Starting phenix.real_space_refine
on Fri Dec  8 15:40:10 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/12_2023/7wz7_32905_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/12_2023/7wz7_32905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/12_2023/7wz7_32905.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/12_2023/7wz7_32905.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/12_2023/7wz7_32905_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/12_2023/7wz7_32905_neut.pdb"
  }
  resolution = 2.83
  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=   0.001 sd=   0.019
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      57      5.16       5
     C    5553      2.51       5
     N    1487      2.21       5
     O    1579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  234": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  235": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8676
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1734
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 205}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 1776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1776
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2130
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 9, 'TRANS': 262}
          Chain breaks: 2
  Time building chain proxies: 4.89, per 1000 atoms: 0.56
  Number of scatterers: 8676
  At special positions: 0
  Unit cell: (93.96, 117.72, 131.76, 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      57     16.00
     O    1579      8.00
     N    1487      7.00
     C    5553      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 147 " - pdb=" SG  CYS C 217 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 657 " - pdb=" SG  CYS R 733 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 2.99
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      38.7% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 38
    Processing helix  chain 'A' and resid 49 through 66
      removed outlier: 3.673A  pdb=" N   ASN A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.863A  pdb=" N   ASN A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 319 through 333
      removed outlier: 3.767A  pdb=" N   VAL A 323 " --> pdb=" O   ARG A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 375
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 28 through 32
    Processing helix  chain 'C' and resid 53 through 56
      removed outlier: 4.168A  pdb=" N   GLY C  56 " --> pdb=" O   SER C  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 53 through 56'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.923A  pdb=" N   THR C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 24
      removed outlier: 3.624A  pdb=" N   ASN E  24 " --> pdb=" O   LYS E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 44
    Processing helix  chain 'E' and resid 45 through 48
      removed outlier: 3.574A  pdb=" N   ASP E  48 " --> pdb=" O   ALA E  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 45 through 48'
    Processing helix  chain 'E' and resid 55 through 59
    Processing helix  chain 'R' and resid 568 through 573
    Processing helix  chain 'R' and resid 578 through 580
      No H-bonds generated for 'chain 'R' and resid 578 through 580'
    Processing helix  chain 'R' and resid 581 through 611
      removed outlier: 4.495A  pdb=" N   TRP R 587 " --> pdb=" O   PRO R 583 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA R 608 " --> pdb=" O   LEU R 604 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 617 through 646
      removed outlier: 3.740A  pdb=" N   THR R 646 " --> pdb=" O   ILE R 642 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 655 through 688
    Processing helix  chain 'R' and resid 694 through 707
    Processing helix  chain 'R' and resid 707 through 722
    Processing helix  chain 'R' and resid 744 through 768
      Proline residue:  R 750  - end of helix
    Processing helix  chain 'R' and resid 785 through 801
      Proline residue:  R 798  - end of helix
    Processing helix  chain 'R' and resid 802 through 805
    Processing helix  chain 'R' and resid 806 through 813
    Processing helix  chain 'R' and resid 814 through 817
      removed outlier: 3.962A  pdb=" N   LEU R 817 " --> pdb=" O   SER R 814 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 814 through 817'
    Processing helix  chain 'R' and resid 818 through 828
    Processing helix  chain 'R' and resid 829 through 837
    Processing helix  chain 'R' and resid 842 through 854
