Starting phenix.real_space_refine
on Wed Jul 23 23:24:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xpd_22285/07_2025/6xpd_22285.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xpd_22285/07_2025/6xpd_22285.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xpd_22285/07_2025/6xpd_22285.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xpd_22285/07_2025/6xpd_22285.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xpd_22285/07_2025/6xpd_22285.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xpd_22285/07_2025/6xpd_22285.cif"
  }
  resolution = 3.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 144 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     S      32      5.16       5
     C    3010      2.51       5
     N     754      2.21       5
     O     822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4622
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2309
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 293}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2309
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 293}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2325  SG  CYS A  53      42.422  21.767  23.908  1.00 88.16           S
  ATOM   2246  SG  CYS B 361      39.757  15.017  23.922  1.00 99.56           S
  ATOM   2271  SG  CYS B 364      39.570  17.025  26.950  1.00 81.28           S
  ATOM     16  SG  CYS B  53      33.976  39.660  23.918  1.00 89.15           S
  ATOM   4555  SG  CYS A 361      36.712  46.426  23.890  1.00100.58           S
  ATOM   4580  SG  CYS A 364      36.887  44.419  26.919  1.00 82.53           S

  Time building chain proxies: 3.44, per 1000 atoms: 0.74
  Number of scatterers: 4622
  At special positions: 0
  Unit cell: (77.19, 62.25, 102.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      4     29.99
     S      32     16.00
     O     822      8.00
     N     754      7.00
     C    3010      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: 1.28
  Conformation dependent library (CDL) restraints added in 545.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" ND1 HIS A 318 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A 301 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B  53 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 364 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS B  54 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 361 "
        pdb="ZN    ZN A 402 " - pdb=" NE2 HIS B  52 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B 301 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B 318 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A  53 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS B 364 "
        pdb="ZN    ZN B 402 " - pdb=" ND1 HIS A  54 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS B 361 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS A  52 "
      Number of angles added : 4


  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      69.0% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 63 through 94
      removed outlier: 3.844A  pdb=" N   TYR B  67 " --> pdb=" O   GLY B  63 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B  77 " --> pdb=" O   LYS B  73 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   GLY B  92 " --> pdb=" O   GLU B  88 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 126
      removed outlier: 4.078A  pdb=" N   HIS B 106 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU B 107 " --> pdb=" O   ASP B 103 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS B 126 " --> pdb=" O   TRP B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 168
    Processing helix  chain 'B' and resid 176 through 196
      removed outlier: 3.637A  pdb=" N   ILE B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 241
      removed outlier: 3.688A  pdb=" N   ASN B 224 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL B 231 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU B 232 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   SER B 234 " --> pdb=" O   SER B 230 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE B 237 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 275
      removed outlier: 4.478A  pdb=" N   ILE B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 293
    Processing helix  chain 'B' and resid 326 through 342
      removed outlier: 3.983A  pdb=" N   VAL B 330 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 365
      removed outlier: 4.655A  pdb=" N   LEU B 362 " --> pdb=" O   PRO B 359 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   PHE B 363 " --> pdb=" O   ASP B 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 94
      removed outlier: 3.843A  pdb=" N   TYR A  67 " --> pdb=" O   GLY A  63 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY A  92 " --> pdb=" O   GLU A  88 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 126
      removed outlier: 4.036A  pdb=" N   HIS A 106 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 107 " --> pdb=" O   ASP A 103 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 108 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS A 126 " --> pdb=" O   TRP A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 168
    Processing helix  chain 'A' and resid 176 through 196
      removed outlier: 3.637A  pdb=" N   ILE A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 182 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 241
