Starting phenix.real_space_refine
on Wed Apr 30 15:57:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g7f_51121/04_2025/9g7f_51121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g7f_51121/04_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_51121/04_2025/9g7f_51121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g7f_51121/04_2025/9g7f_51121.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g7f_51121/04_2025/9g7f_51121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g7f_51121/04_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-5669/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: 6.59, per 1000 atoms: 0.68
  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: 2.52
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.44
  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: 3.63

  Time building geometry restraints manager: 3.01 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:             4.900
  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:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.550
  Find NCS groups from input model:        0.100
  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:16.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.480
-------------------------------------------------------------------------------
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  : 0.981 
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: 1.1456
  time to fit residues: 190.0243
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  : 1.081 
-------------------------------------------------------------------------------
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 = 44)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.135395 restraints weight = 13992.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.89
r_work: 0.3790 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
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  : 1.195 
Fit side-chains
REVERT: B   66 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7572 (ttmt)
REVERT: B   97 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5664 (pp20)
REVERT: B  134 MET cc_start: 0.6896 (tpt) cc_final: 0.6659 (mpp)
REVERT: B  403 MET cc_start: 0.5486 (OUTLIER) cc_final: 0.3903 (ttm)
REVERT: A  169 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7511 (mp10)
REVERT: A  286 GLU cc_start: 0.7890 (pm20) cc_final: 0.7562 (pm20)
REVERT: A  294 GLN cc_start: 0.7479 (tt0) cc_final: 0.7214 (tp-100)
REVERT: A  431 MET cc_start: 0.5036 (ttm) cc_final: 0.4454 (tmm)
REVERT: C   49 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7227 (m-70)
REVERT: C  142 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7729 (pt)
  outliers start: 51
  outliers final: 17
  residues processed: 173
  average time/residue: 1.0229
  time to fit residues: 191.7796
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  : 0.997 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 107 optimal weight:    0.4980
   chunk 93 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9990
   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:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4459 r_free = 0.4459 target = 0.175684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.132578 restraints weight = 14267.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 2.87
r_work: 0.3737 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9924  Z= 0.169
  Angle     :  0.617   8.448  13446  Z= 0.313
  Chirality :  0.046   0.142   1378
  Planarity :  0.004   0.056   1732
  Dihedral  :  5.005  43.961   1314
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  6.66 %
    Allowed  : 24.45 %
    Favored  : 68.89 %
  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: -0.17 (0.25), residues: 1190
  helix:  0.22 (0.25), residues: 398
  sheet: -0.85 (0.36), residues: 226
  loop :  0.17 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 240 
 HIS   0.012   0.001   HIS A 228 
 PHE   0.015   0.002   PHE B 267 
 TYR   0.025   0.002   TYR B 426 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03658 (  340)
  hydrogen bonds       : angle       6.16688 (  975)
  covalent geometry    : bond        0.00400 ( 9924)
  covalent geometry    : angle       0.61748 (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
  204 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 137
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5781 (pp20)
REVERT: B  134 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6733 (mpp)
REVERT: B  258 TRP cc_start: 0.6366 (OUTLIER) cc_final: 0.4732 (t-100)
REVERT: B  403 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4087 (ttm)
REVERT: B  444 MET cc_start: 0.5792 (ptt) cc_final: 0.5580 (pmm)
REVERT: A   49 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7417 (mp)
REVERT: A  169 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7589 (mp10)
REVERT: A  286 GLU cc_start: 0.7909 (pm20) cc_final: 0.7591 (pm20)
REVERT: A  294 GLN cc_start: 0.7645 (tt0) cc_final: 0.7263 (tp-100)
REVERT: A  352 ILE cc_start: 0.5467 (OUTLIER) cc_final: 0.5199 (pp)
REVERT: A  431 MET cc_start: 0.5258 (ttm) cc_final: 0.4565 (tmm)
