Starting phenix.real_space_refine
on Fri Aug 22 15:04:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jps_36488/08_2025/8jps_36488.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jps_36488/08_2025/8jps_36488.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jps_36488/08_2025/8jps_36488.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jps_36488/08_2025/8jps_36488.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jps_36488/08_2025/8jps_36488.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jps_36488/08_2025/8jps_36488.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.041
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      34      5.16       5
     C    3034      2.51       5
     N     751      2.21       5
     O     797      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4616
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1890
          Classifications: {'peptide': 257}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 427
          Classifications: {'peptide': 63}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 3, 'TRANS': 59}
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 129
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "A"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1884
          Classifications: {'peptide': 257}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 415
          Classifications: {'peptide': 63}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 3, 'TRANS': 59}
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 107
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 72
  Time building chain proxies: 1.12, per 1000 atoms: 0.24
  Number of scatterers: 4616
  At special positions: 0
  Unit cell: (132.383, 83.5612, 61.0279, 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      34     16.00
     O     797      8.00
     N     751      7.00
     C    3034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  51 " - pdb=" SG  CYS B 276 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  11 " - pdb=" SG  CYS D  36 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  12 " - pdb=" SG  CYS D  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A 276 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  11 " - pdb=" SG  CYS C  36 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  12 " - pdb=" SG  CYS C  52 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 153.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1188

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 5 sheets defined
      67.0% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'B' and resid 58 through 61
    Processing helix  chain 'B' and resid 62 through 82
      removed outlier: 4.345A  pdb=" N   THR B  68 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 89
      removed outlier: 3.824A  pdb=" N   PHE B  88 " --> pdb=" O   ARG B  85 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG B  89 " --> pdb=" O   PRO B  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 85 through 89'
    Processing helix  chain 'B' and resid 95 through 113
      removed outlier: 3.624A  pdb=" N   LEU B  99 " --> pdb=" O   GLY B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 116
      No H-bonds generated for 'chain 'B' and resid 114 through 116'
    Processing helix  chain 'B' and resid 125 through 158
      removed outlier: 6.542A  pdb=" N   HIS B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   ARG B 156 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 181
    Processing helix  chain 'B' and resid 181 through 187
    Processing helix  chain 'B' and resid 200 through 202
      No H-bonds generated for 'chain 'B' and resid 200 through 202'
    Processing helix  chain 'B' and resid 203 through 226
      removed outlier: 4.483A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      Proline residue:  B 222  - end of helix
    Processing helix  chain 'B' and resid 244 through 246
      No H-bonds generated for 'chain 'B' and resid 244 through 246'
    Processing helix  chain 'B' and resid 247 through 268
      Proline residue:  B 255  - end of helix
      removed outlier: 3.894A  pdb=" N   LEU B 260 " --> pdb=" O   HIS B 256 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLY B 261 " --> pdb=" O   GLY B 257 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 295
    Processing helix  chain 'B' and resid 295 through 311
      Proline residue:  B 301  - end of helix
    Processing helix  chain 'D' and resid 57 through 67
    Processing helix  chain 'A' and resid 58 through 61
    Processing helix  chain 'A' and resid 62 through 82
      removed outlier: 4.613A  pdb=" N   THR A  68 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 89
      removed outlier: 3.692A  pdb=" N   PHE A  88 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG A  89 " --> pdb=" O   PRO A  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 85 through 89'
    Processing helix  chain 'A' and resid 95 through 113
      removed outlier: 3.667A  pdb=" N   LEU A  99 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 117
    Processing helix  chain 'A' and resid 125 through 153
    Processing helix  chain 'A' and resid 153 through 158
    Processing helix  chain 'A' and resid 162 through 181
    Processing helix  chain 'A' and resid 181 through 187
    Processing helix  chain 'A' and resid 203 through 227
      removed outlier: 4.398A  pdb=" N   LEU A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      Proline residue:  A 222  - end of helix
    Processing helix  chain 'A' and resid 244 through 252
    Processing helix  chain 'A' and resid 253 through 268
      removed outlier: 3.742A  pdb=" N   LEU A 260 " --> pdb=" O   HIS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 295
    Processing helix  chain 'A' and resid 295 through 312
      Proline residue:  A 301  - end of helix
      removed outlier: 3.580A  pdb=" N   THR A 312 " --> pdb=" O   CYS A 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 67
      removed outlier: 3.559A  pdb=" N   GLN C  61 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS C  65 " --> pdb=" O   GLN C  61 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 188 through 190
      removed outlier: 3.565A  pdb=" N   GLY B 189 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 25 through 29
      removed outlier: 6.681A  pdb=" N   LYS D  44 " --> pdb=" O   GLU D  26 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   TYR D  28 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   ILE D  42 " --> pdb=" O   TYR D  28 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 52
    Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 191
      removed outlier: 4.021A  pdb=" N   LEU A 194 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 30
      removed outlier: 3.812A  pdb=" N   VAL C  41 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)

    302 hydrogen bonds defined for protein.