      removed outlier: 3.688A  pdb=" N   ASN A 224 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL A 231 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   SER A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 275
      removed outlier: 4.478A  pdb=" N   ILE A 250 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 293
    Processing helix  chain 'A' and resid 326 through 342
      removed outlier: 3.983A  pdb=" N   VAL A 330 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 365
      removed outlier: 4.655A  pdb=" N   LEU A 362 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   PHE A 363 " --> pdb=" O   ASP A 360 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 297 through 304
      removed outlier: 5.680A  pdb=" N   VAL B 300 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ALA B 320 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   SER B 302 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   HIS B 318 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   LEU B 315 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 304
      removed outlier: 5.679A  pdb=" N   VAL A 300 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ALA A 320 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   SER A 302 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   HIS A 318 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   LEU A 315 " --> pdb=" O   THR A 348 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    894 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 1.48 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: 1432
        1.34 -     1.46: 1103
        1.46 -     1.58: 2135
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 4714
  Sorted by residual:
  bond pdb=" CA  THR A 348 "
       pdb=" CB  THR A 348 "
    ideal  model  delta    sigma   weight residual
    1.527  1.498  0.029 2.48e-02 1.63e+03 1.38e+00
  bond pdb=" C   SER B 262 "
       pdb=" O   SER B 262 "
    ideal  model  delta    sigma   weight residual
    1.237  1.250 -0.014 1.17e-02 7.31e+03 1.36e+00
  bond pdb=" CA  THR B 348 "
       pdb=" CB  THR B 348 "
    ideal  model  delta    sigma   weight residual
    1.527  1.499  0.029 2.48e-02 1.63e+03 1.33e+00
  bond pdb=" CG  LEU B 308 "
       pdb=" CD1 LEU B 308 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG  LEU A 308 "
       pdb=" CD1 LEU A 308 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.16e+00
  ... (remaining 4709 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 5932
        1.28 -     2.56: 369
        2.56 -     3.85: 91
        3.85 -     5.13: 22
        5.13 -     6.41: 8
  Bond angle restraints: 6422
  Sorted by residual:
  angle pdb=" C   SER B 353 "
        pdb=" N   PRO B 354 "
        pdb=" CA  PRO B 354 "
      ideal   model   delta    sigma   weight residual
     119.05  122.88   -3.83 1.11e+00 8.12e-01 1.19e+01
  angle pdb=" C   SER A 353 "
        pdb=" N   PRO A 354 "
        pdb=" CA  PRO A 354 "
      ideal   model   delta    sigma   weight residual
     119.05  122.56   -3.51 1.11e+00 8.12e-01 9.98e+00
  angle pdb=" C   ASP B 356 "
        pdb=" N   GLN B 357 "
        pdb=" CA  GLN B 357 "
      ideal   model   delta    sigma   weight residual
     122.41  117.98    4.43 1.41e+00 5.03e-01 9.86e+00
  angle pdb=" C   ASP A 356 "
        pdb=" N   GLN A 357 "
        pdb=" CA  GLN A 357 "
      ideal   model   delta    sigma   weight residual
     122.16  118.05    4.11 1.50e+00 4.44e-01 7.51e+00
  angle pdb=" N   PRO B 354 "
        pdb=" CA  PRO B 354 "
        pdb=" C   PRO B 354 "
      ideal   model   delta    sigma   weight residual
     113.53  110.13    3.40 1.39e+00 5.18e-01 6.00e+00
  ... (remaining 6417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.92: 2330
       12.92 -    25.83: 325
       25.83 -    38.75: 94
       38.75 -    51.67: 28
       51.67 -    64.58: 11
  Dihedral angle restraints: 2788
    sinusoidal: 1008
      harmonic: 1780
  Sorted by residual:
  dihedral pdb=" CA  LEU B 308 "
           pdb=" C   LEU B 308 "
           pdb=" N   THR B 309 "
           pdb=" CA  THR B 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.52  -22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  LEU A 308 "
           pdb=" C   LEU A 308 "
           pdb=" N   THR A 309 "
           pdb=" CA  THR A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.53  -22.47     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  GLU A  88 "
           pdb=" C   GLU A  88 "
           pdb=" N   VAL A  89 "
           pdb=" CA  VAL A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.64   19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 2785 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 520
       0.039 -    0.078: 232
       0.078 -    0.118: 41
       0.118 -    0.157: 5
       0.157 -    0.196: 2
  Chirality restraints: 800
  Sorted by residual:
  chirality pdb=" CA  ASP A 356 "
            pdb=" N   ASP A 356 "
            pdb=" C   ASP A 356 "
            pdb=" CB  ASP A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.61e-01
  chirality pdb=" CA  ASP B 356 "
            pdb=" N   ASP B 356 "
            pdb=" C   ASP B 356 "
            pdb=" CB  ASP B 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.38e-01
  chirality pdb=" CB  ILE A 305 "
            pdb=" CA  ILE A 305 "
            pdb=" CG1 ILE A 305 "
