Starting phenix.real_space_refine
on Sat May 10 02:04:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jps_36488/05_2025/8jps_36488.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jps_36488/05_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_36488/05_2025/8jps_36488.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jps_36488/05_2025/8jps_36488.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jps_36488/05_2025/8jps_36488.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jps_36488/05_2025/8jps_36488.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4}
          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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 72
  Time building chain proxies: 3.62, per 1000 atoms: 0.78
  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: 1.15
  Conformation dependent library (CDL) restraints added in 565.1 milliseconds
  

  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: 0.48
  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: 1.16

  Time building geometry restraints manager: 1.36 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:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.020
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.320
-------------------------------------------------------------------------------
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 : 9.82
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (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
 TRP   0.045   0.002   TRP A 136 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.034   0.002   PHE B 109 
 TYR   0.007   0.002   TYR A 137 
 ARG   0.002   0.000   ARG A 267 

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

*********************** 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  : 0.513 
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: 0.7096 (tt)
REVERT: A  136 TRP cc_start: 0.7612 (t-100) cc_final: 0.7014 (t60)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1408
  time to fit residues: 20.7993
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  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   chunk 16 optimal weight:    0.5980
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.141566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.124652 restraints weight = 10756.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.127597 restraints weight = 6015.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.129505 restraints weight = 4050.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4740  Z= 0.156
  Angle     :  0.671   7.100   6514  Z= 0.341
  Chirality :  0.041   0.131    813
  Planarity :  0.005   0.048    791
  Dihedral  :  4.875  20.294    654
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.58 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.34), residues: 628
  helix:  0.68 (0.29), residues: 366
  sheet:  0.74 (1.13), residues: 24
  loop : -2.00 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 136 
 HIS   0.004   0.001   HIS A 150 
 PHE   0.026   0.002   PHE B  81 
 TYR   0.012   0.002   TYR C  28 
 ARG   0.004   0.001   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  302)
  hydrogen bonds       : angle       4.96297 (  873)
  SS BOND              : bond        0.00265 (    8)
  SS BOND              : angle       1.67689 (   16)
  covalent geometry    : bond        0.00362 ( 4732)
  covalent geometry    : angle       0.66618 ( 6498)

*********************** 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
  105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.504 
Fit side-chains
REVERT: B   55 ASN cc_start: 0.6084 (t0) cc_final: 0.5739 (t0)
REVERT: B  254 TRP cc_start: 0.5812 (t-100) cc_final: 0.5570 (t-100)
REVERT: B  288 LEU cc_start: 0.7441 (tp) cc_final: 0.7135 (tt)
  outliers start: 11
  outliers final: 6
  residues processed: 95
  average time/residue: 0.1187
  time to fit residues: 15.4840
Evaluate side-chains
  96 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  245 ILE
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 16 optimal weight:    0.5980
   chunk 57 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0870
   chunk 44 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0370
   chunk 52 optimal weight:    0.0010
   chunk 60 optimal weight:   10.0000
   chunk 42 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.2242

-------------------------------------------------------------------------------
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
C  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.143801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.127122 restraints weight = 10888.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.130243 restraints weight = 5968.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.132151 restraints weight = 3918.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.1767

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= 0.128
  Angle     :  0.643   8.359   6514  Z= 0.324
  Chirality :  0.041   0.294    813
  Planarity :  0.005   0.045    791
  Dihedral  :  4.680  19.213    654
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.24 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.34), residues: 628
  helix:  0.76 (0.28), residues: 368
  sheet:  0.37 (1.08), residues: 24
  loop : -1.98 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 136 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.021   0.001   PHE B  81 
 TYR   0.008   0.001   TYR D  13 
 ARG   0.001   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (  302)
  hydrogen bonds       : angle       4.70814 (  873)
  SS BOND              : bond        0.00192 (    8)
  SS BOND              : angle       0.85477 (   16)
  covalent geometry    : bond        0.00271 ( 4732)
  covalent geometry    : angle       0.64285 ( 6498)

*********************** 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
  107 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.515 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 100
  average time/residue: 0.1119
  time to fit residues: 15.6755
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  : 0.503 
-------------------------------------------------------------------------------
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  294 ILE
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 3 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.3984

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.138058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.121151 restraints weight = 11351.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.123474 restraints weight = 7085.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.124937 restraints weight = 5228.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4740  Z= 0.206
  Angle     :  0.717   7.321   6514  Z= 0.357
  Chirality :  0.043   0.154    813
  Planarity :  0.005   0.045    791
  Dihedral  :  4.893  18.834    654
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 18.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.34), residues: 628
  helix:  0.56 (0.28), residues: 366
  sheet: -0.11 (1.06), residues: 24
  loop : -2.10 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 136 
 HIS   0.004   0.001   HIS B 296 
 PHE   0.027   0.002   PHE B  81 
 TYR   0.012   0.002   TYR C  28 
 ARG   0.002   0.000   ARG D  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04261 (  302)
  hydrogen bonds       : angle       4.95260 (  873)
  SS BOND              : bond        0.00325 (    8)
  SS BOND              : angle       0.91746 (   16)
  covalent geometry    : bond        0.00487 ( 4732)
  covalent geometry    : angle       0.71641 ( 6498)