    873 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: 0.88

  Time building geometry restraints manager: 0.70 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 1418
        1.34 -     1.46: 1082
        1.46 -     1.58: 2194
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 4732
  Sorted by residual:
  bond pdb=" N   LYS D  18 "
       pdb=" CA  LYS D  18 "
    ideal  model  delta    sigma   weight residual
    1.454  1.479 -0.025 1.34e-02 5.57e+03 3.60e+00
  bond pdb=" N   TRP A 242 "
       pdb=" CA  TRP A 242 "
    ideal  model  delta    sigma   weight residual
    1.454  1.476 -0.022 1.17e-02 7.31e+03 3.50e+00
  bond pdb=" N   GLU B  46 "
       pdb=" CA  GLU B  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.026 1.90e-02 2.77e+03 1.88e+00
  bond pdb=" N   GLU A  46 "
       pdb=" CA  GLU A  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.025 1.90e-02 2.77e+03 1.75e+00
  bond pdb=" C   LEU A 221 "
       pdb=" N   PRO A 222 "
    ideal  model  delta    sigma   weight residual
    1.335  1.349 -0.014 1.30e-02 5.92e+03 1.17e+00
  ... (remaining 4727 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 6160
        1.33 -     2.67: 259
        2.67 -     4.00: 48
        4.00 -     5.33: 24
        5.33 -     6.67: 7
  Bond angle restraints: 6498
  Sorted by residual:
  angle pdb=" N   TRP A 242 "
        pdb=" CA  TRP A 242 "
        pdb=" CB  TRP A 242 "
      ideal   model   delta    sigma   weight residual
     110.39  115.64   -5.25 1.59e+00 3.96e-01 1.09e+01
  angle pdb=" C   GLU B  46 "
        pdb=" N   ALA B  47 "
        pdb=" CA  ALA B  47 "
      ideal   model   delta    sigma   weight residual
     120.88  115.74    5.14 1.62e+00 3.81e-01 1.01e+01
  angle pdb=" CA  LYS D  18 "
        pdb=" C   LYS D  18 "
        pdb=" O   LYS D  18 "
      ideal   model   delta    sigma   weight residual
     121.87  118.23    3.64 1.16e+00 7.43e-01 9.87e+00
  angle pdb=" O   TRP A 242 "
        pdb=" C   TRP A 242 "
        pdb=" N   MET A 243 "
      ideal   model   delta    sigma   weight residual
     121.83  125.84   -4.01 1.28e+00 6.10e-01 9.81e+00
  angle pdb=" C   ALA B  61 "
        pdb=" N   LEU B  62 "
        pdb=" CA  LEU B  62 "
      ideal   model   delta    sigma   weight residual
     120.09  123.81   -3.72 1.25e+00 6.40e-01 8.87e+00
  ... (remaining 6493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 2523
       16.73 -    33.46: 166
       33.46 -    50.19: 43
       50.19 -    66.92: 7
       66.92 -    83.65: 3
  Dihedral angle restraints: 2742
    sinusoidal: 910
      harmonic: 1832
  Sorted by residual:
  dihedral pdb=" CB  CYS B 129 "
           pdb=" SG  CYS B 129 "
           pdb=" SG  CYS B 195 "
           pdb=" CB  CYS B 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.77  -67.77     1      1.00e+01 1.00e-02 5.97e+01
  dihedral pdb=" CB  CYS A  51 "
           pdb=" SG  CYS A  51 "
           pdb=" SG  CYS A 276 "
           pdb=" CB  CYS A 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.90   64.90     1      1.00e+01 1.00e-02 5.53e+01
  dihedral pdb=" CA  ASP B  58 "
           pdb=" C   ASP B  58 "
           pdb=" N   ASP B  59 "
           pdb=" CA  ASP B  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.98  -25.02     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 2739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 504
       0.029 -    0.058: 193
       0.058 -    0.087: 59
       0.087 -    0.116: 49
       0.116 -    0.145: 8
  Chirality restraints: 813
  Sorted by residual:
  chirality pdb=" CA  THR B 300 "
            pdb=" N   THR B 300 "
            pdb=" C   THR B 300 "
            pdb=" CB  THR B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  GLU A  46 "
            pdb=" N   GLU A  46 "
            pdb=" C   GLU A  46 "
            pdb=" CB  GLU A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  THR A 300 "
            pdb=" N   THR A 300 "
            pdb=" C   THR A 300 "
            pdb=" CB  THR A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 810 not shown)

  Planarity restraints: 791
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 136 "   -0.023 2.00e-02 2.50e+03   1.65e-02 6.85e+00
        pdb=" CG  TRP A 136 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 136 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 136 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 136 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 136 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 136 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 136 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 136 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 136 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 216 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" C   ALA A 216 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 216 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE A 217 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 216 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.95e+00