            pdb=" CG2 ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 797 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 220 "   -0.010 2.00e-02 2.50e+03   1.21e-02 2.18e+00
        pdb=" CG  HIS B 220 "    0.026 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 220 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 220 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 220 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 220 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 220 "    0.011 2.00e-02 2.50e+03   1.20e-02 2.16e+00
        pdb=" CG  HIS A 220 "   -0.026 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 220 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 220 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 220 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 220 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 365 "    0.006 2.00e-02 2.50e+03   1.22e-02 1.49e+00
        pdb=" C   GLU B 365 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   GLU B 365 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ASP B 366 "    0.007 2.00e-02 2.50e+03
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.15: 3
        2.15 -     2.84: 1695
        2.84 -     3.52: 7055
        3.52 -     4.21: 10088
        4.21 -     4.90: 17725
  Nonbonded interactions: 36566
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 352 "
            pdb="ZN    ZN A 401 "
     model   vdw
     1.461 2.230
  nonbonded pdb=" OE2 GLU B 352 "
            pdb="ZN    ZN B 401 "
     model   vdw
     1.781 2.230
  nonbonded pdb=" OG1 THR B 348 "
            pdb=" OG1 THR A 348 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   GLN B 227 "
            pdb=" OG  SER B 230 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   GLN A 227 "
            pdb=" OG  SER A 230 "
     model   vdw
     2.185 3.040
  ... (remaining 36561 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.970
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
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      :  0.023   0.723   4728  Z= 0.699
  Angle     :  0.915  26.729   6426  Z= 0.439
  Chirality :  0.043   0.196    800
  Planarity :  0.003   0.022    776
  Dihedral  : 14.372  64.582   1624
  Min Nonbonded Distance : 1.461

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 12.50 %
    Favored  : 87.30 %
  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: -3.83 (0.30), residues: 594
  helix: -1.82 (0.22), residues: 384
  sheet: -3.84 (0.69), residues: 46
  loop : -3.48 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 122 
 HIS   0.014   0.002   HIS B 220 
 PHE   0.020   0.002   PHE A  82 
 TYR   0.011   0.002   TYR B 160 
 ARG   0.001   0.000   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19814 (  306)
  hydrogen bonds       : angle       7.66761 (  894)
  metal coordination   : bond        0.40370 (   14)
  metal coordination   : angle      19.84357 (    4)
  covalent geometry    : bond        0.00700 ( 4714)
  covalent geometry    : angle       0.76998 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
REVERT: B   71 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8312 (ttpp)
REVERT: B  288 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8783 (ttmm)
REVERT: B  295 ASP cc_start: 0.7659 (p0) cc_final: 0.7168 (p0)
REVERT: A   71 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8300 (ttpp)
REVERT: A   85 MET cc_start: 0.6314 (tmm) cc_final: 0.5953 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.2047
  time to fit residues: 33.1931
Evaluate side-chains
  88 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 24 optimal weight:    4.9990
   chunk 47 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.6388

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

Flipped N/Q/H residues before XYZ refinement:
B 172 GLN
B 211 ASN
A 172 GLN
A 211 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.116932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.096119 restraints weight = 8705.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.098599 restraints weight = 5169.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.100176 restraints weight = 3712.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4728  Z= 0.141
  Angle     :  0.578   5.324   6426  Z= 0.300
  Chirality :  0.039   0.111    800
  Planarity :  0.004   0.031    776
  Dihedral  :  4.690  21.139    630
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.62 %
    Favored  : 81.45 %
  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 (0.36), residues: 594
  helix:  0.95 (0.26), residues: 390
  sheet: -3.89 (0.63), residues: 46
  loop : -2.06 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 122 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.016   0.001   PHE A  82 
 TYR   0.007   0.001   TYR A 160 
 ARG   0.002   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05047 (  306)
  hydrogen bonds       : angle       3.80240 (  894)
  metal coordination   : bond        0.00714 (   14)
  metal coordination   : angle       1.08885 (    4)
  covalent geometry    : bond        0.00297 ( 4714)
  covalent geometry    : angle       0.57722 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.490 
Fit side-chains
REVERT: B  344 MET cc_start: 0.8041 (mmm) cc_final: 0.7637 (mmm)
REVERT: A   85 MET cc_start: 0.6302 (tmm) cc_final: 0.5925 (tmm)
  outliers start: 15
  outliers final: 12
  residues processed: 124
  average time/residue: 0.1068
