Starting phenix.real_space_refine
on Wed Jun 18 22:34:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dq1_27646/06_2025/8dq1_27646_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dq1_27646/06_2025/8dq1_27646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dq1_27646/06_2025/8dq1_27646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dq1_27646/06_2025/8dq1_27646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dq1_27646/06_2025/8dq1_27646_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dq1_27646/06_2025/8dq1_27646_trim.cif"
  }
  resolution = 4.1
  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=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4735 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Br      2      7.06       5
     P      34      5.49       5
     S      52      5.16       5
     C    5840      2.51       5
     N    1704      2.21       5
     O    1779      1.98       5
     H    8343      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17754
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 3772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 3772
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 10, 'TRANS': 230}
    Chain: "D"
      Number of atoms: 3728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3728
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 10, 'TRANS': 227}
    Chain: "A"
      Number of atoms: 4749
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 298, 4741
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
      Conformer: "B"
        Number of residues, atoms: 298, 4741
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
          bond proxies already assigned to first conformer: 4787
    Chain: "B"
      Number of atoms: 4733
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 298, 4725
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
      Conformer: "B"
        Number of residues, atoms: 298, 4725
          Classifications: {'peptide': 298}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
          bond proxies already assigned to first conformer: 4771
    Chain: "I"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 363
          Classifications: {'DNA': 18}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 17}
    Chain: "J"
      Number of atoms: 369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 369
          Classifications: {'DNA': 18}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 17}
    Chain: "C"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'K5G': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'K5G': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 12.91, per 1000 atoms: 0.73
  Number of scatterers: 17754
  At special positions: 0
  Unit cell: (77.4, 108.36, 140.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Br      2     34.99
     S      52     16.00
     P      34     15.00
     O    1779      8.00
     N    1704      7.00
     C    5840      6.00
     H    8343      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM17750  O05 K5G D 301 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.50
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 7 sheets defined
      52.0% alpha, 11.9% beta
      6 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 7.79
  Creating SS restraints...
    Processing helix  chain 'C' and resid 5 through 19
    Processing helix  chain 'C' and resid 23 through 35
    Processing helix  chain 'C' and resid 65 through 76
    Processing helix  chain 'C' and resid 76 through 81
      removed outlier: 4.571A  pdb=" N   VAL C  80 " --> pdb=" O   ASN C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 90
      removed outlier: 3.776A  pdb=" N   LEU C  85 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLY C  87 " --> pdb=" O   ALA C  83 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   LEU C  88 " --> pdb=" O   ILE C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 114
      removed outlier: 4.205A  pdb=" N   TRP C 108 " --> pdb=" O   SER C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 169
      removed outlier: 4.601A  pdb=" N   GLU C 149 " --> pdb=" O   SER C 145 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   GLU C 150 " --> pdb=" O   PHE C 146 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE C 151 " --> pdb=" O   GLU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 194
    Processing helix  chain 'C' and resid 197 through 206
    Processing helix  chain 'C' and resid 208 through 224
    Processing helix  chain 'C' and resid 227 through 238
      removed outlier: 3.682A  pdb=" N   ALA C 231 " --> pdb=" O   ASN C 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 19
      removed outlier: 3.994A  pdb=" N   GLY D  13 " --> pdb=" O   LEU D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 39
    Processing helix  chain 'D' and resid 65 through 76
    Processing helix  chain 'D' and resid 81 through 90
      removed outlier: 4.263A  pdb=" N   GLY D  87 " --> pdb=" O   ALA D  83 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU D  88 " --> pdb=" O   ILE D  84 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG D  89 " --> pdb=" O   LEU D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 4.457A  pdb=" N   GLN D 103 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 114