REVERT: C   49 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7225 (m-70)
REVERT: C  122 MET cc_start: 0.3659 (tmm) cc_final: 0.3381 (tmm)
  outliers start: 67
  outliers final: 24
  residues processed: 176
  average time/residue: 1.0607
  time to fit residues: 202.0233
Evaluate side-chains
  156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
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  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  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  126 MET
Chi-restraints excluded: chain C residue  129 TYR
Chi-restraints excluded: chain C residue  159 MET
Chi-restraints excluded: chain C residue  175 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 104 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 99 optimal weight:   30.0000
   chunk 47 optimal weight:   30.0000
   chunk 52 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    2.3586

-------------------------------------------------------------------------------
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  14 ASN
** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 226 HIS
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  48 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.169326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.125856 restraints weight = 14235.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.84
r_work: 0.3631 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.097   9924  Z= 0.304
  Angle     :  0.737  10.358  13446  Z= 0.377
  Chirality :  0.050   0.191   1378
  Planarity :  0.005   0.053   1732
  Dihedral  :  5.321  40.836   1310
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 19.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  7.55 %
    Allowed  : 24.55 %
    Favored  : 67.89 %
  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: -0.36 (0.25), residues: 1190
  helix: -0.05 (0.25), residues: 392
  sheet: -0.91 (0.35), residues: 231
  loop :  0.15 (0.28), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 270 
 HIS   0.015   0.002   HIS A 228 
 PHE   0.024   0.002   PHE B 267 
 TYR   0.045   0.003   TYR B 426 
 ARG   0.004   0.001   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04542 (  340)
  hydrogen bonds       : angle       6.40413 (  975)
  covalent geometry    : bond        0.00720 ( 9924)
  covalent geometry    : angle       0.73733 (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
  212 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 136
  time to evaluate  : 1.093 
Fit side-chains
REVERT: B   50 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7067 (m-30)
REVERT: B   97 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6216 (pp20)
REVERT: B  134 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7058 (mpp)
REVERT: B  205 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8171 (mmmm)
REVERT: B  229 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7424 (mt-10)
REVERT: B  242 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7932 (mp)
REVERT: B  258 TRP cc_start: 0.6807 (OUTLIER) cc_final: 0.5031 (t-100)
REVERT: B  444 MET cc_start: 0.5866 (ptt) cc_final: 0.5317 (ptm)
REVERT: A   49 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7443 (mp)
REVERT: A  231 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7332 (ptt)
REVERT: A  286 GLU cc_start: 0.8050 (pm20) cc_final: 0.7787 (pm20)
REVERT: A  294 GLN cc_start: 0.7962 (tt0) cc_final: 0.7460 (tp-100)
REVERT: A  308 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8373 (mmm160)
REVERT: A  414 SER cc_start: 0.7746 (t) cc_final: 0.7409 (t)
REVERT: A  431 MET cc_start: 0.5447 (ttm) cc_final: 0.4781 (tmm)
REVERT: C   12 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (mp)
REVERT: C   49 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7244 (m-70)
REVERT: C  156 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5380 (mpt)
REVERT: C  201 ARG cc_start: 0.6675 (tmt90) cc_final: 0.6344 (tpp-160)
  outliers start: 76
  outliers final: 26
  residues processed: 183
  average time/residue: 1.0968
  time to fit residues: 217.7046
Evaluate side-chains
  159 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ASP
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  157 LEU
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  242 LEU
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  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  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  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  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:    8.9990
   chunk 102 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 51 optimal weight:   30.0000
   chunk 88 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0070
   chunk 99 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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  14 ASN
** 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 = 0.4445 r_free = 0.4445 target = 0.174665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.131757 restraints weight = 14096.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.86
r_work: 0.3727 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.2259