  time to fit residues: 18.7569
Evaluate side-chains
  99 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 30 optimal weight:   30.0000
   chunk 17 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 211 ASN
A 110 ASN
A 211 ASN
A 224 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.093749 restraints weight = 8792.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.096071 restraints weight = 5308.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.097660 restraints weight = 3856.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4728  Z= 0.179
  Angle     :  0.682  16.814   6426  Z= 0.317
  Chirality :  0.039   0.129    800
  Planarity :  0.004   0.033    776
  Dihedral  :  4.636  22.400    630
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 22.07 %
    Favored  : 73.24 %
  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:  0.46 (0.37), residues: 594
  helix:  1.61 (0.26), residues: 390
  sheet: -3.82 (0.69), residues: 40
  loop : -1.79 (0.55), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 122 
 HIS   0.004   0.001   HIS B 301 
 PHE   0.012   0.001   PHE A  82 
 TYR   0.018   0.002   TYR B  67 
 ARG   0.002   0.000   ARG A 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05038 (  306)
  hydrogen bonds       : angle       3.58610 (  894)
  metal coordination   : bond        0.00920 (   14)
  metal coordination   : angle      11.96174 (    4)
  covalent geometry    : bond        0.00401 ( 4714)
  covalent geometry    : angle       0.61299 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: B  151 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8769 (mm)
REVERT: B  215 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7923 (ttp80)
REVERT: A  151 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8804 (mm)
REVERT: A  215 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7952 (ttp80)
REVERT: A  224 ASN cc_start: 0.7994 (m110) cc_final: 0.7731 (m-40)
  outliers start: 24
  outliers final: 22
  residues processed: 106
  average time/residue: 0.1301
  time to fit residues: 19.2062
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  353 SER
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0270
   chunk 17 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
A 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.116663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.095837 restraints weight = 8846.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098237 restraints weight = 5271.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.099833 restraints weight = 3801.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4728  Z= 0.149
  Angle     :  0.607  10.851   6426  Z= 0.294
  Chirality :  0.038   0.106    800
  Planarity :  0.004   0.033    776
  Dihedral  :  4.422  21.449    630
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 24.80 %
    Favored  : 70.31 %
  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:  0.77 (0.37), residues: 594
  helix:  1.85 (0.26), residues: 390
  sheet: -3.68 (0.64), residues: 46
  loop : -1.57 (0.56), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 122 
 HIS   0.004   0.001   HIS B 301 
 PHE   0.009   0.001   PHE A  82 
 TYR   0.020   0.002   TYR B  67 
 ARG   0.001   0.000   ARG B 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04677 (  306)
  hydrogen bonds       : angle       3.36662 (  894)
  metal coordination   : bond        0.00792 (   14)
  metal coordination   : angle       7.78458 (    4)
  covalent geometry    : bond        0.00330 ( 4714)
  covalent geometry    : angle       0.57499 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.502 
Fit side-chains
REVERT: B  151 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8778 (mm)
REVERT: B  174 GLN cc_start: 0.6267 (tp-100) cc_final: 0.5277 (mt0)
REVERT: B  215 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7722 (ttp-170)
REVERT: A  151 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8762 (mm)
REVERT: A  215 ARG cc_start: 0.8058 (ttt-90) cc_final: 0.7734 (ttp-170)
  outliers start: 25
  outliers final: 20
  residues processed: 108
  average time/residue: 0.1178
  time to fit residues: 17.7380
Evaluate side-chains
  109 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 110 ASN
A 224 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.119778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.099276 restraints weight = 8756.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.101814 restraints weight = 5101.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.103513 restraints weight = 3607.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4728  Z= 0.117
  Angle     :  0.562   8.300   6426  Z= 0.276
  Chirality :  0.037   0.109    800
  Planarity :  0.003   0.035    776
  Dihedral  :  4.134  19.350    630
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 26.95 %
    Favored  : 69.14 %
  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:  1.09 (0.37), residues: 594
  helix:  2.12 (0.26), residues: 384
  sheet: -3.28 (0.75), residues: 40
  loop : -1.56 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.007   0.001   PHE A  82 
 TYR   0.021   0.001   TYR B  67 
 ARG   0.000   0.000   ARG B 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04279 (  306)
  hydrogen bonds       : angle       3.15745 (  894)
  metal coordination   : bond        0.00839 (   14)
  metal coordination   : angle       5.89033 (    4)