      removed outlier: 3.885A  pdb=" N   TRP D 108 " --> pdb=" O   SER D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 169
      removed outlier: 4.323A  pdb=" N   GLU D 149 " --> pdb=" O   SER D 145 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLU D 150 " --> pdb=" O   PHE D 146 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE D 159 " --> pdb=" O   LEU D 155 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLU D 160 " --> pdb=" O   ARG D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 194
      removed outlier: 3.680A  pdb=" N   ASP D 194 " --> pdb=" O   GLN D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 206
    Processing helix  chain 'D' and resid 208 through 224
      removed outlier: 3.556A  pdb=" N   VAL D 212 " --> pdb=" O   SER D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 239
      removed outlier: 3.588A  pdb=" N   ALA D 231 " --> pdb=" O   ASN D 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 56
      removed outlier: 3.588A  pdb=" N   ALA A  50 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 60
      No H-bonds generated for 'chain 'A' and resid 58 through 60'
    Processing helix  chain 'A' and resid 71 through 76
      removed outlier: 3.827A  pdb=" N   GLY A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.525A  pdb=" N   LEU A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 102
      removed outlier: 3.738A  pdb=" N   GLN A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 116
      removed outlier: 4.101A  pdb=" N   VAL A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A 107 " --> pdb=" O   GLU A 103 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL A 108 " --> pdb=" O   SER A 104 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 132
    Processing helix  chain 'A' and resid 198 through 211
      removed outlier: 3.532A  pdb=" N   GLU A 203 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 232
    Processing helix  chain 'A' and resid 232 through 255
    Processing helix  chain 'A' and resid 257 through 270
      removed outlier: 4.049A  pdb=" N   LEU A 261 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 296
      removed outlier: 3.579A  pdb=" N   GLY A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 43
      No H-bonds generated for 'chain 'B' and resid 41 through 43'
    Processing helix  chain 'B' and resid 44 through 56
      removed outlier: 3.539A  pdb=" N   ALA B  50 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ARG B  54 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TRP B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 60
      No H-bonds generated for 'chain 'B' and resid 58 through 60'
    Processing helix  chain 'B' and resid 71 through 75
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 93 through 102
    Processing helix  chain 'B' and resid 106 through 116
    Processing helix  chain 'B' and resid 197 through 210
      removed outlier: 3.760A  pdb=" N   GLU B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
      removed outlier: 3.740A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 227 through 232'
    Processing helix  chain 'B' and resid 232 through 255
    Processing helix  chain 'B' and resid 257 through 274
      removed outlier: 3.778A  pdb=" N   LEU B 261 " --> pdb=" O   SER B 257 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   GLY B 271 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   GLN B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   SER B 273 " --> pdb=" O   TRP B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 297
    Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 62
    Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 62
      removed outlier: 3.699A  pdb=" N   VAL D  94 " --> pdb=" O   THR D 121 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 11
      removed outlier: 6.693A  pdb=" N   LEU A  14 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   TRP A  34 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
      removed outlier: 8.644A  pdb=" N   LEU A  66 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LEU A  36 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   VAL A  90 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL A 137 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ALA A  92 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146
      removed outlier: 6.491A  pdb=" N   HIS A 149 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 9.738A  pdb=" N   VAL A 164 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   GLY A 177 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LEU A 174 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4
      removed outlier: 3.507A  pdb=" N   LEU B 224 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   LEU B 174 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE B 166 " --> pdb=" O   PHE B 175 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 11
      removed outlier: 5.983A  pdb=" N   GLN B   9 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   LEU B  16 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TRP B  34 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   TYR B  64 " --> pdb=" O   TRP B  34 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 184

    429 hydrogen bonds defined for protein.
