Starting phenix.real_space_refine
on Tue May 13 03:50:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g7f_51121/05_2025/9g7f_51121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g7f_51121/05_2025/9g7f_51121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g7f_51121/05_2025/9g7f_51121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g7f_51121/05_2025/9g7f_51121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g7f_51121/05_2025/9g7f_51121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g7f_51121/05_2025/9g7f_51121.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6193      2.51       5
     N    1624      2.21       5
     O    1776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9647
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 4359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4359
          Classifications: {'peptide': 543}
          Link IDs: {'PTRANS': 30, 'TRANS': 512}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3607
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 23, 'TRANS': 424}
    Chain: "C"
      Number of atoms: 1681
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1681
          Classifications: {'peptide': 207}
          Link IDs: {'PTRANS': 10, 'TRANS': 196}
  Time building chain proxies: 6.12, per 1000 atoms: 0.63
  Number of scatterers: 9647
  At special positions: 0
  Unit cell: (104.784, 117.528, 97.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1776      8.00
     N    1624      7.00
     C    6193      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2192

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 14 sheets defined
      39.7% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 24
    Processing helix  chain 'B' and resid 26 through 33
      removed outlier: 3.678A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   HIS B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 40
    Processing helix  chain 'B' and resid 43 through 55
      removed outlier: 4.894A  pdb=" N   ARG B  51 " --> pdb=" O   GLU B  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   HIS B  52 " --> pdb=" O   ALA B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 59
      removed outlier: 4.480A  pdb=" N   ASN B  59 " --> pdb=" O   PHE B  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 56 through 59'
    Processing helix  chain 'B' and resid 76 through 95
      removed outlier: 3.634A  pdb=" N   ASN B  95 " --> pdb=" O   ARG B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 122
      removed outlier: 3.762A  pdb=" N   TYR B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 146
      removed outlier: 3.558A  pdb=" N   VAL B 138 " --> pdb=" O   MET B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 5.126A  pdb=" N   GLU B 158 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE B 160 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 194
      removed outlier: 3.568A  pdb=" N   GLU B 194 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 241
      removed outlier: 4.009A  pdb=" N   GLN B 233 " --> pdb=" O   GLU B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 264
      removed outlier: 3.532A  pdb=" N   TYR B 264 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 272
      removed outlier: 3.644A  pdb=" N   TRP B 270 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 296
    Processing helix  chain 'B' and resid 303 through 314
      removed outlier: 3.549A  pdb=" N   GLY B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 320
      removed outlier: 3.692A  pdb=" N   ALA B 318 " --> pdb=" O   GLY B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 349
    Processing helix  chain 'B' and resid 422 through 429
    Processing helix  chain 'B' and resid 468 through 478
      removed outlier: 4.077A  pdb=" N   VAL B 472 " --> pdb=" O   GLY B 468 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU B 478 " --> pdb=" O   SER B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 527
      removed outlier: 3.651A  pdb=" N   LYS B 516 " --> pdb=" O   SER B 512 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLU B 517 " --> pdb=" O   ASP B 513 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU B 518 " --> pdb=" O   LYS B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 559
    Processing helix  chain 'A' and resid 17 through 24
    Processing helix  chain 'A' and resid 26 through 32
      removed outlier: 3.846A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 49
    Processing helix  chain 'A' and resid 49 through 54
      removed outlier: 3.738A  pdb=" N   GLU A  54 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 95
    Processing helix  chain 'A' and resid 109 through 122
      removed outlier: 3.539A  pdb=" N   TYR A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 146
      removed outlier: 3.600A  pdb=" N   VAL A 138 " --> pdb=" O   MET A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 158
      removed outlier: 4.366A  pdb=" N   GLU A 158 " --> pdb=" O   PRO A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 160
      No H-bonds generated for 'chain 'A' and resid 159 through 160'
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 187 through 192
      removed outlier: 3.771A  pdb=" N   LYS A 192 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 241
      removed outlier: 3.815A  pdb=" N   GLN A 236 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 264
    Processing helix  chain 'A' and resid 266 through 272
      removed outlier: 3.526A  pdb=" N   ASN A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
    Processing helix  chain 'A' and resid 303 through 312
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 4.028A  pdb=" N   ALA A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 422 through 429