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= 0.145
  Angle     :  0.640   9.607  13446  Z= 0.319
  Chirality :  0.046   0.165   1378
  Planarity :  0.004   0.054   1732
  Dihedral  :  4.868  24.699   1308
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 26.74 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.17 (0.25), residues: 1190
  helix:  0.26 (0.26), residues: 393
  sheet: -0.93 (0.36), residues: 217
  loop :  0.15 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.011   0.001   PHE B 209 
 TYR   0.019   0.002   TYR B 187 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03378 (  340)
  hydrogen bonds       : angle       6.02858 (  975)
  covalent geometry    : bond        0.00339 ( 9924)
  covalent geometry    : angle       0.63956 (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
  199 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 139
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5914 (pp20)
REVERT: B  403 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4091 (mtp)
REVERT: B  503 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8416 (pp)
REVERT: B  515 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8896 (pp)
REVERT: A   49 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7246 (mp)
REVERT: A   71 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7394 (t70)
REVERT: A  286 GLU cc_start: 0.7939 (pm20) cc_final: 0.7722 (mp0)
REVERT: A  294 GLN cc_start: 0.7954 (tt0) cc_final: 0.7432 (tp-100)
REVERT: A  431 MET cc_start: 0.5314 (ttm) cc_final: 0.4836 (tmm)
REVERT: C  122 MET cc_start: 0.3500 (tmm) cc_final: 0.2957 (tmm)
REVERT: C  201 ARG cc_start: 0.6379 (tmt90) cc_final: 0.5963 (tpt170)
  outliers start: 60
  outliers final: 27
  residues processed: 179
  average time/residue: 1.0300
  time to fit residues: 200.3288
Evaluate side-chains
  154 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
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  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  366 ILE
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  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   71 ASP
Chi-restraints excluded: chain A residue  116 MET
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  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   77 THR
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  205 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0370
   chunk 55 optimal weight:    0.7980
   chunk 81 optimal weight:    0.3980
   chunk 97 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.4463 r_free = 0.4463 target = 0.176307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.132313 restraints weight = 14236.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 2.97
r_work: 0.3743 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9924  Z= 0.137
  Angle     :  0.636   9.264  13446  Z= 0.317
  Chirality :  0.046   0.195   1378
  Planarity :  0.004   0.054   1732
  Dihedral  :  4.740  23.830   1308
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 26.74 %
    Favored  : 67.50 %
  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: -0.12 (0.25), residues: 1190
  helix:  0.40 (0.26), residues: 396
  sheet: -0.91 (0.36), residues: 220
  loop :  0.12 (0.28), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.010   0.001   PHE B 267 
 TYR   0.021   0.002   TYR B 187 
 ARG   0.006   0.000   ARG C 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03230 (  340)
  hydrogen bonds       : angle       5.88001 (  975)
  covalent geometry    : bond        0.00325 ( 9924)
  covalent geometry    : angle       0.63596 (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
  194 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 136
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5791 (pp20)
REVERT: B  193 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8023 (pm20)
REVERT: B  205 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8522 (mttp)
REVERT: B  403 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.3979 (mtp)
REVERT: B  444 MET cc_start: 0.6353 (pmm) cc_final: 0.6074 (pmm)
REVERT: B  503 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8412 (pp)
REVERT: B  515 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8895 (pp)
REVERT: A   49 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7420 (mp)
REVERT: A   71 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7489 (t70)
REVERT: A  169 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7491 (mp10)
REVERT: A  286 GLU cc_start: 0.7909 (pm20) cc_final: 0.7665 (mp0)
REVERT: A  294 GLN cc_start: 0.8020 (tt0) cc_final: 0.7470 (tp-100)
REVERT: A  352 ILE cc_start: 0.5323 (OUTLIER) cc_final: 0.4923 (pp)
REVERT: A  398 LEU cc_start: 0.7126 (mp) cc_final: 0.6818 (mp)
REVERT: A  431 MET cc_start: 0.5234 (ttm) cc_final: 0.4797 (tmm)
REVERT: C  122 MET cc_start: 0.3605 (tmm) cc_final: 0.2952 (tmm)
REVERT: C  156 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5843 (mpt)
REVERT: C  186 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6854 (ppp80)