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 6.632A  pdb=" N   LYS A  42 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   LEU A 245 " --> pdb=" O   LYS A  42 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU A  44 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   MET A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   LEU A  46 " --> pdb=" O   MET A 247 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   HIS A 345 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.522A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.652A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.039A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.594A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 6.630A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.614A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.620A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.181A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 118 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   MET C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   TYR C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 130
    Processing sheet with id=AB3, first strand: chain 'C' and resid 134 through 136
      removed outlier: 3.652A  pdb=" N   GLU C 234 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   LEU C 166 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   LEU C 175 " --> pdb=" O   LEU C 166 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1239 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.78

  Time building geometry restraints manager: 3.27 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: 2793
        1.34 -     1.46: 2168
        1.46 -     1.59: 3808
        1.59 -     1.71: 0
        1.71 -     1.83: 86
  Bond restraints: 8855
  Sorted by residual:
  bond pdb=" N   TYR C 223 "
       pdb=" CA  TYR C 223 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.14e-02 7.69e+03 1.11e+01
  bond pdb=" CA  ALA B 309 "
       pdb=" C   ALA B 309 "
    ideal  model  delta    sigma   weight residual
    1.524  1.485  0.039 1.31e-02 5.83e+03 8.72e+00
  bond pdb=" N   LYS R 728 "
       pdb=" CA  LYS R 728 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.15e-02 7.56e+03 7.32e+00
  bond pdb=" N   SER C  52 "
       pdb=" CA  SER C  52 "
    ideal  model  delta    sigma   weight residual
    1.454  1.424  0.030 1.16e-02 7.43e+03 6.72e+00
  bond pdb=" CA  LYS R 728 "
       pdb=" C   LYS R 728 "
    ideal  model  delta    sigma   weight residual
    1.524  1.491  0.033 1.31e-02 5.83e+03 6.35e+00
  ... (remaining 8850 not shown)

  Histogram of bond angle deviations from ideal:
       97.94 -   105.20: 133
      105.20 -   112.47: 4646
      112.47 -   119.73: 2921
      119.73 -   127.00: 4186
      127.00 -   134.26: 103
  Bond angle restraints: 11989
  Sorted by residual:
  angle pdb=" N   SER A  13 "
        pdb=" CA  SER A  13 "
        pdb=" C   SER A  13 "
      ideal   model   delta    sigma   weight residual
     107.28  117.82  -10.54 1.75e+00 3.27e-01 3.63e+01
  angle pdb=" C   SER A 339 "
        pdb=" CA  SER A 339 "
        pdb=" CB  SER A 339 "
      ideal   model   delta    sigma   weight residual
     109.83  115.12   -5.29 9.90e-01 1.02e+00 2.86e+01
  angle pdb=" N   GLY B 202 "
        pdb=" CA  GLY B 202 "
        pdb=" C   GLY B 202 "
      ideal   model   delta    sigma   weight residual
     111.04  102.18    8.86 1.77e+00 3.19e-01 2.51e+01
  angle pdb=" C   TYR C 223 "
        pdb=" CA  TYR C 223 "
        pdb=" CB  TYR C 223 "
      ideal   model   delta    sigma   weight residual
     109.56  117.59   -8.03 1.64e+00 3.72e-01 2.40e+01
  angle pdb=" C   SER A  13 "
        pdb=" CA  SER A  13 "
        pdb=" CB  SER A  13 "
      ideal   model   delta    sigma   weight residual
     111.51  105.11    6.40 1.38e+00 5.25e-01 2.15e+01
  ... (remaining 11984 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.49: 4866
       15.49 -    30.98: 290
       30.98 -    46.48: 66
       46.48 -    61.97: 21
       61.97 -    77.46: 2
  Dihedral angle restraints: 5245
    sinusoidal: 2049
      harmonic: 3196
  Sorted by residual:
  dihedral pdb=" CB  CYS R 657 "
           pdb=" SG  CYS R 657 "
           pdb=" SG  CYS R 733 "
           pdb=" CB  CYS R 733 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.67   40.67     1      1.00e+01 1.00e-02 2.32e+01
  dihedral pdb=" CA  GLY B 202 "
           pdb=" C   GLY B 202 "
           pdb=" N   ALA B 203 "
           pdb=" CA  ALA B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.30  -20.70     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  SER A  13 "
           pdb=" C   SER A  13 "
           pdb=" N   ALA A  14 "
           pdb=" CA  ALA A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.02   19.98     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 5242 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1072
       0.064 -    0.129: 273
       0.129 -    0.193: 28
       0.193 -    0.257: 6
       0.257 -    0.321: 3
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  LEU B 308 "
            pdb=" N   LEU B 308 "
            pdb=" C   LEU B 308 "
            pdb=" CB  LEU B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CG  LEU B  55 "
            pdb=" CB  LEU B  55 "
            pdb=" CD1 LEU B  55 "
            pdb=" CD2 LEU B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.99e+00
  ... (remaining 1379 not shown)

  Planarity restraints: 1502
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 817 "    0.014 2.00e-02 2.50e+03   2.79e-02 7.78e+00