      removed outlier: 3.582A  pdb=" N   TYR A 429 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 32
      removed outlier: 3.569A  pdb=" N   LEU C  30 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 58
    Processing helix  chain 'C' and resid 85 through 89
    Processing helix  chain 'C' and resid 111 through 122
    Processing helix  chain 'C' and resid 123 through 127
    Processing helix  chain 'C' and resid 136 through 140
    Processing helix  chain 'C' and resid 148 through 161
    Processing helix  chain 'C' and resid 162 through 164
      No H-bonds generated for 'chain 'C' and resid 162 through 164'
    Processing helix  chain 'C' and resid 174 through 178
      removed outlier: 3.591A  pdb=" N   SER C 177 " --> pdb=" O   GLU C 174 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   HIS C 178 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 174 through 178'
    Processing helix  chain 'C' and resid 192 through 204
    Processing helix  chain 'C' and resid 206 through 210
      removed outlier: 3.935A  pdb=" N   MET C 209 " --> pdb=" O   HIS C 206 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 75
      removed outlier: 5.909A  pdb=" N   ALA B  62 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ILE B 278 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   TYR B  64 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   CYS B 252 " --> pdb=" O   VAL B 277 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   VAL B 279 " --> pdb=" O   CYS B 252 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ILE B 249 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   TYR B 301 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   TRP B 251 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL B 329 " --> pdb=" O   HIS B 353 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   THR B 355 " --> pdb=" O   VAL B 329 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   SER B 331 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 366 " --> pdb=" O   TRP B 356 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 129
      removed outlier: 3.707A  pdb=" N   VAL B 149 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   VAL B 171 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 214
      removed outlier: 3.652A  pdb=" N   LEU B 210 " --> pdb=" O   HIS B 226 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS B 222 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   GLY B 223 " --> pdb=" O   ILE B 419 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ILE B 419 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU B 225 " --> pdb=" O   HIS B 417 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 391
      removed outlier: 7.732A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   SER B 438 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 435 " --> pdb=" O   MET B 431 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 443 through 444
    Processing sheet with id=AA6, first strand: chain 'B' and resid 482 through 492
      removed outlier: 4.170A  pdb=" N   GLU B 484 " --> pdb=" O   ALA B 504 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 73 through 75
      removed outlier: 5.920A  pdb=" N   ALA A  62 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ILE A 278 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   TYR A  64 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS A 252 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   VAL A 279 " --> pdb=" O   CYS A 252 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   ILE A 249 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   TYR A 301 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   TRP A 251 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR A 355 " --> pdb=" O   SER A 331 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 125 through 129
      removed outlier: 6.493A  pdb=" N   VAL A 102 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU A 129 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE A 104 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   VAL A 149 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL A 150 " --> pdb=" O   PHE A 172 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   VAL A 171 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.811A  pdb=" N   HIS A 226 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LEU A 211 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TYR A 213 " --> pdb=" O   LYS A 222 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LYS A 222 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY A 223 " --> pdb=" O   ILE A 419 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   ILE A 419 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU A 225 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 367
    Processing sheet with id=AB2, first strand: chain 'A' and resid 388 through 391
      removed outlier: 7.415A  pdb=" N   GLY A 404 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ASP A 440 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TRP A 435 " --> pdb=" O   MET A 431 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 388 through 391
      removed outlier: 7.415A  pdb=" N   GLY A 404 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ASP A 440 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 14
      removed outlier: 7.010A  pdb=" N   ILE C  63 " --> pdb=" O   PRO C  24 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ASP C  68 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   ILE C  72 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 95 through 97
      removed outlier: 6.462A  pdb=" N   ILE C  96 " --> pdb=" O   MET C 132 " (cutoff:3.500A)
