Starting phenix.real_space_refine
on Sat May 10 00:14:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9k_36110/05_2025/8j9k_36110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9k_36110/05_2025/8j9k_36110.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j9k_36110/05_2025/8j9k_36110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9k_36110/05_2025/8j9k_36110.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9k_36110/05_2025/8j9k_36110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9k_36110/05_2025/8j9k_36110.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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      14      5.16       5
     C    2727      2.51       5
     N     744      2.21       5
     O     799      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4284
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 2542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2542
          Classifications: {'peptide': 359}
          Incomplete info: {'truncation_to_alanine': 89}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 332}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 319
          Unresolved non-hydrogen angles: 388
          Unresolved non-hydrogen dihedrals: 262
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 192
    Chain: "B"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 785
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 957
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 2.97, per 1000 atoms: 0.69
  Number of scatterers: 4284
  At special positions: 0
  Unit cell: (70.3779, 107.419, 106.184, 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      14     16.00
     O     799      8.00
     N     744      7.00
     C    2727      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  47 " - pdb=" SG  CYS B 112 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  48 " - pdb=" SG  CYS D 122 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 509.0 milliseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 12 sheets defined
      6.4% alpha, 45.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'C' and resid 46 through 50
      removed outlier: 3.965A  pdb=" N   LEU C  49 " --> pdb=" O   PRO C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
    Processing helix  chain 'C' and resid 99 through 109
    Processing helix  chain 'C' and resid 160 through 162
      No H-bonds generated for 'chain 'C' and resid 160 through 162'
    Processing helix  chain 'B' and resid 103 through 107
    Processing helix  chain 'D' and resid 88 through 91
    Processing helix  chain 'D' and resid 113 through 117
    Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 118
      removed outlier: 3.547A  pdb=" N   GLY C  40 " --> pdb=" O   PHE C 116 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   THR C   7 " --> pdb=" O   VAL C 389 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   GLU C 391 " --> pdb=" O   THR C   7 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   VAL C   9 " --> pdb=" O   GLU C 391 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.687A  pdb=" N   PHE C 145 " --> pdb=" O   ILE C 169 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS C 171 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 9.600A  pdb=" N   VAL C 143 " --> pdb=" O   LYS C 171 " (cutoff:3.500A)
      removed outlier: 16.110A  pdb=" N   GLN C 173 " --> pdb=" O   CYS C 141 " (cutoff:3.500A)
      removed outlier: 20.660A  pdb=" N   CYS C 141 " --> pdb=" O   GLN C 173 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP C 144 " --> pdb=" O   ALA C  61 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   VAL C  54 " --> pdb=" O   GLN C  86 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   GLN C  86 " --> pdb=" O   VAL C  54 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   VAL C  56 " --> pdb=" O   THR C  84 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   THR C  84 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU C  58 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE C  82 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   CYS C  60 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.687A  pdb=" N   PHE C 145 " --> pdb=" O   ILE C 169 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS C 171 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 9.600A  pdb=" N   VAL C 143 " --> pdb=" O   LYS C 171 " (cutoff:3.500A)
      removed outlier: 16.110A  pdb=" N   GLN C 173 " --> pdb=" O   CYS C 141 " (cutoff:3.500A)
      removed outlier: 20.660A  pdb=" N   CYS C 141 " --> pdb=" O   GLN C 173 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   CYS C 141 " --> pdb=" O   LEU C 130 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN C 131 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU C 289 " --> pdb=" O   GLN C 131 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 187 through 190