        pdb=" C   LEU R 817 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU R 817 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA R 818 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 196 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.79e+00
        pdb=" C   SER C 196 "    0.045 2.00e-02 2.50e+03
        pdb=" O   SER C 196 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY C 197 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  62 "    0.019 2.00e-02 2.50e+03   1.87e-02 5.25e+00
        pdb=" CG  HIS B  62 "   -0.040 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  62 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  62 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  62 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  62 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1499 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1700
        2.76 -     3.30: 8447
        3.30 -     3.83: 14526
        3.83 -     4.37: 17482
        4.37 -     4.90: 30504
  Nonbonded interactions: 72659
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.230 2.440
  nonbonded pdb=" O   LEU A 291 "
            pdb=" OG1 THR A 347 "
     model   vdw
     2.257 2.440
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.266 2.440
  nonbonded pdb=" O   ARG A 314 "
            pdb=" OH  TYR A 326 "
     model   vdw
     2.270 2.440
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.287 2.440
  ... (remaining 72654 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.820
  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:          3.840
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     25.480
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6813
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      :  0.010   0.076   8855  Z= 0.664
  Angle     :  0.954  10.542  11989  Z= 0.541
  Chirality :  0.057   0.321   1382
  Planarity :  0.005   0.046   1502
  Dihedral  : 11.502  77.459   3169
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.69 (0.25), residues: 1086
  helix:  0.60 (0.28), residues: 361
  sheet: -0.86 (0.27), residues: 302
  loop : -0.93 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.026   0.003   TRP B  99 
   HIS   0.018   0.002   HIS B  62 
   PHE   0.034   0.004   PHE B 151 
   TYR   0.032   0.004   TYR B 105 
   ARG   0.009   0.001   ARG B 219 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.9227
  time to fit residues: 212.1829
Evaluate side-chains
  191 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.954 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2512
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.0970
   chunk 82 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0770
   chunk 44 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 33 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B  75 GLN
E  44 HIS
R 820 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8855  Z= 0.211
  Angle     :  0.614   8.699  11989  Z= 0.315
  Chirality :  0.044   0.177   1382
  Planarity :  0.004   0.043   1502
  Dihedral  :  5.087  22.850   1185
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.43 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.26), residues: 1086
  helix:  1.51 (0.28), residues: 359
  sheet: -0.74 (0.28), residues: 283
  loop : -0.84 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.002   TRP B 211 
   HIS   0.006   0.001   HIS A 345 
   PHE   0.018   0.002   PHE A 357 
   TYR   0.014   0.002   TYR C 178 
   ARG   0.007   0.000   ARG R 685 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 0.970 
Fit side-chains
  outliers start: 23
  outliers final: 12
  residues processed: 206
  average time/residue: 0.9815
  time to fit residues: 218.6286
Evaluate side-chains
  197 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 0.975 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 7
  residues processed: 6
  average time/residue: 0.0993
  time to fit residues: 2.4132
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0050
   chunk 27 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0980
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.3172

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 295 ASN
R 820 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8855  Z= 0.187
  Angle     :  0.572   8.024  11989  Z= 0.293
  Chirality :  0.043   0.157   1382
  Planarity :  0.004   0.039   1502
  Dihedral  :  4.773  23.268   1185
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.84 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.21 (0.26), residues: 1086
  helix:  1.95 (0.28), residues: 358
  sheet: -0.72 (0.28), residues: 284
  loop : -0.70 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP B 211 
   HIS   0.008   0.001   HIS A 345 
   PHE   0.021   0.002   PHE A 357 
   TYR   0.014   0.001   TYR C 178 
   ARG   0.009   0.000   ARG R 685 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 1.035 
Fit side-chains
  outliers start: 29
  outliers final: 20
  residues processed: 197
  average time/residue: 0.9751
  time to fit residues: 207.8332
Evaluate side-chains