      removed outlier: 8.512A  pdb=" N   THR C 134 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU C 183 " --> pdb=" O   PHE C 168 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA C 185 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    975 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: 3.01

  Time building geometry restraints manager: 2.75 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: 3018
        1.34 -     1.45: 1624
        1.45 -     1.57: 5182
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 9924
  Sorted by residual:
  bond pdb=" C   MET A 431 "
       pdb=" N   PRO A 432 "
    ideal  model  delta    sigma   weight residual
    1.331  1.368 -0.037 1.27e-02 6.20e+03 8.31e+00
  bond pdb=" C   TRP B 412 "
       pdb=" N   PRO B 413 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.28e-02 6.10e+03 4.42e+00
  bond pdb=" CG  LEU B 244 "
       pdb=" CD1 LEU B 244 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.08e+00
  bond pdb=" C   PRO A 399 "
       pdb=" N   PRO A 400 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.48e+00
  bond pdb=" N   TRP A 258 "
       pdb=" CA  TRP A 258 "
    ideal  model  delta    sigma   weight residual
    1.454  1.471 -0.017 1.15e-02 7.56e+03 2.16e+00
  ... (remaining 9919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 13214
        2.39 -     4.78: 188
        4.78 -     7.17: 36
        7.17 -     9.56: 5
        9.56 -    11.95: 3
  Bond angle restraints: 13446
  Sorted by residual:
  angle pdb=" CB  MET C 156 "
        pdb=" CG  MET C 156 "
        pdb=" SD  MET C 156 "
      ideal   model   delta    sigma   weight residual
     112.70  100.75   11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C   MET A 431 "
        pdb=" N   PRO A 432 "
        pdb=" CA  PRO A 432 "
      ideal   model   delta    sigma   weight residual
     119.90  115.87    4.03 1.02e+00 9.61e-01 1.56e+01
  angle pdb=" C   TRP B 412 "
        pdb=" CA  TRP B 412 "
        pdb=" CB  TRP B 412 "
      ideal   model   delta    sigma   weight residual
     109.11  114.77   -5.66 1.50e+00 4.44e-01 1.42e+01
  angle pdb=" C   GLY C  23 "
        pdb=" N   PRO C  24 "
        pdb=" CA  PRO C  24 "
      ideal   model   delta    sigma   weight residual
     119.83  115.79    4.04 1.08e+00 8.57e-01 1.40e+01
  angle pdb=" C   MET A 134 "
        pdb=" CA  MET A 134 "
        pdb=" CB  MET A 134 "
      ideal   model   delta    sigma   weight residual
     110.51  117.45   -6.94 1.89e+00 2.80e-01 1.35e+01
  ... (remaining 13441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4998
       17.96 -    35.92: 612
       35.92 -    53.88: 173
       53.88 -    71.84: 33
       71.84 -    89.80: 18
  Dihedral angle restraints: 5834
    sinusoidal: 2389
      harmonic: 3445
  Sorted by residual:
  dihedral pdb=" CA  SER C 120 "
           pdb=" C   SER C 120 "
           pdb=" N   MET C 121 "
           pdb=" CA  MET C 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.49  -24.51     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CA  THR B 418 "
           pdb=" C   THR B 418 "
           pdb=" N   ILE B 419 "
           pdb=" CA  ILE B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.39   23.61     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  VAL A 332 "
           pdb=" C   VAL A 332 "
           pdb=" N   GLY A 333 "
           pdb=" CA  GLY A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.48   23.52     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 5831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1070
       0.053 -    0.106: 244
       0.106 -    0.159: 51
       0.159 -    0.212: 11
       0.212 -    0.265: 2
  Chirality restraints: 1378
  Sorted by residual:
  chirality pdb=" CA  TYR A 401 "
            pdb=" N   TYR A 401 "
            pdb=" C   TYR A 401 "
            pdb=" CB  TYR A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  TRP B 412 "
            pdb=" N   TRP B 412 "
            pdb=" C   TRP B 412 "
            pdb=" CB  TRP B 412 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  MET C 156 "
            pdb=" N   MET C 156 "
            pdb=" C   MET C 156 "
            pdb=" CB  MET C 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1375 not shown)

  Planarity restraints: 1732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 412 "   -0.056 5.00e-02 4.00e+02   8.47e-02 1.15e+01
        pdb=" N   PRO A 413 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 413 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 413 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 414 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.41e+00
        pdb=" C   SER A 414 "    0.036 2.00e-02 2.50e+03
        pdb=" O   SER A 414 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 415 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  44 "   -0.034 5.00e-02 4.00e+02   5.22e-02 4.37e+00
        pdb=" N   PRO C  45 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C  45 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C  45 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1729 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1854
        2.77 -     3.30: 9492
        3.30 -     3.83: 16981
        3.83 -     4.37: 20220
        4.37 -     4.90: 33724
  Nonbonded interactions: 82271
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 368 "
            pdb=" O   SER B 378 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OH  TYR B  18 "
            pdb=" O   PRO B 382 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OH  TYR B 301 "
            pdb=" OG1 THR B 355 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG  SER A 109 "
            pdb=" OE1 GLU A 111 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" NZ  LYS C  13 "