      removed outlier: 3.514A  pdb=" N   THR C 187 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU C 201 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR C 223 " --> pdb=" O   HIS C 200 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 209 through 211
      removed outlier: 6.365A  pdb=" N   TYR C 210 " --> pdb=" O   MET C 346 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TYR C 323 " --> pdb=" O   PHE C 343 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU C 345 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   VAL C 321 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 209 through 211
      removed outlier: 6.365A  pdb=" N   TYR C 210 " --> pdb=" O   MET C 346 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TYR C 323 " --> pdb=" O   PHE C 343 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU C 345 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   VAL C 321 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS C 232 " --> pdb=" O   VAL C 330 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE C 233 " --> pdb=" O   GLN C 260 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLN C 260 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31
      removed outlier: 3.560A  pdb=" N   THR B  96 " --> pdb=" O   SER B  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 36
      removed outlier: 3.814A  pdb=" N   ALA B 108 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL B  57 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   TYR B  73 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   TRP B  59 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 36
      removed outlier: 3.814A  pdb=" N   ALA B 108 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 31 through 33
      removed outlier: 3.553A  pdb=" N   CYS D  48 " --> pdb=" O   ALA D 105 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA D 105 " --> pdb=" O   CYS D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 86
      removed outlier: 6.837A  pdb=" N   TRP D  62 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   SER D  76 " --> pdb=" O   ILE D  60 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE D  60 " --> pdb=" O   SER D  76 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TYR D 139 " --> pdb=" O   ARG D 124 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 85 through 86
      removed outlier: 6.837A  pdb=" N   TRP D  62 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   SER D  76 " --> pdb=" O   ILE D  60 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE D  60 " --> pdb=" O   SER D  76 " (cutoff:3.500A)

    166 hydrogen bonds defined for protein.
    405 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: 1.19

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1401
        1.34 -     1.46: 1030
        1.46 -     1.58: 1931
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 4380
  Sorted by residual:
  bond pdb=" C   ASP C 136 "
       pdb=" N   THR C 137 "
    ideal  model  delta    sigma   weight residual
    1.331  1.277  0.053 1.40e-02 5.10e+03 1.44e+01
  bond pdb=" N   GLN B 113 "
       pdb=" CA  GLN B 113 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.25e-02 6.40e+03 5.67e+00
  bond pdb=" C   GLN C 131 "
       pdb=" N   PRO C 132 "
    ideal  model  delta    sigma   weight residual
    1.330  1.352 -0.022 1.22e-02 6.72e+03 3.37e+00
  bond pdb=" CA  VAL C 316 "
       pdb=" CB  VAL C 316 "
    ideal  model  delta    sigma   weight residual
    1.542  1.521  0.021 1.33e-02 5.65e+03 2.49e+00
  bond pdb=" CA  VAL C 273 "
       pdb=" CB  VAL C 273 "
    ideal  model  delta    sigma   weight residual
    1.544  1.521  0.023 1.46e-02 4.69e+03 2.41e+00
  ... (remaining 4375 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 5793
        1.84 -     3.68: 153
        3.68 -     5.52: 25
        5.52 -     7.36: 7
        7.36 -     9.20: 3
  Bond angle restraints: 5981
  Sorted by residual:
  angle pdb=" CA  GLN C 131 "
        pdb=" C   GLN C 131 "
        pdb=" N   PRO C 132 "
      ideal   model   delta    sigma   weight residual
     119.06  112.37    6.69 1.05e+00 9.07e-01 4.06e+01
  angle pdb=" O   GLN C 131 "
        pdb=" C   GLN C 131 "
        pdb=" N   PRO C 132 "
      ideal   model   delta    sigma   weight residual
     121.23  128.12   -6.89 1.13e+00 7.83e-01 3.72e+01
  angle pdb=" C   GLN C 131 "
        pdb=" N   PRO C 132 "
        pdb=" CA  PRO C 132 "
      ideal   model   delta    sigma   weight residual
     120.03  114.14    5.89 9.90e-01 1.02e+00 3.54e+01
  angle pdb=" C   SER B  74 "
        pdb=" N   ALA B  75 "
        pdb=" CA  ALA B  75 "
      ideal   model   delta    sigma   weight residual
     121.54  128.99   -7.45 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" CA  GLN B 113 "
        pdb=" C   GLN B 113 "
        pdb=" O   GLN B 113 "
      ideal   model   delta    sigma   weight residual
     120.66  116.66    4.00 1.15e+00 7.56e-01 1.21e+01
  ... (remaining 5976 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 2342