        pdb=" C   ALA B 216 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ALA B 216 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ILE B 217 "    0.013 2.00e-02 2.50e+03
  ... (remaining 788 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1431
        2.83 -     3.35: 4786
        3.35 -     3.86: 7403
        3.86 -     4.38: 7931
        4.38 -     4.90: 13694
  Nonbonded interactions: 35245
  Sorted by model distance:
  nonbonded pdb=" O   SER A  53 "
            pdb=" ND2 ASN A  55 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" OE1 GLN A 143 "
            pdb=" NE1 TRP A 249 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" O   SER B 122 "
            pdb=" OG1 THR B 123 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   PHE B 264 "
            pdb=" OG  SER B 268 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   SER A 122 "
            pdb=" OG1 THR A 123 "
     model   vdw
     2.365 3.040
  ... (remaining 35240 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 46 through 178 or (resid 179 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 180 through 242 or (resid 243 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 244 through 312))
}
ncs_group {
  reference = (chain 'C' and (resid 8 through 42 or (resid 43 through 44 and (name N or name C \ 
A or name C or name O or name CB )) or resid 45 through 46 or (resid 47 through  \ 
48 and (name N or name CA or name C or name O or name CB )) or resid 49 through  \ 
61 or (resid 62 through 66 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 67 through 70))
  selection = (chain 'D' and (resid 8 through 19 or (resid 20 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 21 through 22 or (resid 23 through 24 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 25 through 31 or (resi \ 
d 32 and (name N or name CA or name C or name O or name CB )) or resid 33 throug \ 
h 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 51 through 55 or (resid 56 through 59 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 60 through 62 or (resid 63 through 66 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 67 through 70))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.110
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
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      :  0.003   0.033   4740  Z= 0.153
  Angle     :  0.691   6.666   6514  Z= 0.379
  Chirality :  0.041   0.145    813
  Planarity :  0.004   0.035    791
  Dihedral  : 12.409  83.654   1530
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.86 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.35), residues: 628
  helix:  0.80 (0.29), residues: 364
  sheet:  0.66 (1.16), residues: 24
  loop : -1.96 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.007   0.002   TYR A 137 
 PHE   0.034   0.002   PHE B 109 
 TRP   0.045   0.002   TRP A 136 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4732)
  covalent geometry    : angle       0.69135 ( 6498)
  SS BOND              : bond        0.00172 (    8)
  SS BOND              : angle       0.62928 (   16)
  hydrogen bonds       : bond        0.13828 (  302)
  hydrogen bonds       : angle       5.54958 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: B   55 ASN cc_start: 0.5704 (t0) cc_final: 0.5482 (t0)
REVERT: B  288 LEU cc_start: 0.7434 (tp) cc_final: 0.7097 (tt)
REVERT: A  136 TRP cc_start: 0.7612 (t-100) cc_final: 0.7013 (t60)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0524
  time to fit residues: 7.8892
Evaluate side-chains
  92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0570
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
B 143 GLN
D  23 GLN
A 143 GLN
A 150 HIS
C  35 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.142357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.125354 restraints weight = 11031.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.128401 restraints weight = 6094.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.130283 restraints weight = 4064.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.131496 restraints weight = 3099.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.132329 restraints weight = 2583.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4740  Z= 0.148
  Angle     :  0.662   7.267   6514  Z= 0.336
  Chirality :  0.041   0.143    813
  Planarity :  0.005   0.048    791
  Dihedral  :  4.848  20.175    654
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.36 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.34), residues: 628