            pdb=" O   THR C  14 "
     model   vdw
     2.289 3.120
  ... (remaining 82266 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.550
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.640
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:11.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
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   0.058   9924  Z= 0.172
  Angle     :  0.742  11.952  13446  Z= 0.397
  Chirality :  0.050   0.265   1378
  Planarity :  0.005   0.085   1732
  Dihedral  : 17.485  89.798   3642
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 30.02 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.24), residues: 1190
  helix: -0.14 (0.25), residues: 381
  sheet: -0.64 (0.37), residues: 210
  loop :  0.01 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 240 
 HIS   0.009   0.001   HIS A 228 
 PHE   0.010   0.001   PHE B 267 
 TYR   0.025   0.002   TYR B 443 
 ARG   0.007   0.001   ARG C 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17621 (  340)
  hydrogen bonds       : angle       8.62519 (  975)
  covalent geometry    : bond        0.00370 ( 9924)
  covalent geometry    : angle       0.74244 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
REVERT: A  431 MET cc_start: 0.5207 (ttm) cc_final: 0.4809 (tmm)
REVERT: C  142 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7873 (pt)
  outliers start: 8
  outliers final: 2
  residues processed: 154
  average time/residue: 1.0985
  time to fit residues: 182.3753
Evaluate side-chains
  128 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  181 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:   30.0000
   chunk 89 optimal weight:    0.8980
   chunk 49 optimal weight:   40.0000
   chunk 30 optimal weight:    0.5980
   chunk 60 optimal weight:    0.3980
   chunk 47 optimal weight:    5.9990
   chunk 92 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 68 optimal weight:    0.3980
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B  88 ASN
B 144 ASN
B 186 ASN
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 HIS
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
B 364 GLN
A  13 HIS
A  14 ASN
** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 GLN
A 294 GLN
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 ASN
C 198 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.178148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.135383 restraints weight = 13992.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 2.90
r_work: 0.3788 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9924  Z= 0.141
  Angle     :  0.610   9.377  13446  Z= 0.313
  Chirality :  0.046   0.171   1378
  Planarity :  0.004   0.059   1732
  Dihedral  :  5.003  46.684   1314
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 26.14 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.24), residues: 1190
  helix:  0.23 (0.26), residues: 391
  sheet: -0.67 (0.38), residues: 204
  loop :  0.10 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 240 
 HIS   0.011   0.001   HIS A 228 
 PHE   0.011   0.001   PHE B 267 
 TYR   0.028   0.002   TYR B 426 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  340)
  hydrogen bonds       : angle       6.53330 (  975)
  covalent geometry    : bond        0.00327 ( 9924)
  covalent geometry    : angle       0.61048 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 145
  time to evaluate  : 1.014 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7576 (ttmt)
REVERT: B   97 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5661 (pp20)
REVERT: B  134 MET cc_start: 0.6891 (tpt) cc_final: 0.6661 (mpp)
REVERT: B  403 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.3904 (ttm)
REVERT: A  169 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7511 (mp10)
REVERT: A  286 GLU cc_start: 0.7885 (pm20) cc_final: 0.7558 (pm20)
REVERT: A  294 GLN cc_start: 0.7469 (tt0) cc_final: 0.7211 (tp-100)
REVERT: A  431 MET cc_start: 0.5045 (ttm) cc_final: 0.4464 (tmm)
REVERT: C   49 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7237 (m-70)
REVERT: C  142 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7732 (pt)
  outliers start: 51
  outliers final: 17
  residues processed: 173
  average time/residue: 1.0139
  time to fit residues: 190.2453
Evaluate side-chains
  145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain C residue   49 HIS
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  181 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.175829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.132643 restraints weight = 14254.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 2.89
r_work: 0.3745 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9924  Z= 0.165
  Angle     :  0.614   8.226  13446  Z= 0.312
  Chirality :  0.046   0.144   1378
  Planarity :  0.004   0.057   1732
  Dihedral  :  5.000  44.332   1314
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 25.45 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1190
  helix:  0.24 (0.25), residues: 398
  sheet: -0.81 (0.36), residues: 224
  loop :  0.15 (0.27), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 240 
 HIS   0.011   0.001   HIS A 228 
 PHE   0.014   0.001   PHE B 267 
 TYR   0.024   0.002   TYR B 426 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  340)
  hydrogen bonds       : angle       6.20804 (  975)
  covalent geometry    : bond        0.00390 ( 9924)
  covalent geometry    : angle       0.61406 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 138
  time to evaluate  : 1.114 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7616 (ttmt)
REVERT: B   97 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5770 (pp20)
REVERT: B  134 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6706 (mpp)