       17.71 -    35.42: 190
       35.42 -    53.13: 54
       53.13 -    70.84: 13
       70.84 -    88.55: 5
  Dihedral angle restraints: 2604
    sinusoidal: 889
      harmonic: 1715
  Sorted by residual:
  dihedral pdb=" CB  CYS B  47 "
           pdb=" SG  CYS B  47 "
           pdb=" SG  CYS B 112 "
           pdb=" CB  CYS B 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.49   57.51     1      1.00e+01 1.00e-02 4.44e+01
  dihedral pdb=" CA  TYR D 128 "
           pdb=" C   TYR D 128 "
           pdb=" N   TYR D 129 "
           pdb=" CA  TYR D 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.72   19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" C   GLN B 113 "
           pdb=" N   GLN B 113 "
           pdb=" CA  GLN B 113 "
           pdb=" CB  GLN B 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.19   -9.41     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 2601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 547
       0.051 -    0.101: 112
       0.101 -    0.151: 35
       0.151 -    0.202: 1
       0.202 -    0.252: 1
  Chirality restraints: 696
  Sorted by residual:
  chirality pdb=" CA  GLN B 113 "
            pdb=" N   GLN B 113 "
            pdb=" C   GLN B 113 "
            pdb=" CB  GLN B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  VAL C 339 "
            pdb=" N   VAL C 339 "
            pdb=" C   VAL C 339 "
            pdb=" CB  VAL C 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CB  VAL C 331 "
            pdb=" CA  VAL C 331 "
            pdb=" CG1 VAL C 331 "
            pdb=" CG2 VAL C 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 693 not shown)

  Planarity restraints: 774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 132 "   -0.013 2.00e-02 2.50e+03   2.51e-02 6.31e+00
        pdb=" C   TYR D 132 "    0.043 2.00e-02 2.50e+03
        pdb=" O   TYR D 132 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   MET D 133 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 240 "   -0.015 2.00e-02 2.50e+03   1.72e-02 5.91e+00
        pdb=" CG  TYR C 240 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 240 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 240 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 240 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 240 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 240 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 240 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 182 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO C 183 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO C 183 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 183 "    0.022 5.00e-02 4.00e+02
  ... (remaining 771 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 917
        2.78 -     3.31: 4008
        3.31 -     3.84: 6709
        3.84 -     4.37: 7482
        4.37 -     4.90: 13639
  Nonbonded interactions: 32755
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B  42 "
            pdb=" OG1 THR B  44 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" NH1 ARG D  64 "
            pdb=" OD1 ASP D 116 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" OE1 GLN D 108 "
            pdb=" ND2 ASN D 110 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" N   GLU D  32 "
            pdb=" OE1 GLU D  32 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" O   GLY C 133 "
            pdb=" N   ASP C 136 "
     model   vdw
     2.359 3.120
  ... (remaining 32750 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.680
  Find NCS groups from input model:        0.030
  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:2.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
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      :  0.004   0.055   4382  Z= 0.216
  Angle     :  0.767   9.204   5985  Z= 0.419
  Chirality :  0.046   0.252    696
  Planarity :  0.005   0.040    774
  Dihedral  : 15.318  88.546   1496
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 19.05 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.39 (0.34), residues: 582
  helix: -3.14 (1.02), residues: 17
  sheet: -1.19 (0.31), residues: 263
  loop : -1.82 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  73 
 HIS   0.003   0.001   HIS C 114 
 PHE   0.012   0.002   PHE C  76 
 TYR   0.037   0.002   TYR C 240 
 ARG   0.004   0.001   ARG C 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23127 (  139)
  hydrogen bonds       : angle      10.46399 (  405)
  SS BOND              : bond        0.00711 (    2)
  SS BOND              : angle       3.02135 (    4)
  covalent geometry    : bond        0.00446 ( 4380)
  covalent geometry    : angle       0.76280 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1566
  time to fit residues: 14.5099
Evaluate side-chains
  51 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0020
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 ASN
C 173 GLN
D 108 GLN