    1223 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      16 hydrogen bonds
      32 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 6.28

  Time building geometry restraints manager: 5.33 seconds

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

  Histogram of bond lengths:
        0.82 -     1.04: 8318
        1.04 -     1.27: 1502
        1.27 -     1.49: 4395
        1.49 -     1.72: 3748
        1.72 -     1.94: 83
  Bond restraints: 18046
  Sorted by residual:
  bond pdb=" C12 K5G D 301 "
       pdb=" C13 K5G D 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.874 -0.354 2.00e-02 2.50e+03 3.13e+02
  bond pdb=" C12 K5G C 301 "
       pdb=" C13 K5G C 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.871 -0.351 2.00e-02 2.50e+03 3.08e+02
  bond pdb=" CA  MET C 173 "
       pdb=" C   MET C 173 "
    ideal  model  delta    sigma   weight residual
    1.524  1.412  0.111 1.27e-02 6.20e+03 7.70e+01
  bond pdb=" C   LEU C 130 "
       pdb=" O   LEU C 130 "
    ideal  model  delta    sigma   weight residual
    1.234  1.141  0.093 1.20e-02 6.94e+03 6.00e+01
  bond pdb=" CA  ARG C  37 "
       pdb=" C   ARG C  37 "
    ideal  model  delta    sigma   weight residual
    1.522  1.423  0.100 1.38e-02 5.25e+03 5.22e+01
  ... (remaining 18041 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 31722
        3.26 -     6.52: 468
        6.52 -     9.77: 33
        9.77 -    13.03: 8
       13.03 -    16.29: 1
  Bond angle restraints: 32232
  Sorted by residual:
  angle pdb=" N   ARG C  36 "
        pdb=" CA  ARG C  36 "
        pdb=" C   ARG C  36 "
      ideal   model   delta    sigma   weight residual
     113.12  102.45   10.67 1.25e+00 6.40e-01 7.28e+01
  angle pdb=" N   LEU C 174 "
        pdb=" CA  LEU C 174 "
        pdb=" C   LEU C 174 "
      ideal   model   delta    sigma   weight residual
     113.38  122.22   -8.84 1.23e+00 6.61e-01 5.17e+01
  angle pdb=" C   PHE A 276 "
        pdb=" CA  PHE A 276 "
        pdb=" CB  PHE A 276 "
      ideal   model   delta    sigma   weight residual
     109.27  120.18  -10.91 1.64e+00 3.72e-01 4.43e+01
  angle pdb=" N   LEU B 117 "
        pdb=" CA  LEU B 117 "
        pdb=" C   LEU B 117 "
      ideal   model   delta    sigma   weight residual
     108.23  119.56  -11.33 1.72e+00 3.38e-01 4.34e+01
  angle pdb=" N   ARG B 114 "
        pdb=" CA  ARG B 114 "
        pdb=" C   ARG B 114 "
      ideal   model   delta    sigma   weight residual
     111.28  104.25    7.03 1.09e+00 8.42e-01 4.15e+01
  ... (remaining 32227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.73: 7687
       26.73 -    53.47: 600
       53.47 -    80.20: 151
       80.20 -   106.94: 12
      106.94 -   133.67: 1
  Dihedral angle restraints: 8451
    sinusoidal: 4790
      harmonic: 3661
  Sorted by residual:
  dihedral pdb=" C   PHE A 276 "
           pdb=" N   PHE A 276 "
           pdb=" CA  PHE A 276 "
           pdb=" CB  PHE A 276 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.46   16.86     0      2.50e+00 1.60e-01 4.55e+01
  dihedral pdb=" CA  GLU C 147 "
           pdb=" C   GLU C 147 "
           pdb=" N   ARG C 148 "
           pdb=" CA  ARG C 148 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.68  -28.32     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" N   PHE A 276 "
           pdb=" C   PHE A 276 "
           pdb=" CA  PHE A 276 "
           pdb=" CB  PHE A 276 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.83  -13.03     0      2.50e+00 1.60e-01 2.72e+01
  ... (remaining 8448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.123: 1374
       0.123 -    0.245: 55
       0.245 -    0.368: 9
       0.368 -    0.490: 3
       0.490 -    0.613: 2
  Chirality restraints: 1443
  Sorted by residual:
  chirality pdb=" CA  PHE A 276 "
            pdb=" N   PHE A 276 "
            pdb=" C   PHE A 276 "