REVERT: B  403 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.4083 (ttm)
REVERT: B  444 MET cc_start: 0.5798 (ptt) cc_final: 0.5575 (pmm)
REVERT: A   49 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7405 (mp)
REVERT: A  169 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7502 (mp10)
REVERT: A  286 GLU cc_start: 0.7895 (pm20) cc_final: 0.7565 (pm20)
REVERT: A  294 GLN cc_start: 0.7654 (tt0) cc_final: 0.7273 (tp-100)
REVERT: A  352 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.5266 (pp)
REVERT: A  431 MET cc_start: 0.5162 (ttm) cc_final: 0.4459 (tmm)
REVERT: C   49 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7286 (m-70)
REVERT: C  156 MET cc_start: 0.5327 (mpt) cc_final: 0.4649 (mpt)
  outliers start: 59
  outliers final: 24
  residues processed: 171
  average time/residue: 0.9840
  time to fit residues: 183.4149
Evaluate side-chains
  157 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   25 VAL
Chi-restraints excluded: chain C residue   49 HIS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  209 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0980
   chunk 30 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 47 optimal weight:   30.0000
   chunk 52 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.172723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.129134 restraints weight = 14174.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 2.89
r_work: 0.3690 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   9924  Z= 0.219
  Angle     :  0.657   9.174  13446  Z= 0.333
  Chirality :  0.047   0.143   1378
  Planarity :  0.005   0.055   1732
  Dihedral  :  4.956  36.756   1310
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 24.95 %
    Favored  : 68.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.25), residues: 1190
  helix:  0.17 (0.25), residues: 394
  sheet: -0.91 (0.35), residues: 231
  loop :  0.23 (0.28), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 270 
 HIS   0.012   0.001   HIS A 228 
 PHE   0.019   0.002   PHE B 267 
 TYR   0.020   0.002   TYR B 187 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03888 (  340)
  hydrogen bonds       : angle       6.17418 (  975)
  covalent geometry    : bond        0.00521 ( 9924)
  covalent geometry    : angle       0.65737 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 135
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5976 (pp20)
REVERT: B  134 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6779 (mpp)
REVERT: B  205 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7994 (mmmm)
REVERT: B  229 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7360 (mt-10)
REVERT: B  258 TRP cc_start: 0.6610 (OUTLIER) cc_final: 0.4923 (t-100)
REVERT: B  503 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8422 (pp)
REVERT: A   49 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7245 (mp)
REVERT: A  169 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7577 (mp10)
REVERT: A  231 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7314 (ptt)
REVERT: A  286 GLU cc_start: 0.7985 (pm20) cc_final: 0.7668 (pm20)
REVERT: A  294 GLN cc_start: 0.7816 (tt0) cc_final: 0.7428 (tp-100)
REVERT: A  352 ILE cc_start: 0.5451 (OUTLIER) cc_final: 0.5092 (pp)
REVERT: A  414 SER cc_start: 0.7713 (t) cc_final: 0.7503 (t)
REVERT: A  431 MET cc_start: 0.5315 (ttm) cc_final: 0.4726 (tmm)
REVERT: C   12 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8297 (mp)
REVERT: C   49 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7234 (m-70)
REVERT: C  201 ARG cc_start: 0.6357 (tmt90) cc_final: 0.6073 (tpp-160)
  outliers start: 69
  outliers final: 27
  residues processed: 176
  average time/residue: 1.0440
  time to fit residues: 199.9034
Evaluate side-chains
  161 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 122
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  134 MET
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  231 MET
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 HIS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 46 optimal weight:   20.0000
   chunk 102 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0020
   chunk 88 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  48 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.176017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.133422 restraints weight = 14077.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.81
r_work: 0.3762 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9924  Z= 0.138
  Angle     :  0.606   9.464  13446  Z= 0.305
  Chirality :  0.045   0.154   1378
  Planarity :  0.004   0.052   1732
  Dihedral  :  4.795  31.076   1310
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 25.25 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.25), residues: 1190
  helix:  0.38 (0.26), residues: 394
  sheet: -0.85 (0.36), residues: 220
  loop :  0.18 (0.28), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 270 
 HIS   0.007   0.001   HIS A 228 
 PHE   0.010   0.001   PHE B 209 
 TYR   0.034   0.002   TYR B 426 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03266 (  340)
  hydrogen bonds       : angle       5.90407 (  975)
  covalent geometry    : bond        0.00325 ( 9924)
  covalent geometry    : angle       0.60578 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 136
  time to evaluate  : 1.088 
Fit side-chains
REVERT: B   88 ASN cc_start: 0.8484 (m-40) cc_final: 0.8269 (m110)
REVERT: B   97 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5765 (pp20)
REVERT: B  157 LEU cc_start: 0.7852 (tm) cc_final: 0.7637 (mt)
REVERT: B  205 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.7730 (mmmm)
REVERT: B  229 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7105 (mt-10)