D 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.120680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.095458 restraints weight = 9809.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.098500 restraints weight = 5479.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.100429 restraints weight = 3899.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4382  Z= 0.142
  Angle     :  0.642   8.447   5985  Z= 0.322
  Chirality :  0.045   0.156    696
  Planarity :  0.005   0.038    774
  Dihedral  :  4.769  27.722    638
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.05 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.23 (0.34), residues: 582
  helix: -3.07 (0.88), residues: 23
  sheet: -0.93 (0.31), residues: 259
  loop : -1.83 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  62 
 HIS   0.002   0.001   HIS C 114 
 PHE   0.009   0.001   PHE B  95 
 TYR   0.012   0.002   TYR C 240 
 ARG   0.003   0.000   ARG D  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03391 (  139)
  hydrogen bonds       : angle       6.36922 (  405)
  SS BOND              : bond        0.00555 (    2)
  SS BOND              : angle       1.81863 (    4)
  covalent geometry    : bond        0.00334 ( 4380)
  covalent geometry    : angle       0.64087 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 TYR cc_start: 0.8649 (m-10) cc_final: 0.8430 (m-10)
REVERT: B  118 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6711 (m-30)
REVERT: D   95 THR cc_start: 0.8551 (p) cc_final: 0.8307 (p)
REVERT: D  108 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7923 (tm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1269
  time to fit residues: 12.5692
Evaluate side-chains
  64 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0030
   chunk 29 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0770
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.5548

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

Flipped N/Q/H residues before XYZ refinement:
C 114 HIS
C 123 ASN
B  30 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.120690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.095581 restraints weight = 9941.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.098634 restraints weight = 5527.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.100610 restraints weight = 3915.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4382  Z= 0.132
  Angle     :  0.603   7.647   5985  Z= 0.300
  Chirality :  0.043   0.154    696
  Planarity :  0.004   0.038    774
  Dihedral  :  4.540  27.951    638
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.50 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 18.57 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.07 (0.33), residues: 582
  helix: -2.92 (0.94), residues: 23
  sheet: -0.77 (0.31), residues: 260
  loop : -1.77 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 140 
 HIS   0.002   0.000   HIS C 114 
 PHE   0.008   0.001   PHE C 117 
 TYR   0.015   0.001   TYR C 240 
 ARG   0.007   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02853 (  139)
  hydrogen bonds       : angle       5.46611 (  405)
  SS BOND              : bond        0.00513 (    2)
  SS BOND              : angle       1.53527 (    4)
  covalent geometry    : bond        0.00313 ( 4380)
  covalent geometry    : angle       0.60216 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 ASN cc_start: 0.8660 (m-40) cc_final: 0.8442 (m-40)
REVERT: C  122 GLN cc_start: 0.7936 (pm20) cc_final: 0.7293 (pt0)
REVERT: B   60 TYR cc_start: 0.8647 (m-10) cc_final: 0.8414 (m-10)
REVERT: B   63 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8598 (mmmm)
REVERT: B  118 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6699 (m-30)
REVERT: D  128 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6538 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1190
  time to fit residues: 12.5695
Evaluate side-chains
  71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  123 ASN
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 44 optimal weight:    0.0980
   chunk 19 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 GLN
D 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.120225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.094912 restraints weight = 9960.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.098009 restraints weight = 5492.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.100014 restraints weight = 3865.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4382  Z= 0.144
  Angle     :  0.592   6.026   5985  Z= 0.300
  Chirality :  0.043   0.151    696
  Planarity :  0.005   0.075    774
  Dihedral  :  4.481  28.201    638
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.50 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 20.24 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.03 (0.33), residues: 582
  helix: -2.90 (0.94), residues: 23
  sheet: -0.80 (0.31), residues: 272
