Starting phenix.real_space_refine
on Sun Apr 27 05:16:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jps_36488/04_2025/8jps_36488.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jps_36488/04_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_36488/04_2025/8jps_36488.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jps_36488/04_2025/8jps_36488.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jps_36488/04_2025/8jps_36488.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jps_36488/04_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 3.68, per 1000 atoms: 0.80
  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: 1.38
  Conformation dependent library (CDL) restraints added in 581.5 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: 1.21

  Time building geometry restraints manager: 1.43 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:             1.680
  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:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.390
  Find NCS groups from input model:        0.160
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.300
-------------------------------------------------------------------------------
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  : 0.576 
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: 0.1386
  time to fit residues: 20.5788
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  : 0.495 
-------------------------------------------------------------------------------
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 = 52)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.124683 restraints weight = 10756.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.127599 restraints weight = 6002.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.129465 restraints weight = 4054.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
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       1.67691 (   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  : 0.465 
Fit side-chains
REVERT: B   55 ASN cc_start: 0.6085 (t0) cc_final: 0.5740 (t0)
REVERT: B  254 TRP cc_start: 0.5812 (t-100) cc_final: 0.5570 (t-100)
REVERT: B  288 LEU cc_start: 0.7443 (tp) cc_final: 0.7136 (tt)
  outliers start: 11
  outliers final: 6
  residues processed: 95
  average time/residue: 0.1218
  time to fit residues: 15.6401
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  : 0.486 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0370
   chunk 52 optimal weight:    0.0060
   chunk 60 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.4074

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.143245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.127091 restraints weight = 10884.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.129884 restraints weight = 6187.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.131601 restraints weight = 4218.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4740  Z= 0.131
  Angle     :  0.649   8.245   6514  Z= 0.327
  Chirality :  0.041   0.292    813
  Planarity :  0.005   0.045    791
  Dihedral  :  4.724  19.139    654
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.67 %
    Favored  : 80.60 %
  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: -0.43 (0.34), residues: 628
  helix:  0.73 (0.28), residues: 368
  sheet:  0.35 (1.08), residues: 24
  loop : -2.00 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 136 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.022   0.002   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        0.03817 (  302)
  hydrogen bonds       : angle       4.74614 (  873)
  SS BOND              : bond        0.00207 (    8)
  SS BOND              : angle       0.87438 (   16)
  covalent geometry    : bond        0.00286 ( 4732)
  covalent geometry    : angle       0.64803 ( 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
  104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.494 
Fit side-chains
REVERT: B  112 VAL cc_start: 0.8179 (p) cc_final: 0.7818 (t)
REVERT: B  288 LEU cc_start: 0.7476 (tp) cc_final: 0.7182 (tt)
  outliers start: 8
  outliers final: 6
  residues processed: 97
  average time/residue: 0.1105
  time to fit residues: 15.1803
Evaluate side-chains
  97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.138839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.122003 restraints weight = 11364.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.124311 restraints weight = 7027.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.125779 restraints weight = 5178.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.2135

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= 0.184
  Angle     :  0.695   7.951   6514  Z= 0.347
  Chirality :  0.042   0.157    813
  Planarity :  0.005   0.045    791
  Dihedral  :  4.859  18.940    654
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.53 %
    Favored  : 77.37 %
  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: -0.64 (0.34), residues: 628
  helix:  0.60 (0.28), residues: 366
  sheet: -0.15 (1.05), residues: 24
  loop : -2.11 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 136 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.025   0.002   PHE B  81 
 TYR   0.013   0.002   TYR C  28 
 ARG   0.002   0.000   ARG D  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  302)
  hydrogen bonds       : angle       4.89754 (  873)
  SS BOND              : bond        0.00284 (    8)
  SS BOND              : angle       0.88848 (   16)
  covalent geometry    : bond        0.00432 ( 4732)
  covalent geometry    : angle       0.69485 ( 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
  114 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.474 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7825 (mp)
REVERT: B  147 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6676 (mm)
REVERT: B  288 LEU cc_start: 0.7576 (tp) cc_final: 0.7247 (tt)
REVERT: D   23 GLN cc_start: 0.8397 (tp40) cc_final: 0.8188 (tp-100)
REVERT: A  221 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6592 (tt)
REVERT: C   16 ILE cc_start: 0.5148 (OUTLIER) cc_final: 0.4836 (mp)
  outliers start: 19
  outliers final: 11
  residues processed: 102
  average time/residue: 0.1313
  time to fit residues: 18.1763
Evaluate side-chains
  105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  131 LEU
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  245 ILE
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:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   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 279 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 = 0.140097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.122939 restraints weight = 10999.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.125921 restraints weight = 6140.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.127758 restraints weight = 4158.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.2218