REVERT: B  403 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.3927 (mtp)
REVERT: B  503 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8422 (pp)
REVERT: B  515 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8898 (pp)
REVERT: A   49 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7314 (mp)
REVERT: A  169 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7618 (mp10)
REVERT: A  286 GLU cc_start: 0.7858 (pm20) cc_final: 0.7515 (pm20)
REVERT: A  294 GLN cc_start: 0.7782 (tt0) cc_final: 0.7424 (tp-100)
REVERT: A  398 LEU cc_start: 0.6994 (mp) cc_final: 0.6754 (mp)
REVERT: A  431 MET cc_start: 0.5358 (ttm) cc_final: 0.4781 (tmm)
REVERT: C   49 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7222 (m-70)
REVERT: C  156 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5832 (mpt)
REVERT: C  184 MET cc_start: 0.5915 (mmm) cc_final: 0.5614 (mmm)
REVERT: C  201 ARG cc_start: 0.6196 (tmt90) cc_final: 0.5812 (tpt170)
  outliers start: 68
  outliers final: 25
  residues processed: 173
  average time/residue: 1.0204
  time to fit residues: 191.5011
Evaluate side-chains
  161 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 HIS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  209 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0040
   chunk 55 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 110 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
B 193 GLN
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN
** A 328 HIS ** 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 = 0.4465 r_free = 0.4465 target = 0.176240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.133333 restraints weight = 14066.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.87
r_work: 0.3771 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9924  Z= 0.135
  Angle     :  0.625   9.855  13446  Z= 0.310
  Chirality :  0.046   0.192   1378
  Planarity :  0.004   0.051   1732
  Dihedral  :  4.746  29.874   1310
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 26.44 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.25), residues: 1190
  helix:  0.52 (0.26), residues: 394
  sheet: -0.82 (0.36), residues: 220
  loop :  0.23 (0.28), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 270 
 HIS   0.008   0.001   HIS A 228 
 PHE   0.011   0.001   PHE B 267 
 TYR   0.027   0.002   TYR B 426 
 ARG   0.005   0.000   ARG C 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03161 (  340)
  hydrogen bonds       : angle       5.80251 (  975)
  covalent geometry    : bond        0.00320 ( 9924)
  covalent geometry    : angle       0.62467 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 135
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8500 (m-40) cc_final: 0.8260 (m-40)
REVERT: B   97 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5728 (pp20)
REVERT: B  193 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8097 (pm20)
REVERT: B  403 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.3922 (mtp)
REVERT: B  444 MET cc_start: 0.6392 (pmm) cc_final: 0.6175 (pmm)
REVERT: B  503 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8404 (pp)
REVERT: B  515 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8842 (pp)
REVERT: A   49 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7214 (mp)
REVERT: A  169 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7631 (mp10)
REVERT: A  286 GLU cc_start: 0.7859 (pm20) cc_final: 0.7532 (pm20)
REVERT: A  294 GLN cc_start: 0.7804 (tt0) cc_final: 0.7466 (tp-100)
REVERT: A  352 ILE cc_start: 0.5310 (OUTLIER) cc_final: 0.4967 (pp)
REVERT: A  398 LEU cc_start: 0.7110 (mp) cc_final: 0.6814 (mp)
REVERT: A  431 MET cc_start: 0.5373 (ttm) cc_final: 0.4744 (tmm)
REVERT: C  141 ASP cc_start: 0.4887 (p0) cc_final: 0.4612 (p0)
REVERT: C  186 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6876 (ppp80)
REVERT: C  201 ARG cc_start: 0.6241 (tmt90) cc_final: 0.5903 (tpt170)
  outliers start: 55
  outliers final: 29
  residues processed: 172
  average time/residue: 1.0499
  time to fit residues: 195.4861
Evaluate side-chains
  164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 126
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  186 ARG
Chi-restraints excluded: chain C residue  205 TYR
Chi-restraints excluded: chain C residue  209 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 105 optimal weight:    0.3980
   chunk 108 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0870
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  11 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.178192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.135818 restraints weight = 14113.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.85
r_work: 0.3790 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9924  Z= 0.125
  Angle     :  0.625  10.116  13446  Z= 0.309
  Chirality :  0.045   0.165   1378
  Planarity :  0.004   0.054   1732
  Dihedral  :  4.706  29.404   1310
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 26.94 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1190
  helix:  0.60 (0.26), residues: 394
  sheet: -0.82 (0.36), residues: 220
  loop :  0.25 (0.28), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.010   0.001   PHE A 105 
 TYR   0.025   0.002   TYR C  33 
 ARG   0.007   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02987 (  340)
  hydrogen bonds       : angle       5.71761 (  975)
  covalent geometry    : bond        0.00295 ( 9924)
  covalent geometry    : angle       0.62495 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 133
  time to evaluate  : 1.069 
Fit side-chains
REVERT: B   88 ASN cc_start: 0.8511 (m-40) cc_final: 0.8300 (m-40)
REVERT: B   97 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5623 (pp20)
