bonds       : angle       4.55777 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 179
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  312 THR cc_start: 0.9358 (m) cc_final: 0.9105 (t)
REVERT: A   41 LYS cc_start: 0.8037 (mppt) cc_final: 0.7696 (mppt)
REVERT: B   85 TYR cc_start: 0.8900 (m-10) cc_final: 0.8287 (m-10)
REVERT: B  291 ASP cc_start: 0.8433 (m-30) cc_final: 0.7788 (m-30)
REVERT: B  295 ASN cc_start: 0.7847 (m-40) cc_final: 0.7156 (m-40)
REVERT: G   11 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8686 (tp-100)
REVERT: G   15 LEU cc_start: 0.9166 (mt) cc_final: 0.8437 (mt)
REVERT: G   18 GLN cc_start: 0.8230 (tp40) cc_final: 0.7500 (tm-30)
REVERT: G   22 GLU cc_start: 0.7795 (mt-10) cc_final: 0.6945 (mm-30)
REVERT: H   34 MET cc_start: 0.8819 (mmm) cc_final: 0.8368 (mmm)
REVERT: H  111 TRP cc_start: 0.8468 (m-10) cc_final: 0.8057 (m-10)
REVERT: H  229 CYS cc_start: 0.5371 (p) cc_final: 0.5106 (p)
  outliers start: 33
  outliers final: 26
  residues processed: 200
  average time/residue: 0.0758
  time to fit residues: 21.7961
Evaluate side-chains
  191 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  111 LEU
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  149 ASN
Chi-restraints excluded: chain P residue  322 THR
Chi-restraints excluded: chain P residue  328 VAL
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 108 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 96 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
P 149 ASN
P 154 ASN
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.088712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.073155 restraints weight = 30819.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.075568 restraints weight = 14019.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.077122 restraints weight = 8448.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.078101 restraints weight = 6053.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.078658 restraints weight = 4858.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.6137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8510  Z= 0.152
  Angle     :  0.630  12.297  11647  Z= 0.319
  Chirality :  0.044   0.241   1379
  Planarity :  0.004   0.044   1511
  Dihedral  :  4.334  19.319   1284
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.11 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.54 (0.25), residues: 1185
  helix:  2.65 (0.24), residues: 423
  sheet:  0.21 (0.33), residues: 260
  loop :  0.12 (0.30), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 202 
 TYR   0.024   0.002   TYR H 228 
 PHE   0.019   0.002   PHE P 138 
 TRP   0.032   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8506)
  covalent geometry    : angle       0.62808 (11639)
  SS BOND              : bond        0.00392 (    4)
  SS BOND              : angle       1.95743 (    8)
  hydrogen bonds       : bond        0.03365 (  486)
  hydrogen bonds       : angle       4.35370 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  312 THR cc_start: 0.9285 (m) cc_final: 0.9039 (t)
REVERT: A   41 LYS cc_start: 0.8033 (mppt) cc_final: 0.7691 (mppt)
REVERT: A  225 SER cc_start: 0.9140 (p) cc_final: 0.8833 (t)
REVERT: B   85 TYR cc_start: 0.8847 (m-10) cc_final: 0.8240 (m-10)
REVERT: B  291 ASP cc_start: 0.8392 (m-30) cc_final: 0.7707 (m-30)
REVERT: G   11 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8691 (tp-100)
REVERT: G   15 LEU cc_start: 0.9194 (mt) cc_final: 0.8449 (mt)
REVERT: G   18 GLN cc_start: 0.8239 (tp40) cc_final: 0.7613 (tm-30)
REVERT: G   22 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6890 (mm-30)
REVERT: H   34 MET cc_start: 0.8755 (mmm) cc_final: 0.8199 (mmm)
REVERT: H  111 TRP cc_start: 0.8510 (m-10) cc_final: 0.8184 (m-10)
REVERT: H  229 CYS cc_start: 0.5588 (p) cc_final: 0.5296 (p)
  outliers start: 25
  outliers final: 21
  residues processed: 198
  average time/residue: 0.0714
  time to fit residues: 20.7052
Evaluate side-chains
  191 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  111 LEU
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  283 LEU
Chi-restraints excluded: chain P residue  322 THR
Chi-restraints excluded: chain P residue  328 VAL
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0270