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     :  0.664   6.941   6514  Z= 0.333
  Chirality :  0.041   0.148    813
  Planarity :  0.005   0.044    791
  Dihedral  :  4.757  18.587    654
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.26 %
    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: -0.57 (0.34), residues: 628
  helix:  0.68 (0.28), residues: 368
  sheet: -1.20 (0.88), residues: 34
  loop : -2.02 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 136 
 HIS   0.006   0.001   HIS B 296 
 PHE   0.020   0.002   PHE B  81 
 TYR   0.009   0.001   TYR D  28 
 ARG   0.001   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  302)
  hydrogen bonds       : angle       4.75850 (  873)
  SS BOND              : bond        0.00258 (    8)
  SS BOND              : angle       0.70642 (   16)
  covalent geometry    : bond        0.00337 ( 4732)
  covalent geometry    : angle       0.66353 ( 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
  108 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.473 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7923 (mp)
REVERT: B  288 LEU cc_start: 0.7505 (tp) cc_final: 0.7190 (tt)
REVERT: A  147 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6644 (mm)
  outliers start: 17
  outliers final: 11
  residues processed: 99
  average time/residue: 0.1207
  time to fit residues: 16.3268
Evaluate side-chains
  103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
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 B residue  186 LEU
Chi-restraints excluded: chain B residue  245 ILE
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  215 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 40 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0270
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4199 r_free = 0.4199 target = 0.140659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.123414 restraints weight = 10821.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.126436 restraints weight = 5992.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.128316 restraints weight = 4035.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.2363

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= 0.143
  Angle     :  0.661   8.244   6514  Z= 0.331
  Chirality :  0.041   0.146    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.637  17.894    654
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.91 %
    Favored  : 75.22 %
  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:  0.71 (0.28), residues: 368
  sheet: -1.33 (0.89), residues: 34
  loop : -1.94 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.028   0.002   PHE A 264 
 TYR   0.011   0.001   TYR C  28 
 ARG   0.001   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  302)
  hydrogen bonds       : angle       4.75974 (  873)
  SS BOND              : bond        0.00245 (    8)
  SS BOND              : angle       0.67451 (   16)
  covalent geometry    : bond        0.00332 ( 4732)
  covalent geometry    : angle       0.66097 ( 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
  115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.517 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7910 (mp)
REVERT: B  147 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6465 (mm)
REVERT: B  254 TRP cc_start: 0.5830 (t-100) cc_final: 0.5575 (t-100)
REVERT: B  288 LEU cc_start: 0.7497 (tp) cc_final: 0.7157 (tt)
REVERT: A  147 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6616 (mm)
REVERT: A  221 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6663 (tt)
  outliers start: 18
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1287
  time to fit residues: 17.9582
Evaluate side-chains
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  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  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 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  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:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.4201 r_free = 0.4201 target = 0.140776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.123835 restraints weight = 10815.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.126799 restraints weight = 6090.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.128637 restraints weight = 4133.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.2445

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     :  0.689  12.905   6514  Z= 0.339
  Chirality :  0.041   0.143    813
  Planarity :  0.005   0.042    791
  Dihedral  :  4.627  17.575    654
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.41 %
    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 (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 (0.34), residues: 628
  helix:  0.77 (0.28), residues: 368
  sheet: -1.38 (0.90), residues: 34
  loop : -1.92 (0.40), 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   0.018   0.002   PHE A 264 
 TYR   0.007   0.001   TYR A 199 
 ARG   0.001   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  302)
  hydrogen bonds       : angle       4.80809 (  873)
  SS BOND              : bond        0.00248 (    8)
  SS BOND              : angle       0.62832 (   16)
  covalent geometry    : bond        0.00338 ( 4732)
  covalent geometry    : angle       0.68912 ( 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
  112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.474 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7901 (mp)
REVERT: B  147 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6401 (mm)
REVERT: B  254 TRP cc_start: 0.5791 (t-100) cc_final: 0.5577 (t-100)
REVERT: B  288 LEU cc_start: 0.7490 (tp) cc_final: 0.7284 (tp)
REVERT: A  147 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6691 (mm)
REVERT: A  221 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6583 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 103
  average time/residue: 0.1171
  time to fit residues: 16.5648
Evaluate side-chains
  105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.140351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.123408 restraints weight = 11024.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.126395 restraints weight = 6130.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.128267 restraints weight = 4138.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.2574