REVERT: B  205 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8446 (mttp)
REVERT: B  403 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.3744 (mtp)
REVERT: B  503 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8383 (pp)
REVERT: B  515 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8863 (pp)
REVERT: A   49 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7186 (mp)
REVERT: A  169 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7618 (mp10)
REVERT: A  286 GLU cc_start: 0.7869 (pm20) cc_final: 0.7630 (mp0)
REVERT: A  294 GLN cc_start: 0.7768 (tt0) cc_final: 0.7457 (tp-100)
REVERT: A  352 ILE cc_start: 0.5317 (OUTLIER) cc_final: 0.4994 (pp)
REVERT: A  398 LEU cc_start: 0.7129 (mp) cc_final: 0.6883 (mp)
REVERT: A  431 MET cc_start: 0.5371 (ttm) cc_final: 0.4844 (tmm)
REVERT: C  147 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7365 (mmtp)
REVERT: C  156 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5868 (mpt)
REVERT: C  201 ARG cc_start: 0.6195 (tmt90) cc_final: 0.5877 (tpt170)
  outliers start: 51
  outliers final: 27
  residues processed: 163
  average time/residue: 1.0903
  time to fit residues: 192.4918
Evaluate side-chains
  157 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  205 TYR
Chi-restraints excluded: chain C residue  209 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 108 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 19 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 193 GLN
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.175437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.132464 restraints weight = 14173.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.90
r_work: 0.3766 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9924  Z= 0.173
  Angle     :  0.669  10.262  13446  Z= 0.332
  Chirality :  0.046   0.154   1378
  Planarity :  0.005   0.055   1732
  Dihedral  :  4.880  33.192   1310
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 26.54 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.25), residues: 1190
  helix:  0.54 (0.26), residues: 394
  sheet: -0.79 (0.37), residues: 217
  loop :  0.18 (0.28), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 270 
 HIS   0.008   0.001   HIS A 228 
 PHE   0.016   0.002   PHE B 267 
 TYR   0.027   0.002   TYR C  33 
 ARG   0.007   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03397 (  340)
  hydrogen bonds       : angle       5.82454 (  975)
  covalent geometry    : bond        0.00413 ( 9924)
  covalent geometry    : angle       0.66853 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 127
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8536 (m-40) cc_final: 0.8300 (m110)
REVERT: B   97 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5793 (pp20)
REVERT: B  193 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7978 (pm20)
REVERT: B  205 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8504 (mttp)
REVERT: B  403 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.4458 (mmp)
REVERT: B  443 TYR cc_start: 0.5668 (p90) cc_final: 0.4950 (p90)
REVERT: B  503 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8396 (pp)
REVERT: B  515 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8848 (pp)
REVERT: A   49 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7266 (mp)
REVERT: A  169 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7617 (mp10)
REVERT: A  286 GLU cc_start: 0.7918 (pm20) cc_final: 0.7673 (mp0)
REVERT: A  294 GLN cc_start: 0.7896 (tt0) cc_final: 0.7523 (tp-100)
REVERT: A  398 LEU cc_start: 0.7155 (mp) cc_final: 0.6871 (mp)
REVERT: A  431 MET cc_start: 0.5253 (ttm) cc_final: 0.4880 (tmm)
REVERT: C  147 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7648 (mmtp)
REVERT: C  156 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5486 (mpt)
REVERT: C  201 ARG cc_start: 0.6275 (tmt90) cc_final: 0.5977 (tpt170)
  outliers start: 57
  outliers final: 29
  residues processed: 166
  average time/residue: 1.0288
  time to fit residues: 185.3706
Evaluate side-chains
  163 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   25 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 67 optimal weight:    0.1980
   chunk 7 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 105 optimal weight:    0.4980
   chunk 104 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 193 GLN
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
** A 328 HIS ** 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 = 0.4462 r_free = 0.4462 target = 0.175876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.133643 restraints weight = 14144.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 2.85
r_work: 0.3761 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9924  Z= 0.154
  Angle     :  0.676  12.133  13446  Z= 0.334
  Chirality :  0.046   0.158   1378
  Planarity :  0.004   0.056   1732
  Dihedral  :  4.892  31.038   1310
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 27.34 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.25), residues: 1190
  helix:  0.52 (0.26), residues: 394
  sheet: -0.81 (0.36), residues: 217
  loop :  0.17 (0.28), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.012   0.001   PHE B 267 
 TYR   0.024   0.002   TYR B 187 
 ARG   0.007   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03253 (  340)
  hydrogen bonds       : angle       5.79396 (  975)
  covalent geometry    : bond        0.00368 ( 9924)
  covalent geometry    : angle       0.67591 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 ASN cc_start: 0.8549 (m-40) cc_final: 0.8297 (m-40)
REVERT: B   97 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5699 (pp20)
REVERT: B  193 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7875 (pm20)