  helix:  0.69 (0.29), residues: 366
  sheet:  0.78 (1.13), residues: 24
  loop : -2.00 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 124 
 TYR   0.012   0.002   TYR C  28 
 PHE   0.026   0.002   PHE B 109 
 TRP   0.029   0.002   TRP A 136 
 HIS   0.003   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4732)
  covalent geometry    : angle       0.65815 ( 6498)
  SS BOND              : bond        0.00259 (    8)
  SS BOND              : angle       1.64574 (   16)
  hydrogen bonds       : bond        0.04186 (  302)
  hydrogen bonds       : angle       4.90518 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.166 
Fit side-chains
REVERT: B   55 ASN cc_start: 0.6135 (t0) cc_final: 0.5779 (t0)
REVERT: B  254 TRP cc_start: 0.5795 (t-100) cc_final: 0.5536 (t-100)
REVERT: B  288 LEU cc_start: 0.7416 (tp) cc_final: 0.7108 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0448
  time to fit residues: 6.1403
Evaluate side-chains
  97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 45 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0870
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
B 279 GLN
D  23 GLN
A 279 GLN
C  35 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.142596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.125961 restraints weight = 10932.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.128913 restraints weight = 6008.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.130734 restraints weight = 4023.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.131948 restraints weight = 3083.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.132608 restraints weight = 2564.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4740  Z= 0.137
  Angle     :  0.654   8.204   6514  Z= 0.329
  Chirality :  0.041   0.281    813
  Planarity :  0.005   0.045    791
  Dihedral  :  4.724  18.629    654
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.67 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.34), residues: 628
  helix:  0.69 (0.28), residues: 368
  sheet:  0.44 (1.09), residues: 24
  loop : -1.98 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.008   0.001   TYR D  28 
 PHE   0.023   0.002   PHE B  81 
 TRP   0.025   0.001   TRP A 136 
 HIS   0.002   0.001   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4732)
  covalent geometry    : angle       0.65370 ( 6498)
  SS BOND              : bond        0.00233 (    8)
  SS BOND              : angle       0.90109 (   16)
  hydrogen bonds       : bond        0.03835 (  302)
  hydrogen bonds       : angle       4.77598 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.102 
Fit side-chains
REVERT: B  288 LEU cc_start: 0.7486 (tp) cc_final: 0.7173 (tt)
  outliers start: 10
  outliers final: 6
  residues processed: 99
  average time/residue: 0.0370
  time to fit residues: 5.2556
Evaluate side-chains
  98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0770
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.141834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.124974 restraints weight = 11022.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.127886 restraints weight = 6138.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.129705 restraints weight = 4155.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.130911 restraints weight = 3196.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.131631 restraints weight = 2676.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4740  Z= 0.136
  Angle     :  0.643   7.954   6514  Z= 0.321
  Chirality :  0.041   0.209    813
  Planarity :  0.005   0.044    791
  Dihedral  :  4.631  18.501    654
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.69 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.34), residues: 628
  helix:  0.77 (0.28), residues: 368
  sheet: -0.01 (1.03), residues: 24
  loop : -1.95 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.013   0.001   TYR C  28 
 PHE   0.020   0.002   PHE B  81 
 TRP   0.027   0.001   TRP A 136 
 HIS   0.007   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4732)
  covalent geometry    : angle       0.64222 ( 6498)
  SS BOND              : bond        0.00237 (    8)
  SS BOND              : angle       0.75421 (   16)
  hydrogen bonds       : bond        0.03685 (  302)
  hydrogen bonds       : angle       4.70937 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.121 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7970 (mp)
REVERT: D   23 GLN cc_start: 0.8365 (tp40) cc_final: 0.8140 (tp-100)
  outliers start: 10
  outliers final: 6
  residues processed: 99
  average time/residue: 0.0457
  time to fit residues: 6.3822
Evaluate side-chains
  102 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 101 GLN