            pdb=" CB  PHE A 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.39e+00
  chirality pdb=" CA  LEU B 117 "
            pdb=" N   LEU B 117 "
            pdb=" C   LEU B 117 "
            pdb=" CB  LEU B 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.46e+00
  chirality pdb=" CA  ARG D 156 "
            pdb=" N   ARG D 156 "
            pdb=" C   ARG D 156 "
            pdb=" CB  ARG D 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.36e+00
  ... (remaining 1440 not shown)

  Planarity restraints: 2605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 129 "   -0.285 2.00e-02 2.50e+03   3.09e-01 1.43e+03
        pdb=" CG  ASN C 129 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 129 "    0.274 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 129 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN C 129 "    0.449 2.00e-02 2.50e+03
        pdb="HD22 ASN C 129 "   -0.462 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 115 "   -0.204 2.00e-02 2.50e+03   2.41e-01 8.73e+02
        pdb=" CD  GLN B 115 "    0.015 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 115 "    0.195 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 115 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN B 115 "    0.364 2.00e-02 2.50e+03
        pdb="HE22 GLN B 115 "   -0.370 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 121 "    0.205 2.00e-02 2.50e+03   2.29e-01 7.89e+02
        pdb=" CD  GLN B 121 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 121 "   -0.185 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 121 "    0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN B 121 "   -0.337 2.00e-02 2.50e+03
        pdb="HE22 GLN B 121 "    0.353 2.00e-02 2.50e+03
  ... (remaining 2602 not shown)

  Histogram of nonbonded interaction distances:
        0.86 -     1.63: 6
        1.63 -     2.40: 7039
        2.40 -     3.17: 55063
        3.17 -     3.93: 74460
        3.93 -     4.70: 122223
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 258791
  Sorted by model distance:
  nonbonded pdb="HH11 ARG C  37 "
            pdb="HD23 LEU A 211 "
     model   vdw
     0.863 2.270
  nonbonded pdb=" HB3 ARG B  43 "
            pdb="HD23 LEU B 117 "
     model   vdw
     1.095 2.440
  nonbonded pdb="HG12 VAL D  60 "
            pdb="BR1  K5G D 301 "
     model   vdw
     1.389 3.070
  nonbonded pdb="HH11 ARG C  37 "
            pdb=" CD2 LEU A 211 "
     model   vdw
     1.513 2.750
  nonbonded pdb=" OE1 GLN B 115 "
            pdb=" HG3 PRO B 278 "
     model   vdw
     1.539 2.620
  ... (remaining 258786 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' and (resid 1 through 59 or resid 61 through 117 or (resid 118 and (na \ 
me N or name CA or name C or name O or name CB or name CG or name CD or name NE  \ 
or name CZ or name NH1 or name NH2)) or (resid 119 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 120 through 244 or resid 246 through 254 or \ 
 (resid 255 and (name N or name CA or name C or name O )) or resid 256 through 2 \ 
98))
  selection = (chain 'B' and (resid 1 through 59 or resid 61 through 230 or (resid 231 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 232 through 244 or re \ 
sid 246 through 298))
}
ncs_group {
  reference = (chain 'C' and (resid 4 through 49 or (resid 50 and (name N or name CA or name C \ 
 or name O or name CB or name OG1 or name CG2)) or resid 51 through 68 or (resid \ 
 69 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ 
 or name CD2)) or resid 70 through 129 or (resid 130 and (name N or name CA or n \ 
ame C or name O or name CB or name CG or name CD1 or name CD2)) or resid 131 thr \ 
ough 155 or (resid 156 and (name N or name CA or name C or name O or name CB or  \ 
name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 157  \ 
through 161 or (resid 162 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD1 or name CD2)) or resid 163 through 211 or (resid 212 and  \ 