REVERT: B  205 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8529 (mttp)
REVERT: B  403 MET cc_start: 0.4991 (OUTLIER) cc_final: 0.4381 (mmp)
REVERT: B  443 TYR cc_start: 0.5621 (p90) cc_final: 0.4916 (p90)
REVERT: B  503 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8382 (pp)
REVERT: B  515 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8849 (pp)
REVERT: A   49 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7237 (mp)
REVERT: A  169 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7620 (mp10)
REVERT: A  286 GLU cc_start: 0.7898 (pm20) cc_final: 0.7665 (mp0)
REVERT: A  294 GLN cc_start: 0.7882 (tt0) cc_final: 0.7527 (tp-100)
REVERT: A  398 LEU cc_start: 0.7183 (mp) cc_final: 0.6934 (mp)
REVERT: A  431 MET cc_start: 0.5280 (ttm) cc_final: 0.4989 (tmm)
REVERT: C  156 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5372 (mpt)
REVERT: C  201 ARG cc_start: 0.6292 (tmt90) cc_final: 0.6006 (tpt170)
  outliers start: 49
  outliers final: 30
  residues processed: 156
  average time/residue: 0.9955
  time to fit residues: 171.6753
Evaluate side-chains
  159 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 120
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  398 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   25 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 93 optimal weight:    7.9990
   chunk 77 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 99 optimal weight:   30.0000
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B 193 GLN
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.175414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.133199 restraints weight = 14236.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 2.86
r_work: 0.3747 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9924  Z= 0.163
  Angle     :  0.699  11.976  13446  Z= 0.342
  Chirality :  0.046   0.172   1378
  Planarity :  0.004   0.055   1732
  Dihedral  :  4.922  31.996   1310
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 27.63 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1190
  helix:  0.50 (0.26), residues: 394
  sheet: -0.82 (0.36), residues: 217
  loop :  0.17 (0.28), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A 270 
 HIS   0.006   0.001   HIS B  52 
 PHE   0.014   0.001   PHE B 267 
 TYR   0.019   0.002   TYR C 136 
 ARG   0.007   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 (  340)
  hydrogen bonds       : angle       5.79656 (  975)
  covalent geometry    : bond        0.00390 ( 9924)
  covalent geometry    : angle       0.69934 (13446)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
REVERT: B   69 LYS cc_start: 0.7657 (tptp) cc_final: 0.7405 (ttpp)
REVERT: B   88 ASN cc_start: 0.8528 (m-40) cc_final: 0.8269 (m-40)
REVERT: B   97 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5766 (pp20)
REVERT: B  193 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7992 (pm20)
REVERT: B  205 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (mttp)
REVERT: B  403 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4486 (mmp)
REVERT: B  443 TYR cc_start: 0.5629 (p90) cc_final: 0.4924 (p90)
REVERT: B  503 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8389 (pp)
REVERT: B  515 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8882 (pp)
REVERT: A   49 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7243 (mp)
REVERT: A  169 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7593 (mp10)
REVERT: A  286 GLU cc_start: 0.7913 (pm20) cc_final: 0.7673 (mp0)
REVERT: A  294 GLN cc_start: 0.7897 (tt0) cc_final: 0.7542 (tp-100)
REVERT: A  346 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7291 (mppt)
REVERT: A  398 LEU cc_start: 0.7213 (mp) cc_final: 0.6999 (mt)
REVERT: A  431 MET cc_start: 0.5253 (ttm) cc_final: 0.4994 (tmm)
REVERT: C  201 ARG cc_start: 0.6289 (tmt90) cc_final: 0.5975 (tpt170)
  outliers start: 47
  outliers final: 29
  residues processed: 157
  average time/residue: 1.0312
  time to fit residues: 175.7913
Evaluate side-chains
  154 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 117
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  205 LYS
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  470 PHE
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  547 SER
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   25 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  205 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0000
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 69 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 193 GLN
** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** 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 = 0.4472 r_free = 0.4472 target = 0.176703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.134928 restraints weight = 14130.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.87
r_work: 0.3773 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9924  Z= 0.139
  Angle     :  0.695  12.944  13446  Z= 0.341
  Chirality :  0.046   0.152   1378
  Planarity :  0.004   0.055   1732
  Dihedral  :  4.897  30.186   1310
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 28.03 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.25), residues: 1190
  helix:  0.55 (0.26), residues: 393
  sheet: -0.82 (0.36), residues: 217
  loop :  0.18 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.011   0.001   PHE B 267 
 TYR   0.025   0.002   TYR B 187 
 ARG   0.007   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03127 (  340)
  hydrogen bonds       : angle       5.75355 (  975)
  covalent geometry    : bond        0.00331 ( 9924)
  covalent geometry    : angle       0.69538 (13446)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8036.09 seconds
wall clock time: 138 minutes 54.19 seconds (8334.19 seconds total)