B 279 GLN
A 143 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.141743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.124683 restraints weight = 10982.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.127663 restraints weight = 6106.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.129458 restraints weight = 4122.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.130454 restraints weight = 3190.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.131348 restraints weight = 2734.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4740  Z= 0.138
  Angle     :  0.655   6.590   6514  Z= 0.326
  Chirality :  0.041   0.244    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.606  18.123    654
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.04 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.34), residues: 628
  helix:  0.71 (0.28), residues: 370
  sheet: -0.34 (1.03), residues: 24
  loop : -1.85 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.006   0.001   TYR D  28 
 PHE   0.024   0.001   PHE A 264 
 TRP   0.024   0.002   TRP A 136 
 HIS   0.005   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4732)
  covalent geometry    : angle       0.65507 ( 6498)
  SS BOND              : bond        0.00226 (    8)
  SS BOND              : angle       0.64802 (   16)
  hydrogen bonds       : bond        0.03631 (  302)
  hydrogen bonds       : angle       4.69766 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: B  146 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7928 (mp)
REVERT: B  147 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6416 (mm)
REVERT: B  267 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.6994 (tpp80)
REVERT: A  221 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6592 (tt)
REVERT: A  242 TRP cc_start: 0.6271 (t-100) cc_final: 0.5530 (t-100)
  outliers start: 18
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0470
  time to fit residues: 6.8514
Evaluate side-chains
  107 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0050
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
B 207 GLN
D  23 GLN
A 143 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.141753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.124585 restraints weight = 11102.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.127656 restraints weight = 6150.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.129502 restraints weight = 4142.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.130675 restraints weight = 3194.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.131364 restraints weight = 2693.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4740  Z= 0.138
  Angle     :  0.656   7.247   6514  Z= 0.328
  Chirality :  0.041   0.216    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.557  17.329    654
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 19.61 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.35), residues: 628
  helix:  0.69 (0.28), residues: 370
  sheet: -1.16 (0.88), residues: 34
  loop : -1.74 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.011   0.001   TYR C  28 
 PHE   0.017   0.001   PHE A 264 
 TRP   0.024   0.001   TRP A 136 
 HIS   0.004   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4732)
  covalent geometry    : angle       0.65614 ( 6498)
  SS BOND              : bond        0.00231 (    8)
  SS BOND              : angle       0.62675 (   16)
  hydrogen bonds       : bond        0.03608 (  302)
  hydrogen bonds       : angle       4.72755 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.172 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7929 (mp)
REVERT: B  147 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6407 (mm)
REVERT: B  267 ARG cc_start: 0.7305 (mmm-85) cc_final: 0.7021 (tpp80)
REVERT: A  221 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6563 (tt)
REVERT: A  242 TRP cc_start: 0.6153 (t-100) cc_final: 0.5881 (t-100)
  outliers start: 17
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0449
  time to fit residues: 6.6355
Evaluate side-chains
  109 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   chunk 56 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0870
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
B 207 GLN
A 143 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.141236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.124136 restraints weight = 10956.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.127170 restraints weight = 6131.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.128993 restraints weight = 4138.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.130214 restraints weight = 3208.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.130955 restraints weight = 2683.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4740  Z= 0.145