  200 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.994 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 8
  residues processed: 14
  average time/residue: 0.2042
  time to fit residues: 5.2650
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0870
   chunk 94 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
R 820 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8855  Z= 0.352
  Angle     :  0.640   9.543  11989  Z= 0.327
  Chirality :  0.045   0.277   1382
  Planarity :  0.004   0.048   1502
  Dihedral  :  4.977  26.542   1185
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.04 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.26), residues: 1086
  helix:  1.81 (0.28), residues: 359
  sheet: -0.77 (0.29), residues: 289
  loop : -0.67 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B 211 
   HIS   0.005   0.001   HIS A 345 
   PHE   0.021   0.002   PHE R 823 
   TYR   0.018   0.002   TYR C 178 
   ARG   0.011   0.001   ARG R 685 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 1.010 
Fit side-chains
  outliers start: 28
  outliers final: 16
  residues processed: 193
  average time/residue: 1.0146
  time to fit residues: 211.1729
Evaluate side-chains
  194 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 178
  time to evaluate  : 0.937 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 9
  residues processed: 8
  average time/residue: 0.1138
  time to fit residues: 2.8334
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
B  75 GLN
B 176 GLN
R 820 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8855  Z= 0.254
  Angle     :  0.607   9.558  11989  Z= 0.307
  Chirality :  0.044   0.186   1382
  Planarity :  0.004   0.050   1502
  Dihedral  :  4.854  24.876   1185
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.67 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.28 (0.26), residues: 1086
  helix:  1.93 (0.28), residues: 358
  sheet: -0.55 (0.29), residues: 280
  loop : -0.69 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B 211 
   HIS   0.007   0.001   HIS A 345 
   PHE   0.019   0.002   PHE A 357 
   TYR   0.015   0.002   TYR C 178 
   ARG   0.008   0.000   ARG R 685 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 174
  time to evaluate  : 0.961 
Fit side-chains
  outliers start: 32
  outliers final: 25
  residues processed: 190
  average time/residue: 1.0463
  time to fit residues: 214.7524
Evaluate side-chains
  200 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.981 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 14
  residues processed: 12
  average time/residue: 0.2630
  time to fit residues: 5.3451
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0170
   chunk 87 optimal weight:    0.0470
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
R 820 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8855  Z= 0.233
  Angle     :  0.585   9.392  11989  Z= 0.297
  Chirality :  0.043   0.147   1382
  Planarity :  0.004   0.041   1502
  Dihedral  :  4.732  24.911   1185
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.09 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.31 (0.26), residues: 1086
  helix:  1.96 (0.28), residues: 360
  sheet: -0.52 (0.30), residues: 272
  loop : -0.71 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B 211 
   HIS   0.008   0.001   HIS A 345 
   PHE   0.015   0.002   PHE A 212 
   TYR   0.015   0.002   TYR C 178 
   ARG   0.007   0.000   ARG B 219 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 0.964 
Fit side-chains
  outliers start: 37
  outliers final: 20
  residues processed: 197
  average time/residue: 1.0150
  time to fit residues: 215.9283
Evaluate side-chains
  200 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.923 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 14
  residues processed: 7
  average time/residue: 0.2644
  time to fit residues: 3.7022
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 60 optimal weight:    0.0060
   chunk 77 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 48 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
R 820 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8855  Z= 0.224
  Angle     :  0.579  10.248  11989  Z= 0.295
  Chirality :  0.043   0.159   1382
  Planarity :  0.004   0.040   1502
  Dihedral  :  4.696  23.812   1185
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.09 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.42 (0.26), residues: 1086
  helix:  2.09 (0.28), residues: 360
  sheet: -0.58 (0.30), residues: 281
  loop : -0.59 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.002   TRP B 211 
   HIS   0.005   0.001   HIS A 345 
   PHE   0.014   0.002   PHE A 212 
   TYR   0.014   0.001   TYR C 178 
   ARG   0.007   0.000   ARG A  34 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 178
  time to evaluate  : 0.957 
Fit side-chains
  outliers start: 39
  outliers final: 19
  residues processed: 200
  average time/residue: 0.9572
  time to fit residues: 207.4415
Evaluate side-chains
  191 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.875 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 13