  covalent geometry    : bond        0.00240 ( 4714)
  covalent geometry    : angle       0.54216 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.477 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6413 (tp-100) cc_final: 0.5310 (mt0)
  outliers start: 20
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0931
  time to fit residues: 14.6272
Evaluate side-chains
  99 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:   30.0000
   chunk 10 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.119243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.098720 restraints weight = 8781.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.101177 restraints weight = 5222.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.102870 restraints weight = 3753.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4728  Z= 0.131
  Angle     :  0.606   7.997   6426  Z= 0.293
  Chirality :  0.038   0.116    800
  Planarity :  0.004   0.035    776
  Dihedral  :  4.091  18.433    630
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.54 %
    Favored  : 67.77 %
  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:  1.09 (0.36), residues: 594
  helix:  2.02 (0.26), residues: 392
  sheet: -3.12 (0.70), residues: 46
  loop : -1.45 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 122 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.031   0.001   PHE B 240 
 TYR   0.020   0.001   TYR B  67 
 ARG   0.001   0.000   ARG A 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04354 (  306)
  hydrogen bonds       : angle       3.22073 (  894)
  metal coordination   : bond        0.00757 (   14)
  metal coordination   : angle       5.59481 (    4)
  covalent geometry    : bond        0.00282 ( 4714)
  covalent geometry    : angle       0.58988 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.491 
Fit side-chains
  outliers start: 24
  outliers final: 22
  residues processed: 105
  average time/residue: 0.0995
  time to fit residues: 15.0063
Evaluate side-chains
  107 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0270
   chunk 35 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    3.4046

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

Flipped N/Q/H residues before XYZ refinement:
B 174 GLN
A 189 ASN
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.095122 restraints weight = 8818.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.097482 restraints weight = 5319.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.099038 restraints weight = 3838.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4728  Z= 0.191
  Angle     :  0.666   8.540   6426  Z= 0.328
  Chirality :  0.040   0.127    800
  Planarity :  0.004   0.038    776
  Dihedral  :  4.496  23.263    630
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 28.32 %
    Favored  : 66.21 %
  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:  0.92 (0.36), residues: 594
  helix:  1.85 (0.26), residues: 390
  sheet: -3.21 (0.68), residues: 46
  loop : -1.33 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 122 
 HIS   0.004   0.001   HIS B 220 
 PHE   0.034   0.002   PHE A 240 
 TYR   0.019   0.002   TYR B  67 
 ARG   0.001   0.000   ARG B 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04889 (  306)
  hydrogen bonds       : angle       3.49342 (  894)
  metal coordination   : bond        0.00729 (   14)
  metal coordination   : angle       6.26388 (    4)
  covalent geometry    : bond        0.00430 ( 4714)
  covalent geometry    : angle       0.64771 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 GLN cc_start: 0.6206 (tp-100) cc_final: 0.5835 (pm20)
REVERT: A  151 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8877 (mm)
  outliers start: 28
  outliers final: 24
  residues processed: 114
  average time/residue: 0.1130
  time to fit residues: 17.6751
Evaluate side-chains
  108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0570
   overall best weight:    1.3104

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 ASN ** 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 = 0.3559 r_free = 0.3559 target = 0.119500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.099334 restraints weight = 8725.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.101823 restraints weight = 5171.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.103325 restraints weight = 3698.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4728  Z= 0.131
  Angle     :  0.638   8.991   6426  Z= 0.308
  Chirality :  0.039   0.143    800
  Planarity :  0.004   0.036    776
  Dihedral  :  4.285  22.912    630
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 30.66 %
    Favored  : 65.23 %
  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:  1.06 (0.36), residues: 594
  helix:  1.97 (0.26), residues: 392
  sheet: -2.98 (0.71), residues: 46
  loop : -1.41 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 122 
 HIS   0.014   0.001   HIS B 220 
 PHE   0.030   0.002   PHE A 240 
 TYR   0.021   0.001   TYR B  67 
 ARG   0.000   0.000   ARG B 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  306)
  hydrogen bonds       : angle       3.38599 (  894)
  metal coordination   : bond        0.00626 (   14)
  metal coordination   : angle       4.24815 (    4)
  covalent geometry    : bond        0.00278 ( 4714)
  covalent geometry    : angle       0.62893 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.483 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6441 (tp-100) cc_final: 0.5361 (mt0)