  Angle     :  0.670   6.137   6514  Z= 0.335
  Chirality :  0.041   0.146    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.560  16.994    654
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 21.77 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.35), residues: 628
  helix:  0.77 (0.28), residues: 368
  sheet: -1.18 (0.89), residues: 34
  loop : -1.80 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.006   0.001   TYR A 199 
 PHE   0.027   0.001   PHE A 264 
 TRP   0.029   0.002   TRP B 254 
 HIS   0.003   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4732)
  covalent geometry    : angle       0.67020 ( 6498)
  SS BOND              : bond        0.00240 (    8)
  SS BOND              : angle       0.61038 (   16)
  hydrogen bonds       : bond        0.03663 (  302)
  hydrogen bonds       : angle       4.74100 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.157 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7933 (mp)
REVERT: B  147 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6414 (mm)
REVERT: B  267 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.7025 (tpp80)
REVERT: A  147 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6592 (mm)
REVERT: A  221 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6583 (tt)
  outliers start: 20
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0490
  time to fit residues: 7.0114
Evaluate side-chains
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.140939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.124361 restraints weight = 11137.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.127124 restraints weight = 6394.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.128866 restraints weight = 4417.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.129861 restraints weight = 3460.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.130693 restraints weight = 2970.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4740  Z= 0.150
  Angle     :  0.702  12.578   6514  Z= 0.341
  Chirality :  0.042   0.216    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.582  16.958    654
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 21.98 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.35), residues: 628
  helix:  0.81 (0.28), residues: 366
  sheet: -1.26 (0.90), residues: 34
  loop : -1.80 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  38 
 TYR   0.012   0.001   TYR C  28 
 PHE   0.028   0.002   PHE B 264 
 TRP   0.057   0.002   TRP B 254 
 HIS   0.003   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4732)
  covalent geometry    : angle       0.70260 ( 6498)
  SS BOND              : bond        0.00252 (    8)
  SS BOND              : angle       0.65232 (   16)
  hydrogen bonds       : bond        0.03731 (  302)
  hydrogen bonds       : angle       4.85854 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.148 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7931 (mp)
REVERT: B  147 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6575 (mm)
REVERT: B  267 ARG cc_start: 0.7276 (mmm-85) cc_final: 0.7006 (tpp80)
REVERT: D   23 GLN cc_start: 0.8384 (tp40) cc_final: 0.8174 (tp-100)
REVERT: A  147 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6624 (mm)
REVERT: A  221 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6606 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 108
  average time/residue: 0.0579
  time to fit residues: 8.2530
Evaluate side-chains
  110 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 143 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.139913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.122841 restraints weight = 10790.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.125723 restraints weight = 6089.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.127536 restraints weight = 4156.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.128730 restraints weight = 3229.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.129358 restraints weight = 2723.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4740  Z= 0.168
  Angle     :  0.737  12.844   6514  Z= 0.356
  Chirality :  0.043   0.229    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.662  16.900    654
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.63 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.34), residues: 628
  helix:  0.75 (0.28), residues: 366
  sheet: -1.39 (0.91), residues: 34
  loop : -1.83 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  38 
 TYR   0.006   0.002   TYR A 199 
 PHE   0.032   0.002   PHE A 264 
 TRP   0.044   0.002   TRP B 254 
 HIS   0.003   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4732)
  covalent geometry    : angle       0.73684 ( 6498)