  loop : -1.72 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  59 
 HIS   0.005   0.001   HIS C 347 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.013   0.001   TYR C 240 
 ARG   0.006   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02682 (  139)
  hydrogen bonds       : angle       5.28772 (  405)
  SS BOND              : bond        0.00557 (    2)
  SS BOND              : angle       1.46077 (    4)
  covalent geometry    : bond        0.00340 ( 4380)
  covalent geometry    : angle       0.59066 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: C   16 ASN cc_start: 0.8678 (m-40) cc_final: 0.8476 (m-40)
REVERT: C  122 GLN cc_start: 0.7838 (pm20) cc_final: 0.7389 (pt0)
REVERT: B   63 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8585 (mmmm)
REVERT: B  118 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6674 (m-30)
REVERT: D  128 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.6582 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1232
  time to fit residues: 11.9908
Evaluate side-chains
  69 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 43 optimal weight:    0.3980
   chunk 50 optimal weight:    0.0270
   chunk 32 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0980
   overall best weight:    0.2438

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

Flipped N/Q/H residues before XYZ refinement:
C 102 GLN
D 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.122758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.097884 restraints weight = 10025.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.101021 restraints weight = 5507.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.103051 restraints weight = 3864.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   4382  Z= 0.097
  Angle     :  0.551   5.976   5985  Z= 0.278
  Chirality :  0.042   0.148    696
  Planarity :  0.005   0.066    774
  Dihedral  :  4.257  27.291    638
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.47 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.95 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.33), residues: 582
  helix: -2.95 (0.82), residues: 29
  sheet: -0.47 (0.31), residues: 262
  loop : -1.62 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 140 
 HIS   0.006   0.001   HIS C 347 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.014   0.001   TYR C 240 
 ARG   0.004   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02481 (  139)
  hydrogen bonds       : angle       4.94478 (  405)
  SS BOND              : bond        0.00403 (    2)
  SS BOND              : angle       0.93771 (    4)
  covalent geometry    : bond        0.00228 ( 4380)
  covalent geometry    : angle       0.55103 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: C   16 ASN cc_start: 0.8663 (m-40) cc_final: 0.8462 (m-40)
REVERT: C  103 ASP cc_start: 0.8326 (t70) cc_final: 0.8084 (t0)
REVERT: C  122 GLN cc_start: 0.7816 (pm20) cc_final: 0.7281 (pt0)
REVERT: C  240 TYR cc_start: 0.8382 (m-80) cc_final: 0.8147 (m-80)
REVERT: D  128 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6943 (m-80)
  outliers start: 16
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1253
  time to fit residues: 13.5111
Evaluate side-chains
  69 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0170
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.6222

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.121155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.096631 restraints weight = 9868.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.099795 restraints weight = 5351.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101814 restraints weight = 3763.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4382  Z= 0.136
  Angle     :  0.578   7.163   5985  Z= 0.288
  Chirality :  0.043   0.169    696
  Planarity :  0.005   0.054    774
  Dihedral  :  4.315  28.519    638
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.84 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 21.90 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.34), residues: 582
  helix: -2.86 (0.82), residues: 29
  sheet: -0.48 (0.31), residues: 267
  loop : -1.62 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  59 
 HIS   0.004   0.001   HIS C 347 
 PHE   0.009   0.001   PHE C 116 
 TYR   0.018   0.001   TYR C 240 
 ARG   0.005   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02511 (  139)
  hydrogen bonds       : angle       4.95719 (  405)
  SS BOND              : bond        0.00517 (    2)
  SS BOND              : angle       1.43862 (    4)
  covalent geometry    : bond        0.00325 ( 4380)
  covalent geometry    : angle       0.57663 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: C  103 ASP cc_start: 0.8399 (t70) cc_final: 0.7870 (t0)
REVERT: C  122 GLN cc_start: 0.7879 (pm20) cc_final: 0.7401 (pt0)
REVERT: C  240 TYR cc_start: 0.8531 (m-80) cc_final: 0.8225 (m-80)
REVERT: D  128 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.6804 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 70