REVERT: C  201 ARG cc_start: 0.6333 (tmt90) cc_final: 0.5932 (tpt170)
  outliers start: 58
  outliers final: 26
  residues processed: 173
  average time/residue: 1.1261
  time to fit residues: 210.7236
Evaluate side-chains
  165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
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  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  414 SER
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  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   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  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  186 ARG
Chi-restraints excluded: chain C residue  205 TYR
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:    0.8980
   chunk 87 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0060
   overall best weight:    1.3600

-------------------------------------------------------------------------------
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 328 HIS ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.172518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.129092 restraints weight = 14197.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.85
r_work: 0.3697 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   9924  Z= 0.200
  Angle     :  0.679  10.256  13446  Z= 0.338
  Chirality :  0.047   0.177   1378
  Planarity :  0.005   0.056   1732
  Dihedral  :  4.850  24.130   1308
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 27.24 %
    Favored  : 67.20 %
  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 (0.25), residues: 1190
  helix:  0.33 (0.26), residues: 394
  sheet: -0.77 (0.38), residues: 205
  loop :  0.06 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 270 
 HIS   0.007   0.001   HIS A 228 
 PHE   0.018   0.002   PHE B 267 
 TYR   0.025   0.002   TYR C  33 
 ARG   0.005   0.000   ARG C  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03594 (  340)
  hydrogen bonds       : angle       5.97881 (  975)
  covalent geometry    : bond        0.00479 ( 9924)
  covalent geometry    : angle       0.67925 (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
  178 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 122
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5994 (pp20)
REVERT: B  403 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4097 (mtp)
REVERT: B  444 MET cc_start: 0.6381 (pmm) cc_final: 0.6116 (pmm)
REVERT: B  503 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8411 (pp)
REVERT: B  515 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8884 (pp)
REVERT: A   49 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7286 (mp)
REVERT: A   71 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7498 (t70)
REVERT: A  169 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7492 (mp10)
REVERT: A  286 GLU cc_start: 0.7986 (pm20) cc_final: 0.7736 (mp0)
REVERT: A  294 GLN cc_start: 0.8080 (tt0) cc_final: 0.7487 (tp-100)
REVERT: A  398 LEU cc_start: 0.7193 (mp) cc_final: 0.6884 (mp)
REVERT: A  431 MET cc_start: 0.5243 (ttm) cc_final: 0.5011 (tmm)
REVERT: C  147 LYS cc_start: 0.7915 (mtmp) cc_final: 0.7554 (mttt)
REVERT: C  156 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5459 (mpt)
REVERT: C  201 ARG cc_start: 0.6476 (tmt90) cc_final: 0.6082 (tpt170)
  outliers start: 56
  outliers final: 28
  residues processed: 160
  average time/residue: 1.0897
  time to fit residues: 188.8899
Evaluate side-chains
  153 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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  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  542 LEU
Chi-restraints excluded: chain B residue  547 SER
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  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   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  151 GLU
Chi-restraints excluded: chain C residue  156 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 108 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4441 r_free = 0.4441 target = 0.174080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.131290 restraints weight = 14279.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.89
r_work: 0.3714 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2564

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= 0.163
  Angle     :  0.675  10.405  13446  Z= 0.332
  Chirality :  0.046   0.161   1378
  Planarity :  0.004   0.058   1732
  Dihedral  :  4.812  25.781   1308
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 27.63 %
    Favored  : 66.70 %
  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:  0.41 (0.26), residues: 396
  sheet: -0.76 (0.38), residues: 205
  loop :  0.08 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.013   0.001   PHE B 267 
 TYR   0.025   0.002   TYR C  33 
 ARG   0.004   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (  340)
  hydrogen bonds       : angle       5.89939 (  975)
  covalent geometry    : bond        0.00388 ( 9924)
  covalent geometry    : angle       0.67477 (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