(name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or r \ 
esid 213 through 241 or resid 301))
  selection = (chain 'D' and (resid 4 through 9 or (resid 10 and (name N or name CA or name C  \ 
or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2  \ 
or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 11 through 35 or (res \ 
id 36 and (name N or name CA or name C or name O or name CB or name CG or name C \ 
D or name NE or name CZ or name NH1 or name NH2)) or resid 37 or (resid 38 and ( \ 
name N or name CA or name C or name O or name CB or name CG or name CD1 or name  \ 
CD2)) or resid 39 through 173 or (resid 174 and (name N or name CA or name C or  \ 
name O or name CB or name CG or name CD1 or name CD2)) or resid 175 through 241  \ 
or resid 301))
}

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=0.00 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:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.180
  Construct map_model_manager:             0.300
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.120
  Set scattering table:                    0.210
  Process input model:                     49.470
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
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      :  0.011   0.354   9703  Z= 0.578
  Angle     :  1.104  11.602  13309  Z= 0.600
  Chirality :  0.065   0.613   1443
  Planarity :  0.007   0.086   1599
  Dihedral  : 19.210 133.673   3695
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  1.52 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.30 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.25), residues: 1069
  helix:  0.07 (0.23), residues: 482
  sheet: -1.96 (0.40), residues: 144
  loop : -1.60 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP A 100 
 HIS   0.020   0.003   HIS B  74 
 PHE   0.037   0.003   PHE A  25 
 TYR   0.041   0.004   TYR B 201 
 ARG   0.033   0.001   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17804 (  445)
  hydrogen bonds       : angle       6.81786 ( 1255)
  covalent geometry    : bond        0.01065 ( 9703)
  covalent geometry    : angle       1.10372 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 302
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   41 ASP cc_start: 0.7948 (m-30) cc_final: 0.7590 (m-30)
REVERT: C   55 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7300 (ttm110)
REVERT: C   75 GLN cc_start: 0.7361 (mt0) cc_final: 0.6917 (mt0)
REVERT: C   76 ASN cc_start: 0.8454 (t0) cc_final: 0.8175 (t0)
REVERT: C   85 LEU cc_start: 0.8336 (mt) cc_final: 0.8097 (mt)
REVERT: C  109 ASN cc_start: 0.7980 (m110) cc_final: 0.7630 (m-40)
REVERT: C  142 ASN cc_start: 0.7395 (m110) cc_final: 0.7098 (t0)
REVERT: C  218 ASN cc_start: 0.7852 (m110) cc_final: 0.7600 (m110)
REVERT: D   55 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7708 (tmm160)
REVERT: D   74 MET cc_start: 0.7536 (mmt) cc_final: 0.7256 (mmm)
REVERT: D   76 ASN cc_start: 0.8728 (t0) cc_final: 0.8408 (t0)
REVERT: D   77 TYR cc_start: 0.7363 (m-80) cc_final: 0.5795 (m-80)
REVERT: D  106 MET cc_start: 0.4932 (tmm) cc_final: 0.4706 (tpp)
REVERT: D  107 LEU cc_start: 0.7668 (mm) cc_final: 0.7429 (tp)
REVERT: D  109 ASN cc_start: 0.7576 (m-40) cc_final: 0.7259 (m110)
REVERT: D  147 GLU cc_start: 0.8012 (tt0) cc_final: 0.7591 (tt0)
REVERT: D  156 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6875 (ttm-80)
REVERT: D  214 PHE cc_start: 0.7954 (t80) cc_final: 0.7541 (t80)
REVERT: A   13 ASP cc_start: 0.8533 (p0) cc_final: 0.8094 (p0)
REVERT: A  122 ARG cc_start: 0.7441 (mpp80) cc_final: 0.7230 (mtt90)
REVERT: A  144 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8518 (mm-30)
REVERT: A  161 ASP cc_start: 0.8461 (m-30) cc_final: 0.8099 (m-30)
REVERT: A  256 GLU cc_start: 0.5493 (tt0) cc_final: 0.4896 (mt-10)
REVERT: A  276 PHE cc_start: 0.8958 (p90) cc_final: 0.8742 (p90)