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= 0.154
  Angle     :  0.730  11.802   6514  Z= 0.359
  Chirality :  0.042   0.140    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.644  17.267    654
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 23.49 %
    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: -0.53 (0.34), residues: 628
  helix:  0.67 (0.28), residues: 368
  sheet: -1.41 (0.90), residues: 34
  loop : -1.89 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.030   0.002   PHE A 264 
 TYR   0.012   0.001   TYR C  28 
 ARG   0.001   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  302)
  hydrogen bonds       : angle       4.87036 (  873)
  SS BOND              : bond        0.00297 (    8)
  SS BOND              : angle       2.87016 (   16)
  covalent geometry    : bond        0.00367 ( 4732)
  covalent geometry    : angle       0.71643 ( 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
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.468 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7922 (mp)
REVERT: B  147 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6415 (mm)
REVERT: B  254 TRP cc_start: 0.5826 (t-100) cc_final: 0.5587 (t-100)
REVERT: A  147 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6688 (mm)
REVERT: A  221 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6605 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1178
  time to fit residues: 16.2791
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  : 0.480 
-------------------------------------------------------------------------------
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  152 SER
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 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:    0.0050
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   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 ** 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 = 0.4206 r_free = 0.4206 target = 0.141009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.123920 restraints weight = 11077.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.126978 restraints weight = 6088.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.128890 restraints weight = 4075.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.2614

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= 0.147
  Angle     :  0.726  11.044   6514  Z= 0.356
  Chirality :  0.042   0.140    813
  Planarity :  0.005   0.043    791
  Dihedral  :  4.595  17.031    654
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 24.14 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.35), residues: 628
  helix:  0.70 (0.28), residues: 370
  sheet: -1.39 (0.91), residues: 34
  loop : -1.77 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.021   0.001   PHE A 264 
 TYR   0.007   0.001   TYR A 199 
 ARG   0.001   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  302)
  hydrogen bonds       : angle       4.81461 (  873)
  SS BOND              : bond        0.00314 (    8)
  SS BOND              : angle       2.36400 (   16)
  covalent geometry    : bond        0.00345 ( 4732)
  covalent geometry    : angle       0.71690 ( 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
  109 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7929 (mp)
REVERT: B  147 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6413 (mm)
REVERT: B  254 TRP cc_start: 0.5817 (t-100) cc_final: 0.5566 (t-100)
REVERT: D   23 GLN cc_start: 0.8449 (tp40) cc_final: 0.8224 (tp-100)
REVERT: A  147 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6647 (mm)
REVERT: A  221 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6576 (tt)
  outliers start: 19
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1179
  time to fit residues: 16.3950
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  : 0.576 
-------------------------------------------------------------------------------
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  152 SER
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 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:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4203 r_free = 0.4203 target = 0.140754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.123847 restraints weight = 10904.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.126765 restraints weight = 6094.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.128648 restraints weight = 4129.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.2676

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= 0.153
  Angle     :  0.731  13.166   6514  Z= 0.359
  Chirality :  0.042   0.140    813
  Planarity :  0.005   0.042    791
  Dihedral  :  4.568  16.891    654
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  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: -0.44 (0.35), residues: 628
  helix:  0.71 (0.28), residues: 370
  sheet: -1.43 (0.92), residues: 34
  loop : -1.78 (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   0.034   0.002   PHE A 264 
 TYR   0.013   0.001   TYR C  28 
 ARG   0.001   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  302)
  hydrogen bonds       : angle       4.83497 (  873)
  SS BOND              : bond        0.00313 (    8)
  SS BOND              : angle       2.14467 (   16)
  covalent geometry    : bond        0.00359 ( 4732)
  covalent geometry    : angle       0.72455 ( 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
  109 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.466 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7928 (mp)
REVERT: B  147 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6420 (mm)
REVERT: B  254 TRP cc_start: 0.5828 (t-100) cc_final: 0.5583 (t-100)
REVERT: D   23 GLN cc_start: 0.8506 (tp40) cc_final: 0.8286 (tp-100)
REVERT: A  147 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6643 (mm)
REVERT: A  221 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6572 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 100
  average time/residue: 0.1195
  time to fit residues: 16.7234
Evaluate side-chains
  103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
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  152 SER
Chi-restraints excluded: chain B residue  184 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
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:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 40 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0570
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.141983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.125268 restraints weight = 10906.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.128242 restraints weight = 6075.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.130137 restraints weight = 4075.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4740  Z= 0.140
  Angle     :  0.729  12.783   6514  Z= 0.352
  Chirality :  0.041   0.142    813
  Planarity :  0.005   0.042    791
  Dihedral  :  4.490  16.625    654
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 25.43 %
    Favored  : 70.91 %
  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:  0.77 (0.28), residues: 370
  sheet: -1.44 (0.91), residues: 34
  loop : -1.70 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 136 
 HIS   0.003   0.001   HIS B 296 
 PHE   0.032   0.001   PHE A 264 
 TYR   0.007   0.001   TYR A 199 
 ARG   0.001   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  302)
  hydrogen bonds       : angle       4.75701 (  873)
  SS BOND              : bond        0.00283 (    8)
  SS BOND              : angle       1.92971 (   16)
  covalent geometry    : bond        0.00322 ( 4732)
  covalent geometry    : angle       0.72337 ( 6498)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1734.08 seconds
wall clock time: 30 minutes 48.84 seconds (1848.84 seconds total)