  residues processed: 6
  average time/residue: 0.2694
  time to fit residues: 3.2507
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0570
   chunk 71 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
R 820 HIS
** R 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8855  Z= 0.278
  Angle     :  0.612  11.423  11989  Z= 0.310
  Chirality :  0.044   0.163   1382
  Planarity :  0.004   0.042   1502
  Dihedral  :  4.768  24.602   1185
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.71 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.26), residues: 1086
  helix:  1.99 (0.27), residues: 361
  sheet: -0.49 (0.29), residues: 278
  loop : -0.67 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B 211 
   HIS   0.005   0.001   HIS A 345 
   PHE   0.019   0.002   PHE A 343 
   TYR   0.016   0.002   TYR B  85 
   ARG   0.006   0.001   ARG B 219 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.897 
Fit side-chains
  outliers start: 26
  outliers final: 21
  residues processed: 188
  average time/residue: 1.0218
  time to fit residues: 207.1397
Evaluate side-chains
  190 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.967 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 13
  residues processed: 8
  average time/residue: 0.4401
  time to fit residues: 5.4764
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 42 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 88 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 103 optimal weight:    0.3980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 176 GLN
R 820 HIS
R 827 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8855  Z= 0.205
  Angle     :  0.591  11.847  11989  Z= 0.296
  Chirality :  0.043   0.153   1382
  Planarity :  0.004   0.040   1502
  Dihedral  :  4.663  23.433   1185
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.86 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.44 (0.26), residues: 1086
  helix:  2.12 (0.27), residues: 360
  sheet: -0.54 (0.29), residues: 283
  loop : -0.61 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B 211 
   HIS   0.005   0.001   HIS R 820 
   PHE   0.018   0.002   PHE A 343 
   TYR   0.013   0.001   TYR C 178 
   ARG   0.007   0.000   ARG B 219 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.979 
Fit side-chains
  outliers start: 22
  outliers final: 19
  residues processed: 186
  average time/residue: 0.9778
  time to fit residues: 196.6669
Evaluate side-chains
  188 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 0.871 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 15
  residues processed: 5
  average time/residue: 0.3956
  time to fit residues: 3.5552
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 108 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 92 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
R 820 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8855  Z= 0.278
  Angle     :  0.620  12.476  11989  Z= 0.311
  Chirality :  0.044   0.150   1382
  Planarity :  0.004   0.041   1502
  Dihedral  :  4.736  24.826   1185
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 21.07 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.42 (0.26), residues: 1086
  helix:  2.03 (0.27), residues: 362
  sheet: -0.59 (0.29), residues: 294
  loop : -0.53 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B 211 
   HIS   0.005   0.001   HIS A 345 
   PHE   0.027   0.002   PHE A 282 
   TYR   0.016   0.002   TYR B 124 
   ARG   0.007   0.001   ARG A  34 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.960 
Fit side-chains
  outliers start: 22
  outliers final: 20
  residues processed: 190
  average time/residue: 0.9352
  time to fit residues: 192.7571
Evaluate side-chains
  190 residues out of total 955 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 0.909 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 15
  residues processed: 6
  average time/residue: 0.5513
  time to fit residues: 5.1119
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0370
   chunk 88 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
R 820 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.180447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.151926 restraints weight = 12335.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 2.35
r_work: 0.3852 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8855  Z= 0.268
  Angle     :  0.621  11.852  11989  Z= 0.310
  Chirality :  0.044   0.155   1382
  Planarity :  0.004   0.042   1502
  Dihedral  :  4.748  24.508   1185
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.17 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.40 (0.26), residues: 1086
  helix:  1.99 (0.27), residues: 362
  sheet: -0.53 (0.29), residues: 289
  loop : -0.56 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP R 804 
   HIS   0.005   0.001   HIS R 820 
   PHE   0.026   0.002   PHE A 282 
   TYR   0.015   0.002   TYR C 178 
   ARG   0.007   0.001   ARG A  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3838.25 seconds
wall clock time: 68 minutes 53.79 seconds (4133.79 seconds total)