REVERT: A  289 MET cc_start: 0.8645 (ttt) cc_final: 0.8430 (ttp)
REVERT: B  167 TYR cc_start: 0.7656 (t80) cc_final: 0.7339 (t80)
REVERT: B  264 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6935 (tt0)
  outliers start: 8
  outliers final: 4
  residues processed: 305
  average time/residue: 0.4772
  time to fit residues: 196.8181
Evaluate side-chains
  263 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 258
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 129 ASN
C 142 ASN
C 164 GLN
C 215 HIS
D  86 ASN
D 220 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.166650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.127081 restraints weight = 38491.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.132584 restraints weight = 16356.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.136114 restraints weight = 8733.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9703  Z= 0.150
  Angle     :  0.579   6.355  13309  Z= 0.307
  Chirality :  0.038   0.136   1443
  Planarity :  0.005   0.061   1599
  Dihedral  : 17.910  89.558   1610
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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 (0.26), residues: 1069
  helix:  0.86 (0.24), residues: 486
  sheet: -1.81 (0.41), residues: 149
  loop : -1.33 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 100 
 HIS   0.009   0.001   HIS B 282 
 PHE   0.016   0.001   PHE A  25 
 TYR   0.031   0.002   TYR C  72 
 ARG   0.005   0.000   ARG B 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04549 (  445)
  hydrogen bonds       : angle       5.37536 ( 1255)
  covalent geometry    : bond        0.00332 ( 9703)
  covalent geometry    : angle       0.57857 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   55 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7344 (ttm110)
REVERT: C   75 GLN cc_start: 0.7148 (mt0) cc_final: 0.6773 (mt0)
REVERT: C  105 ARG cc_start: 0.6388 (mtt-85) cc_final: 0.5826 (mtt-85)
REVERT: C  109 ASN cc_start: 0.8081 (m110) cc_final: 0.7832 (m-40)
REVERT: D   74 MET cc_start: 0.7137 (mmt) cc_final: 0.6896 (mmm)
REVERT: D   89 ARG cc_start: 0.7664 (mmm160) cc_final: 0.7160 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7664 (tt0) cc_final: 0.7452 (tt0)
REVERT: D  157 CYS cc_start: 0.9020 (m) cc_final: 0.8627 (m)
REVERT: D  214 PHE cc_start: 0.7990 (t80) cc_final: 0.7370 (t80)
REVERT: A   13 ASP cc_start: 0.8162 (p0) cc_final: 0.7623 (p0)
REVERT: A   28 ARG cc_start: 0.8626 (ttt90) cc_final: 0.8288 (ttt-90)
REVERT: A   87 ASN cc_start: 0.8810 (p0) cc_final: 0.8546 (p0)
REVERT: A  196 ASP cc_start: 0.6940 (m-30) cc_final: 0.6685 (m-30)
REVERT: A  244 LEU cc_start: 0.9055 (tp) cc_final: 0.8812 (tp)
REVERT: A  289 MET cc_start: 0.8673 (ttt) cc_final: 0.8285 (ttp)
REVERT: B   13 ASP cc_start: 0.7801 (p0) cc_final: 0.7366 (p0)
REVERT: B  155 GLU cc_start: 0.7527 (tt0) cc_final: 0.7172 (tt0)
REVERT: B  162 ASP cc_start: 0.8092 (p0) cc_final: 0.7887 (p0)
REVERT: B  185 GLU cc_start: 0.8169 (pm20) cc_final: 0.7806 (pm20)
REVERT: B  232 ASP cc_start: 0.8784 (p0) cc_final: 0.8099 (p0)
REVERT: B  264 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7203 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.4720
  time to fit residues: 181.7936
Evaluate side-chains
  253 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 79 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C  61 HIS
B 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.165075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.124767 restraints weight = 39639.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.130067 restraints weight = 16598.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.133723 restraints weight = 8880.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9703  Z= 0.149
  Angle     :  0.548   5.903  13309  Z= 0.290
  Chirality :  0.037   0.134   1443