  SS BOND              : bond        0.00291 (    8)
  SS BOND              : angle       0.73525 (   16)
  hydrogen bonds       : bond        0.03831 (  302)
  hydrogen bonds       : angle       4.93364 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.104 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7935 (mp)
REVERT: B  147 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6503 (mm)
REVERT: B  267 ARG cc_start: 0.7324 (mmm-85) cc_final: 0.7050 (tpp80)
REVERT: A  147 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6566 (mm)
REVERT: A  221 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6660 (tt)
  outliers start: 20
  outliers final: 14
  residues processed: 104
  average time/residue: 0.0469
  time to fit residues: 6.7193
Evaluate side-chains
  112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 44 optimal weight:    0.0770
   chunk 21 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B 207 GLN
D  23 GLN
A 143 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.141489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.124511 restraints weight = 11003.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.127447 restraints weight = 6136.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.129300 restraints weight = 4152.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.130499 restraints weight = 3204.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.131131 restraints weight = 2686.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4740  Z= 0.146
  Angle     :  0.731  12.109   6514  Z= 0.354
  Chirality :  0.042   0.238    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.605  16.824    654
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 23.49 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.35), residues: 628
  helix:  0.82 (0.28), residues: 366
  sheet: -1.46 (0.91), residues: 34
  loop : -1.75 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 267 
 TYR   0.012   0.001   TYR C  28 
 PHE   0.030   0.002   PHE A 264 
 TRP   0.044   0.002   TRP B 254 
 HIS   0.003   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4732)
  covalent geometry    : angle       0.73081 ( 6498)
  SS BOND              : bond        0.00248 (    8)
  SS BOND              : angle       0.64768 (   16)
  hydrogen bonds       : bond        0.03667 (  302)
  hydrogen bonds       : angle       4.85537 (  873)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.169 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7912 (mp)
REVERT: B  147 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6288 (mm)
REVERT: B  267 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.6851 (tpp80)
REVERT: A  147 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6656 (mm)
REVERT: A  221 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6594 (tt)
  outliers start: 17
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0451
  time to fit residues: 6.3516
Evaluate side-chains
  109 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  207 GLN
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  143 GLN
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0970
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
B 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.141220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.124270 restraints weight = 11090.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.127237 restraints weight = 6184.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.129061 restraints weight = 4181.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.130259 restraints weight = 3231.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.130907 restraints weight = 2716.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.196   4740  Z= 0.290
  Angle     :  1.250  59.195   6514  Z= 0.707
  Chirality :  0.048   0.691    813
  Planarity :  0.005   0.076    791
  Dihedral  :  4.606  16.860    654
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.71 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.35), residues: 628
  helix:  0.83 (0.28), residues: 366
  sheet: -1.46 (0.91), residues: 34
  loop : -1.75 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 124 
 TYR   0.008   0.001   TYR C  28 
 PHE   0.024   0.001   PHE A 264 
 TRP   0.038   0.002   TRP B 254 
 HIS   0.003   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 4732)
  covalent geometry    : angle       1.25145 ( 6498)
  SS BOND              : bond        0.00264 (    8)
  SS BOND              : angle       0.63672 (   16)
  hydrogen bonds       : bond        0.03704 (  302)
  hydrogen bonds       : angle       4.87595 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 859.41 seconds
wall clock time: 15 minutes 28.69 seconds (928.69 seconds total)