   chunk 42 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    1.7242

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

Flipped N/Q/H residues before XYZ refinement:
P 149 ASN
** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 198 ASN
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.089156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.073619 restraints weight = 30917.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.076043 restraints weight = 14056.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.077618 restraints weight = 8465.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.078617 restraints weight = 6050.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.079180 restraints weight = 4843.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.6203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8510  Z= 0.148
  Angle     :  0.635  12.367  11647  Z= 0.317
  Chirality :  0.045   0.294   1379
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.215  19.903   1284
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.15 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.57 (0.25), residues: 1185
  helix:  2.74 (0.24), residues: 424
  sheet:  0.18 (0.33), residues: 261
  loop :  0.11 (0.30), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 202 
 TYR   0.024   0.002   TYR H 228 
 PHE   0.019   0.002   PHE B 335 
 TRP   0.057   0.003   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8506)
  covalent geometry    : angle       0.63337 (11639)
  SS BOND              : bond        0.00499 (    4)
  SS BOND              : angle       1.88665 (    8)
  hydrogen bonds       : bond        0.03299 (  486)
  hydrogen bonds       : angle       4.30357 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  312 THR cc_start: 0.9286 (m) cc_final: 0.9042 (t)
REVERT: A   41 LYS cc_start: 0.8049 (mppt) cc_final: 0.7793 (mppt)
REVERT: A  191 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7789 (mm-30)
REVERT: A  225 SER cc_start: 0.9030 (p) cc_final: 0.8798 (t)
REVERT: B   85 TYR cc_start: 0.8837 (m-10) cc_final: 0.8233 (m-10)
REVERT: B  291 ASP cc_start: 0.8320 (m-30) cc_final: 0.7686 (m-30)
REVERT: G   11 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8657 (tp-100)
REVERT: G   15 LEU cc_start: 0.9178 (mt) cc_final: 0.8386 (mt)
REVERT: G   18 GLN cc_start: 0.8177 (tp40) cc_final: 0.7864 (tm-30)
REVERT: H   34 MET cc_start: 0.8765 (mmm) cc_final: 0.8233 (mmm)
REVERT: H  111 TRP cc_start: 0.8420 (m-10) cc_final: 0.8151 (m-10)
REVERT: H  216 ILE cc_start: 0.8842 (mm) cc_final: 0.8465 (tp)
REVERT: H  229 CYS cc_start: 0.5659 (p) cc_final: 0.5379 (p)
  outliers start: 26
  outliers final: 23
  residues processed: 191
  average time/residue: 0.0713
  time to fit residues: 19.7141
Evaluate side-chains
  192 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  111 LEU
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  283 LEU
Chi-restraints excluded: chain P residue  322 THR
Chi-restraints excluded: chain P residue  328 VAL
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 24 optimal weight:   50.0000
   chunk 102 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 57 optimal weight:   30.0000
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
P 149 ASN
** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 198 ASN
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.089161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.073527 restraints weight = 30874.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.075945 restraints weight = 14118.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.077508 restraints weight = 8530.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.078493 restraints weight = 6103.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.079060 restraints weight = 4899.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.6296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8510  Z= 0.148
  Angle     :  0.662  14.810  11647  Z= 0.329
  Chirality :  0.045   0.341   1379
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.191  19.854   1284
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 25.44 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.58 (0.25), residues: 1185