  Planarity :  0.005   0.054   1599
  Dihedral  : 17.434  88.432   1610
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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: -0.43 (0.26), residues: 1069
  helix:  1.06 (0.23), residues: 498
  sheet: -1.76 (0.42), residues: 140
  loop : -1.31 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 100 
 HIS   0.004   0.001   HIS A 282 
 PHE   0.018   0.001   PHE A  25 
 TYR   0.026   0.002   TYR C  72 
 ARG   0.007   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  445)
  hydrogen bonds       : angle       5.10934 ( 1255)
  covalent geometry    : bond        0.00337 ( 9703)
  covalent geometry    : angle       0.54801 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4388 (ttp) cc_final: 0.2914 (tmm)
REVERT: C   55 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7284 (ttm110)
REVERT: C   75 GLN cc_start: 0.7154 (mt0) cc_final: 0.6805 (mt0)
REVERT: D   89 ARG cc_start: 0.7684 (mmm160) cc_final: 0.7319 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7718 (tt0) cc_final: 0.7397 (tt0)
REVERT: D  157 CYS cc_start: 0.8934 (m) cc_final: 0.8585 (m)
REVERT: D  214 PHE cc_start: 0.8032 (t80) cc_final: 0.7512 (t80)
REVERT: A   13 ASP cc_start: 0.8193 (p0) cc_final: 0.7644 (p0)
REVERT: A   28 ARG cc_start: 0.8643 (ttt90) cc_final: 0.8409 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9183 (tp) cc_final: 0.8925 (tp)
REVERT: A  244 LEU cc_start: 0.9051 (tp) cc_final: 0.8830 (tp)
REVERT: A  289 MET cc_start: 0.8802 (ttt) cc_final: 0.8367 (ttp)
REVERT: A  291 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7295 (tp30)
REVERT: B   13 ASP cc_start: 0.8116 (p0) cc_final: 0.7225 (p0)
REVERT: B  155 GLU cc_start: 0.7626 (tt0) cc_final: 0.7355 (tt0)
REVERT: B  162 ASP cc_start: 0.8080 (p0) cc_final: 0.7766 (p0)
REVERT: B  171 ARG cc_start: 0.8583 (ptp-110) cc_final: 0.8100 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8913 (p0) cc_final: 0.8468 (p0)
REVERT: B  264 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7314 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.4865
  time to fit residues: 180.9361
Evaluate side-chains
  241 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.164314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.123767 restraints weight = 35451.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.129001 restraints weight = 15448.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.132392 restraints weight = 8470.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3288
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3288 r_free = 0.3288    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3288 r_free = 0.3288    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3288
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9703  Z= 0.150
  Angle     :  0.526   4.238  13309  Z= 0.281
  Chirality :  0.037   0.139   1443
  Planarity :  0.005   0.078   1599
  Dihedral  : 17.212  85.893   1610
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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: -0.35 (0.26), residues: 1069
  helix:  1.15 (0.23), residues: 504
  sheet: -1.77 (0.42), residues: 142
  loop : -1.34 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 100 
 HIS   0.005   0.001   HIS D  49 
 PHE   0.017   0.001   PHE A  25 
 TYR   0.027   0.002   TYR C  72 
 ARG   0.010   0.000   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03836 (  445)
  hydrogen bonds       : angle       5.03276 ( 1255)
  covalent geometry    : bond        0.00340 ( 9703)
  covalent geometry    : angle       0.52639 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 1.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4591 (ttp) cc_final: 0.3059 (tmm)
REVERT: C   55 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7325 (ttm110)
REVERT: C   75 GLN cc_start: 0.7155 (mt0) cc_final: 0.6847 (mt0)
REVERT: D   34 GLU cc_start: 0.6545 (tp30) cc_final: 0.6249 (tp30)