*********************** 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
  115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.484 
Fit side-chains
REVERT: B  147 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6695 (mm)
REVERT: D   23 GLN cc_start: 0.8361 (tp40) cc_final: 0.8143 (tp-100)
REVERT: A  221 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6608 (tt)
REVERT: C   16 ILE cc_start: 0.5025 (OUTLIER) cc_final: 0.4722 (mp)
  outliers start: 20
  outliers final: 11
  residues processed: 102
  average time/residue: 0.1280
  time to fit residues: 17.5734
Evaluate side-chains
  105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 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   78 THR
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  221 LEU
Chi-restraints excluded: chain A residue  296 HIS
Chi-restraints excluded: chain C residue   16 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 42 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.140419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.123290 restraints weight = 10980.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.126234 restraints weight = 6142.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.128085 restraints weight = 4162.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.2173

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= 0.143
  Angle     :  0.663   6.982   6514  Z= 0.331
  Chirality :  0.041   0.148    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.748  18.624    654
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.34), residues: 628
  helix:  0.70 (0.28), residues: 368
  sheet: -0.45 (1.06), residues: 24
  loop : -2.02 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 136 
 HIS   0.006   0.001   HIS B 296 
 PHE   0.020   0.002   PHE B  81 
 TYR   0.007   0.001   TYR B 199 
 ARG   0.001   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (  302)
  hydrogen bonds       : angle       4.76036 (  873)
  SS BOND              : bond        0.00250 (    8)
  SS BOND              : angle       0.70745 (   16)
  covalent geometry    : bond        0.00329 ( 4732)
  covalent geometry    : angle       0.66247 ( 6498)

*********************** 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
  109 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.500 
Fit side-chains
REVERT: B  179 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8144 (mp)
REVERT: A  147 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6628 (mm)
  outliers start: 16
  outliers final: 9
  residues processed: 100
  average time/residue: 0.1173
  time to fit residues: 16.1740
Evaluate side-chains
  103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
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  179 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  184 VAL
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 40 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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**
B 279 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 = 0.4189 r_free = 0.4189 target = 0.139324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.122624 restraints weight = 11191.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.124982 restraints weight = 6971.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.126457 restraints weight = 5156.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4740  Z= 0.158
  Angle     :  0.678   7.222   6514  Z= 0.339
  Chirality :  0.041   0.143    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.708  18.103    654
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.12 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.34), residues: 628
  helix:  0.66 (0.28), residues: 368
  sheet: -1.26 (0.91), residues: 34
  loop : -1.95 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.027   0.002   PHE A 264 
 TYR   0.010   0.002   TYR C  28 
 ARG   0.001   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03889 (  302)
  hydrogen bonds       : angle       4.86160 (  873)
  SS BOND              : bond        0.00266 (    8)
  SS BOND              : angle       0.72977 (   16)
  covalent geometry    : bond        0.00373 ( 4732)
  covalent geometry    : angle       0.67822 ( 6498)

*********************** 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
  112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.485 
Fit side-chains
REVERT: B  147 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6525 (mm)
REVERT: A  147 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6751 (mm)
REVERT: A  221 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6553 (tt)
  outliers start: 18
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1173
  time to fit residues: 16.3353
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  : 0.507 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain D residue   38 ARG
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4192 r_free = 0.4192 target = 0.139347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.122955 restraints weight = 11113.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.125442 restraints weight = 6859.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.126955 restraints weight = 5004.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4740  Z= 0.168
  Angle     :  0.729  13.490   6514  Z= 0.355
  Chirality :  0.043   0.146    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.741  17.907    654
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 23.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.34), residues: 628
  helix:  0.67 (0.28), residues: 368
  sheet: -1.34 (0.92), residues: 34
  loop : -1.95 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.021   0.002   PHE A 264 
 TYR   0.006   0.001   TYR B 199 
 ARG   0.002   0.000   ARG C  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  302)
  hydrogen bonds       : angle       4.95141 (  873)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       0.72476 (   16)
  covalent geometry    : bond        0.00398 ( 4732)
  covalent geometry    : angle       0.72874 ( 6498)

*********************** 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
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.532 
Fit side-chains
REVERT: B  147 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6469 (mm)
REVERT: A  147 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6676 (mm)
REVERT: A  221 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6521 (tt)
  outliers start: 19
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1276
  time to fit residues: 17.4735
Evaluate side-chains
  105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain D residue   38 ARG
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0870
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    7.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.139986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.123349 restraints weight = 11247.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.125740 restraints weight = 6981.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.127248 restraints weight = 5130.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.2512