  helix:  2.79 (0.24), residues: 424
  sheet:  0.15 (0.33), residues: 257
  loop :  0.09 (0.30), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 202 
 TYR   0.023   0.002   TYR H 228 
 PHE   0.019   0.002   PHE B 335 
 TRP   0.063   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8506)
  covalent geometry    : angle       0.66099 (11639)
  SS BOND              : bond        0.00436 (    4)
  SS BOND              : angle       1.81530 (    8)
  hydrogen bonds       : bond        0.03263 (  486)
  hydrogen bonds       : angle       4.27732 ( 1377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  312 THR cc_start: 0.9291 (m) cc_final: 0.9045 (t)
REVERT: A   41 LYS cc_start: 0.8013 (mppt) cc_final: 0.7807 (mppt)
REVERT: A  225 SER cc_start: 0.9034 (p) cc_final: 0.8791 (t)
REVERT: A  301 ASP cc_start: 0.7453 (t0) cc_final: 0.7234 (p0)
REVERT: B   50 THR cc_start: 0.8428 (m) cc_final: 0.8102 (t)
REVERT: B   61 MET cc_start: 0.8547 (ppp) cc_final: 0.8114 (ptm)
REVERT: B   85 TYR cc_start: 0.8820 (m-10) cc_final: 0.8244 (m-10)
REVERT: B  291 ASP cc_start: 0.8386 (m-30) cc_final: 0.7918 (m-30)
REVERT: G   11 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8644 (tp-100)
REVERT: G   15 LEU cc_start: 0.9184 (mt) cc_final: 0.8378 (mt)
REVERT: G   18 GLN cc_start: 0.8179 (tp40) cc_final: 0.7795 (tm-30)
REVERT: H   34 MET cc_start: 0.8775 (mmm) cc_final: 0.8246 (mmm)
REVERT: H  111 TRP cc_start: 0.8390 (m-10) cc_final: 0.8190 (m-10)
REVERT: H  216 ILE cc_start: 0.8830 (mm) cc_final: 0.8507 (tp)
REVERT: H  229 CYS cc_start: 0.5690 (p) cc_final: 0.5407 (p)
  outliers start: 24
  outliers final: 20
  residues processed: 188
  average time/residue: 0.0757
  time to fit residues: 20.8452
Evaluate side-chains
  191 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   75 THR
Chi-restraints excluded: chain P residue  111 LEU
Chi-restraints excluded: chain P residue  124 HIS
Chi-restraints excluded: chain P residue  283 LEU
Chi-restraints excluded: chain P residue  322 THR
Chi-restraints excluded: chain P residue  328 VAL
Chi-restraints excluded: chain P residue  376 ARG
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 57 optimal weight:   30.0000
   chunk 23 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0570
   chunk 3 optimal weight:   50.0000
   chunk 9 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   overall best weight:    3.1704

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

Flipped N/Q/H residues before XYZ refinement:
P 149 ASN
** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 198 ASN
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.087478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.071618 restraints weight = 31002.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.073957 restraints weight = 14214.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.075478 restraints weight = 8720.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.076441 restraints weight = 6304.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.077063 restraints weight = 5098.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.6530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8510  Z= 0.217
  Angle     :  0.683  13.856  11647  Z= 0.344
  Chirality :  0.046   0.308   1379
  Planarity :  0.004   0.043   1511
  Dihedral  :  4.313  16.007   1284
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.85 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 are not related in a simple way.
  whole:  1.46 (0.26), residues: 1185
  helix:  2.73 (0.24), residues: 423
  sheet:  0.03 (0.32), residues: 277
  loop :  0.01 (0.30), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 129 
 TYR   0.022   0.002   TYR H 228 
 PHE   0.020   0.002   PHE B 335 
 TRP   0.063   0.003   TRP B  82 
 HIS   0.005   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8506)
  covalent geometry    : angle       0.68192 (11639)
  SS BOND              : bond        0.00521 (    4)
  SS BOND              : angle       1.65248 (    8)
  hydrogen bonds       : bond        0.03402 (  486)
  hydrogen bonds       : angle       4.40913 ( 1377)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1672.07 seconds
wall clock time: 29 minutes 21.96 seconds (1761.96 seconds total)