  average time/residue: 0.1173
  time to fit residues: 11.4171
Evaluate side-chains
  68 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
C  86 GLN
C 182 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.119498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.094161 restraints weight = 10015.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.097166 restraints weight = 5567.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099069 restraints weight = 3984.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   4382  Z= 0.225
  Angle     :  0.638   7.030   5985  Z= 0.322
  Chirality :  0.045   0.174    696
  Planarity :  0.005   0.037    774
  Dihedral  :  4.659  28.555    638
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.04 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 22.38 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.33), residues: 582
  helix: -2.78 (0.93), residues: 23
  sheet: -0.67 (0.31), residues: 275
  loop : -1.69 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  73 
 HIS   0.004   0.001   HIS C 114 
 PHE   0.010   0.001   PHE C 117 
 TYR   0.020   0.002   TYR C 240 
 ARG   0.004   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02759 (  139)
  hydrogen bonds       : angle       5.22564 (  405)
  SS BOND              : bond        0.00682 (    2)
  SS BOND              : angle       1.84307 (    4)
  covalent geometry    : bond        0.00538 ( 4380)
  covalent geometry    : angle       0.63657 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 50
  time to evaluate  : 0.498 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8429 (t70) cc_final: 0.7668 (t0)
REVERT: C  122 GLN cc_start: 0.7934 (pm20) cc_final: 0.7452 (pt0)
REVERT: C  240 TYR cc_start: 0.8518 (m-80) cc_final: 0.8120 (m-80)
REVERT: B  118 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6981 (m-30)
REVERT: D  128 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7436 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1210
  time to fit residues: 11.3441
Evaluate side-chains
  66 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 GLN
D 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.119373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.094760 restraints weight = 9715.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.097820 restraints weight = 5394.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.099722 restraints weight = 3809.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4382  Z= 0.169
  Angle     :  0.604   7.741   5985  Z= 0.302
  Chirality :  0.044   0.170    696
  Planarity :  0.004   0.036    774
  Dihedral  :  4.574  28.913    638
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.01 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.10 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.34), residues: 582
  helix: -2.47 (0.99), residues: 23
  sheet: -0.62 (0.31), residues: 271
  loop : -1.70 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  73 
 HIS   0.006   0.001   HIS C 347 
 PHE   0.009   0.001   PHE C 117 
 TYR   0.019   0.002   TYR C 240 
 ARG   0.004   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02584 (  139)
  hydrogen bonds       : angle       5.09809 (  405)
  SS BOND              : bond        0.00625 (    2)
  SS BOND              : angle       1.46329 (    4)
  covalent geometry    : bond        0.00404 ( 4380)
  covalent geometry    : angle       0.60319 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.511 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8410 (t70) cc_final: 0.7633 (t0)
REVERT: C  122 GLN cc_start: 0.7907 (pm20) cc_final: 0.7444 (pt0)
REVERT: C  240 TYR cc_start: 0.8545 (m-80) cc_final: 0.8116 (m-80)
REVERT: B  118 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.7019 (m-30)
REVERT: D  108 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8231 (tm-30)
REVERT: D  128 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7238 (m-80)
  outliers start: 19
  outliers final: 15
  residues processed: 72
  average time/residue: 0.1240
  time to fit residues: 12.2303
Evaluate side-chains
  71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  108 GLN
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 55 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  86 GLN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.119587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.095053 restraints weight = 9981.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.098071 restraints weight = 5519.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.100038 restraints weight = 3930.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4382  Z= 0.154
  Angle     :  0.614   7.304   5985  Z= 0.308
  Chirality :  0.044   0.163    696
  Planarity :  0.004   0.035    774
  Dihedral  :  4.537  28.778    638
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.01 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.33 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.34), residues: 582