  185 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 128
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5948 (pp20)
REVERT: B  193 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7986 (pm20)
REVERT: B  205 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8621 (mttp)
REVERT: B  403 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.3951 (mtp)
REVERT: B  444 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.6171 (pmm)
REVERT: B  503 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8409 (pp)
REVERT: B  515 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8879 (pp)
REVERT: A   49 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7200 (mp)
REVERT: A   71 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7493 (t70)
REVERT: A  169 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7464 (mp10)
REVERT: A  286 GLU cc_start: 0.7937 (pm20) cc_final: 0.7695 (mp0)
REVERT: A  294 GLN cc_start: 0.8101 (tt0) cc_final: 0.7494 (tp-100)
REVERT: A  398 LEU cc_start: 0.7201 (mp) cc_final: 0.6963 (mt)
REVERT: A  431 MET cc_start: 0.5257 (ttm) cc_final: 0.4975 (tmt)
REVERT: C  122 MET cc_start: 0.3540 (tmm) cc_final: 0.3002 (tmm)
REVERT: C  147 LYS cc_start: 0.7905 (mtmp) cc_final: 0.7557 (mttt)
REVERT: C  201 ARG cc_start: 0.6378 (tmt90) cc_final: 0.5997 (tpt170)
  outliers start: 57
  outliers final: 29
  residues processed: 163
  average time/residue: 1.0965
  time to fit residues: 193.2524
Evaluate side-chains
  157 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 118
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
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  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  414 SER
Chi-restraints excluded: chain B residue  444 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  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  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   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  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  175 ILE
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:    7.9990
   chunk 67 optimal weight:    0.4980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 ** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.174962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.132420 restraints weight = 14187.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 2.83
r_work: 0.3727 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2602

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= 0.160
  Angle     :  0.678  11.308  13446  Z= 0.334
  Chirality :  0.046   0.157   1378
  Planarity :  0.005   0.058   1732
  Dihedral  :  4.845  26.347   1308
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 28.23 %
    Favored  : 66.70 %
  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: -0.06 (0.25), residues: 1190
  helix:  0.42 (0.26), residues: 395
  sheet: -0.79 (0.37), residues: 205
  loop :  0.09 (0.28), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.013   0.001   PHE B 267 
 TYR   0.025   0.002   TYR C  33 
 ARG   0.004   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03368 (  340)
  hydrogen bonds       : angle       5.88594 (  975)
  covalent geometry    : bond        0.00381 ( 9924)
  covalent geometry    : angle       0.67831 (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
  175 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 124
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: B   97 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5848 (pp20)
REVERT: B  205 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8615 (mttp)
REVERT: B  403 MET cc_start: 0.5126 (OUTLIER) cc_final: 0.3873 (mtp)
REVERT: B  503 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8396 (pp)
REVERT: B  515 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8858 (pp)
REVERT: A   49 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7172 (mp)
REVERT: A   71 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7500 (t70)
REVERT: A  169 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7452 (mp10)
REVERT: A  286 GLU cc_start: 0.7937 (pm20) cc_final: 0.7700 (mp0)
REVERT: A  294 GLN cc_start: 0.8122 (tt0) cc_final: 0.7526 (tp-100)
REVERT: A  398 LEU cc_start: 0.7217 (mp) cc_final: 0.6990 (mt)
REVERT: A  431 MET cc_start: 0.5260 (ttm) cc_final: 0.5018 (tmt)
REVERT: C  122 MET cc_start: 0.3614 (tmm) cc_final: 0.3094 (tmm)
REVERT: C  147 LYS cc_start: 0.7872 (mtmp) cc_final: 0.7550 (mttt)
REVERT: C  156 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5779 (mpt)
REVERT: C  201 ARG cc_start: 0.6387 (tmt90) cc_final: 0.6031 (tpt170)
  outliers start: 51
  outliers final: 30
  residues processed: 153
  average time/residue: 0.9957
  time to fit residues: 166.8234
Evaluate side-chains
  157 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 118
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
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  403 MET
Chi-restraints excluded: chain B residue  414 SER
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  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  153 THR