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= 0.146
  Angle     :  0.709  12.175   6514  Z= 0.345
  Chirality :  0.042   0.252    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.665  17.656    654
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.35), residues: 628
  helix:  0.74 (0.28), residues: 368
  sheet: -1.38 (0.92), residues: 34
  loop : -1.86 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.034   0.002   PHE A 264 
 TYR   0.012   0.001   TYR C  28 
 ARG   0.002   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03731 (  302)
  hydrogen bonds       : angle       4.89297 (  873)
  SS BOND              : bond        0.00262 (    8)
  SS BOND              : angle       0.65797 (   16)
  covalent geometry    : bond        0.00343 ( 4732)
  covalent geometry    : angle       0.70885 ( 6498)

*********************** 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
  107 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.486 
Fit side-chains
REVERT: B  147 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6505 (mm)
REVERT: D   23 GLN cc_start: 0.8376 (tp40) cc_final: 0.8140 (tp-100)
REVERT: A  147 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6706 (mm)
REVERT: A  221 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6518 (tt)
  outliers start: 17
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1156
  time to fit residues: 15.4780
Evaluate side-chains
  103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  296 HIS
Chi-restraints excluded: chain D residue   38 ARG
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 6 optimal weight:    0.0270
   chunk 30 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7440

-------------------------------------------------------------------------------
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 = 0.4200 r_free = 0.4200 target = 0.140025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.123904 restraints weight = 11066.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.126408 restraints weight = 6719.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.127932 restraints weight = 4826.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6862
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4740  Z= 0.152
  Angle     :  0.718  11.799   6514  Z= 0.348
  Chirality :  0.043   0.254    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.650  17.403    654
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 23.28 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.35), residues: 628
  helix:  0.76 (0.28), residues: 368
  sheet: -1.43 (0.93), residues: 34
  loop : -1.82 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.020   0.002   PHE A 264 
 TYR   0.007   0.001   TYR A 199 
 ARG   0.001   0.000   ARG C  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03731 (  302)
  hydrogen bonds       : angle       4.90291 (  873)
  SS BOND              : bond        0.00276 (    8)
  SS BOND              : angle       0.67911 (   16)
  covalent geometry    : bond        0.00357 ( 4732)
  covalent geometry    : angle       0.71763 ( 6498)

*********************** 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
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.476 
Fit side-chains
REVERT: B  147 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6520 (mm)
REVERT: A  147 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6703 (mm)
REVERT: A  221 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6539 (tt)
  outliers start: 21
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1138
  time to fit residues: 16.1000
Evaluate side-chains
  106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain B residue  152 SER
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 D residue   38 ARG
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
Chi-restraints excluded: chain A residue  298 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0970
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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**
D  23 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 = 0.4207 r_free = 0.4207 target = 0.140444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.124188 restraints weight = 11195.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.126686 restraints weight = 6871.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.128247 restraints weight = 4978.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4740  Z= 0.154
  Angle     :  0.762  11.419   6514  Z= 0.372
  Chirality :  0.043   0.258    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.653  17.267    654
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 24.78 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.35), residues: 628
  helix:  0.68 (0.28), residues: 370
  sheet: -1.44 (0.93), residues: 34
  loop : -1.74 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.036   0.002   PHE A 264 
 TYR   0.013   0.001   TYR C  28 
 ARG   0.001   0.000   ARG A 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  302)
  hydrogen bonds       : angle       4.92926 (  873)
  SS BOND              : bond        0.00485 (    8)
  SS BOND              : angle       3.03185 (   16)
  covalent geometry    : bond        0.00362 ( 4732)
  covalent geometry    : angle       0.74757 ( 6498)

********************** 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
  105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.527 
Fit side-chains
REVERT: B  147 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6628 (mm)
REVERT: A  147 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6737 (mm)
REVERT: A  221 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6477 (tt)
  outliers start: 17
  outliers final: 14
  residues processed: 96
  average time/residue: 0.1151
  time to fit residues: 15.2622
Evaluate side-chains
  103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain B residue  152 SER
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 D residue   38 ARG
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
Chi-restraints excluded: chain A residue  298 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.139853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.122600 restraints weight = 11086.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.125634 restraints weight = 6245.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.127494 restraints weight = 4259.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4740  Z= 0.156
  Angle     :  0.757  11.287   6514  Z= 0.368
  Chirality :  0.043   0.245    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.619  17.199    654
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.57 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.34), residues: 628
  helix:  0.78 (0.28), residues: 366
  sheet: -1.41 (0.94), residues: 34
  loop : -1.81 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.019   0.002   PHE A 264 
 TYR   0.007   0.001   TYR A 199 
 ARG   0.001   0.000   ARG C  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (  302)
  hydrogen bonds       : angle       4.93591 (  873)
  SS BOND              : bond        0.00342 (    8)
  SS BOND              : angle       2.63818 (   16)
  covalent geometry    : bond        0.00368 ( 4732)
  covalent geometry    : angle       0.74629 ( 6498)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1700.15 seconds
wall clock time: 30 minutes 26.94 seconds (1826.94 seconds total)