  helix: -2.35 (1.01), residues: 23
  sheet: -0.51 (0.32), residues: 271
  loop : -1.68 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  73 
 HIS   0.004   0.001   HIS C 114 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.017   0.001   TYR C 240 
 ARG   0.004   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02545 (  139)
  hydrogen bonds       : angle       5.05126 (  405)
  SS BOND              : bond        0.00564 (    2)
  SS BOND              : angle       1.36909 (    4)
  covalent geometry    : bond        0.00372 ( 4380)
  covalent geometry    : angle       0.61312 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.459 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8378 (t70) cc_final: 0.7597 (t0)
REVERT: C  122 GLN cc_start: 0.7925 (pm20) cc_final: 0.7438 (pt0)
REVERT: C  240 TYR cc_start: 0.8573 (m-80) cc_final: 0.8162 (m-80)
REVERT: C  289 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7885 (pp)
REVERT: B  118 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6991 (m-30)
REVERT: B  128 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8241 (tttm)
REVERT: D  128 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7049 (m-80)
  outliers start: 18
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1160
  time to fit residues: 11.4025
Evaluate side-chains
  73 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    0.1980
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 102 GLN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.120013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.095460 restraints weight = 9728.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.098526 restraints weight = 5362.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.100396 restraints weight = 3818.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4382  Z= 0.145
  Angle     :  0.604   6.822   5985  Z= 0.303
  Chirality :  0.043   0.160    696
  Planarity :  0.004   0.035    774
  Dihedral  :  4.507  28.553    638
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.01 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.33 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.35), residues: 582
  helix: -2.29 (1.01), residues: 23
  sheet: -0.43 (0.32), residues: 271
  loop : -1.61 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  73 
 HIS   0.004   0.001   HIS C 114 
 PHE   0.009   0.001   PHE C 117 
 TYR   0.017   0.001   TYR C 240 
 ARG   0.003   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02542 (  139)
  hydrogen bonds       : angle       4.97253 (  405)
  SS BOND              : bond        0.00555 (    2)
  SS BOND              : angle       1.30502 (    4)
  covalent geometry    : bond        0.00346 ( 4380)
  covalent geometry    : angle       0.60346 ( 5981)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.516 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8397 (t70) cc_final: 0.7597 (t0)
REVERT: C  122 GLN cc_start: 0.7913 (pm20) cc_final: 0.7408 (pt0)
REVERT: C  240 TYR cc_start: 0.8585 (m-80) cc_final: 0.8158 (m-80)
REVERT: C  289 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (pp)
REVERT: D  128 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6776 (m-80)
  outliers start: 19
  outliers final: 14
  residues processed: 69
  average time/residue: 0.1190
  time to fit residues: 11.6808
Evaluate side-chains
  69 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0970
   chunk 19 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.118429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093629 restraints weight = 9827.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.096710 restraints weight = 5441.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.098581 restraints weight = 3861.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4382  Z= 0.192
  Angle     :  0.627   6.677   5985  Z= 0.316
  Chirality :  0.044   0.162    696
  Planarity :  0.004   0.036    774
  Dihedral  :  4.640  28.399    638
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.53 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.57 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.35), residues: 582
  helix: -2.07 (1.07), residues: 23
  sheet: -0.60 (0.31), residues: 286
  loop : -1.58 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  62 
 HIS   0.005   0.001   HIS D  61 
 PHE   0.009   0.001   PHE C 117 
 TYR   0.018   0.002   TYR C 240 
 ARG   0.005   0.000   ARG C 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02714 (  139)
  hydrogen bonds       : angle       5.08616 (  405)
  SS BOND              : bond        0.00651 (    2)
  SS BOND              : angle       1.59934 (    4)
  covalent geometry    : bond        0.00454 ( 4380)
  covalent geometry    : angle       0.62606 ( 5981)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1763.06 seconds
wall clock time: 31 minutes 30.91 seconds (1890.91 seconds total)