REVERT: A  225 LEU cc_start: 0.9162 (tt) cc_final: 0.8683 (tp)
REVERT: A  226 PHE cc_start: 0.8298 (m-80) cc_final: 0.8086 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1040
  time to fit residues: 16.1475
Evaluate side-chains
  107 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 ASN ** 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 = 0.3548 r_free = 0.3548 target = 0.118463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.098461 restraints weight = 8981.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.100848 restraints weight = 5319.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102355 restraints weight = 3819.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4728  Z= 0.155
  Angle     :  0.689   9.733   6426  Z= 0.331
  Chirality :  0.040   0.168    800
  Planarity :  0.004   0.037    776
  Dihedral  :  4.362  26.528    630
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 30.27 %
    Favored  : 66.02 %
  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:  1.03 (0.36), residues: 594
  helix:  1.86 (0.25), residues: 390
  sheet: -2.93 (0.71), residues: 46
  loop : -1.14 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP A 152 
 HIS   0.013   0.001   HIS B 220 
 PHE   0.027   0.002   PHE A 240 
 TYR   0.021   0.002   TYR A  67 
 ARG   0.001   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04551 (  306)
  hydrogen bonds       : angle       3.44152 (  894)
  metal coordination   : bond        0.00625 (   14)
  metal coordination   : angle       4.82550 (    4)
  covalent geometry    : bond        0.00344 ( 4714)
  covalent geometry    : angle       0.67899 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.533 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6490 (tp-100) cc_final: 0.5379 (mt0)
  outliers start: 19
  outliers final: 19
  residues processed: 109
  average time/residue: 0.1043
  time to fit residues: 16.2945
Evaluate side-chains
  111 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0670
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.4126

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 ASN ** 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 = 0.3549 r_free = 0.3549 target = 0.118379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098331 restraints weight = 8879.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.100631 restraints weight = 5358.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102235 restraints weight = 3899.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4728  Z= 0.164
  Angle     :  0.690   9.989   6426  Z= 0.335
  Chirality :  0.040   0.174    800
  Planarity :  0.004   0.036    776
  Dihedral  :  4.433  26.972    630
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 30.47 %
    Favored  : 65.43 %
  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:  1.03 (0.36), residues: 594
  helix:  1.81 (0.26), residues: 390
  sheet: -3.03 (0.84), residues: 34
  loop : -1.14 (0.52), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A 152 
 HIS   0.013   0.001   HIS B 220 
 PHE   0.025   0.002   PHE A 240 
 TYR   0.021   0.002   TYR A  67 
 ARG   0.001   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04700 (  306)
  hydrogen bonds       : angle       3.53315 (  894)
  metal coordination   : bond        0.00619 (   14)
  metal coordination   : angle       4.65440 (    4)
  covalent geometry    : bond        0.00367 ( 4714)
  covalent geometry    : angle       0.68009 ( 6422)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.530 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6464 (tp-100) cc_final: 0.5340 (mt0)
  outliers start: 21
  outliers final: 20
  residues processed: 107
  average time/residue: 0.1003
  time to fit residues: 15.4235
Evaluate side-chains
  112 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue   93 HIS
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  163 CYS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 224 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.119009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.098971 restraints weight = 8900.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.101332 restraints weight = 5323.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102911 restraints weight = 3844.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4728  Z= 0.154
  Angle     :  0.678   9.900   6426  Z= 0.328
  Chirality :  0.040   0.160    800
  Planarity :  0.004   0.036    776
  Dihedral  :  4.360  23.936    630
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 30.08 %
    Favored  : 65.04 %
  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:  1.06 (0.36), residues: 594
  helix:  1.82 (0.26), residues: 390
  sheet: -2.66 (1.00), residues: 28
  loop : -1.28 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 152 
 HIS   0.012   0.001   HIS B 220 
 PHE   0.024   0.001   PHE A 240 
 TYR   0.021   0.002   TYR B  67 
 ARG   0.001   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04626 (  306)
  hydrogen bonds       : angle       3.49299 (  894)
  metal coordination   : bond        0.00606 (   14)
  metal coordination   : angle       4.31080 (    4)
  covalent geometry    : bond        0.00340 ( 4714)
  covalent geometry    : angle       0.66931 ( 6422)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1560.07 seconds
wall clock time: 27 minutes 50.29 seconds (1670.29 seconds total)