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   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  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  175 ILE
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:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 99 optimal weight:   20.0000
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4454 r_free = 0.4454 target = 0.175175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.132839 restraints weight = 14348.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 2.85
r_work: 0.3732 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2711

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= 0.160
  Angle     :  0.693  12.299  13446  Z= 0.341
  Chirality :  0.046   0.164   1378
  Planarity :  0.005   0.057   1732
  Dihedral  :  4.869  27.897   1308
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 28.63 %
    Favored  : 66.70 %
  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: -0.10 (0.25), residues: 1190
  helix:  0.41 (0.26), residues: 395
  sheet: -0.91 (0.36), residues: 217
  loop :  0.13 (0.28), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 270 
 HIS   0.007   0.001   HIS B  52 
 PHE   0.013   0.001   PHE B 267 
 TYR   0.025   0.002   TYR B 187 
 ARG   0.007   0.000   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  340)
  hydrogen bonds       : angle       5.87296 (  975)
  covalent geometry    : bond        0.00384 ( 9924)
  covalent geometry    : angle       0.69274 (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
  169 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 122
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
REVERT: B   69 LYS cc_start: 0.7689 (tptp) cc_final: 0.7464 (ttpp)
REVERT: B   97 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5865 (pp20)
REVERT: B  193 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7902 (pm20)
REVERT: B  205 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8602 (mttp)
REVERT: B  443 TYR cc_start: 0.5661 (p90) cc_final: 0.4992 (p90)
REVERT: B  503 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8397 (pp)
REVERT: B  515 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8896 (pp)
REVERT: A   49 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7168 (mp)
REVERT: A   71 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7506 (t70)
REVERT: A  169 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7452 (mp10)
REVERT: A  286 GLU cc_start: 0.7929 (pm20) cc_final: 0.7699 (mp0)
REVERT: A  294 GLN cc_start: 0.8113 (tt0) cc_final: 0.7501 (tp-100)
REVERT: A  398 LEU cc_start: 0.7220 (mp) cc_final: 0.7000 (mt)
REVERT: C   46 ARG cc_start: 0.8586 (tpm170) cc_final: 0.8240 (tpm-80)
REVERT: C  122 MET cc_start: 0.3672 (tmm) cc_final: 0.3160 (tmm)
REVERT: C  147 LYS cc_start: 0.7760 (mtmp) cc_final: 0.7457 (mttt)
REVERT: C  156 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5574 (mpt)
REVERT: C  201 ARG cc_start: 0.6390 (tmt90) cc_final: 0.6027 (tpt170)
  outliers start: 47
  outliers final: 28
  residues processed: 150
  average time/residue: 1.0344
  time to fit residues: 168.4182
Evaluate side-chains
  153 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
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  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  414 SER
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  554 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue  153 THR
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  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   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  151 GLU
Chi-restraints excluded: chain C residue  156 MET
Chi-restraints excluded: chain C residue  175 ILE
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:    0.0270
   chunk 89 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0030
   chunk 67 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.4448

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.176903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.134749 restraints weight = 14207.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.88
r_work: 0.3775 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9924  Z= 0.134
  Angle     :  0.672  12.731  13446  Z= 0.330
  Chirality :  0.046   0.162   1378
  Planarity :  0.004   0.057   1732
  Dihedral  :  4.819  27.551   1308
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 29.32 %
    Favored  : 66.50 %
  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:  0.49 (0.26), residues: 395
  sheet: -0.86 (0.36), residues: 212
  loop :  0.16 (0.28), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 270 
 HIS   0.008   0.001   HIS B  52 
 PHE   0.009   0.001   PHE A 209 
 TYR   0.027   0.002   TYR B 187 
 ARG   0.007   0.000   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03141 (  340)
  hydrogen bonds       : angle       5.77894 (  975)
  covalent geometry    : bond        0.00319 ( 9924)
  covalent geometry    : angle       0.67246 (13446)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8492.84 seconds
wall clock time: 146 minutes 20.06 seconds (8780.06 seconds total)