REVERT: D   89 ARG cc_start: 0.7528 (mmm160) cc_final: 0.7049 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7729 (tt0) cc_final: 0.7448 (tt0)
REVERT: D  157 CYS cc_start: 0.9052 (m) cc_final: 0.8736 (m)
REVERT: D  214 PHE cc_start: 0.8056 (t80) cc_final: 0.7456 (t80)
REVERT: A   13 ASP cc_start: 0.8177 (p0) cc_final: 0.7640 (p0)
REVERT: A   28 ARG cc_start: 0.8629 (ttt90) cc_final: 0.8379 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9139 (tp) cc_final: 0.8910 (tp)
REVERT: A  196 ASP cc_start: 0.6916 (m-30) cc_final: 0.6534 (m-30)
REVERT: A  289 MET cc_start: 0.8835 (ttt) cc_final: 0.8454 (ttp)
REVERT: B  162 ASP cc_start: 0.8029 (p0) cc_final: 0.7700 (p0)
REVERT: B  171 ARG cc_start: 0.8626 (ptp-110) cc_final: 0.8167 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8302 (t0) cc_final: 0.8032 (t0)
REVERT: B  264 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7212 (tt0)
REVERT: B  286 MET cc_start: 0.8600 (mpp) cc_final: 0.8348 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.4830
  time to fit residues: 175.6505
Evaluate side-chains
  239 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 272 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 = 0.3651 r_free = 0.3651 target = 0.163939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.123525 restraints weight = 37308.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.128798 restraints weight = 15940.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.132212 restraints weight = 8627.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9703  Z= 0.146
  Angle     :  0.527   4.670  13309  Z= 0.281
  Chirality :  0.037   0.144   1443
  Planarity :  0.005   0.073   1599
  Dihedral  : 17.124  82.509   1610
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  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: -0.21 (0.26), residues: 1069
  helix:  1.28 (0.23), residues: 504
  sheet: -1.74 (0.43), residues: 143
  loop : -1.26 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 100 
 HIS   0.005   0.001   HIS A 282 
 PHE   0.016   0.001   PHE A  25 
 TYR   0.016   0.002   TYR C 234 
 ARG   0.004   0.000   ARG B 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  445)
  hydrogen bonds       : angle       4.99260 ( 1255)
  covalent geometry    : bond        0.00330 ( 9703)
  covalent geometry    : angle       0.52683 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4617 (ttp) cc_final: 0.3093 (tmm)
REVERT: C   55 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7278 (ttm110)
REVERT: C   75 GLN cc_start: 0.7166 (mt0) cc_final: 0.6849 (mt0)
REVERT: C  214 PHE cc_start: 0.7043 (t80) cc_final: 0.6663 (t80)
REVERT: D   89 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7062 (mmm-85)
REVERT: D   98 ASP cc_start: 0.8336 (t70) cc_final: 0.8123 (t0)
REVERT: D  147 GLU cc_start: 0.7724 (tt0) cc_final: 0.7417 (tt0)
REVERT: D  157 CYS cc_start: 0.8833 (m) cc_final: 0.8521 (m)
REVERT: D  214 PHE cc_start: 0.8061 (t80) cc_final: 0.7467 (t80)
REVERT: A   13 ASP cc_start: 0.8156 (p0) cc_final: 0.7623 (p0)
REVERT: A   28 ARG cc_start: 0.8613 (ttt90) cc_final: 0.8377 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9156 (tp) cc_final: 0.8926 (tp)
REVERT: A  196 ASP cc_start: 0.6894 (m-30) cc_final: 0.6559 (m-30)
REVERT: A  291 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7376 (tp30)
REVERT: B  162 ASP cc_start: 0.8229 (p0) cc_final: 0.7759 (p0)
REVERT: B  171 ARG cc_start: 0.8633 (ptp-110) cc_final: 0.8204 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8249 (t0) cc_final: 0.7990 (t0)
REVERT: B  264 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7216 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.4688
  time to fit residues: 167.2016
Evaluate side-chains
  239 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
** B 272 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 = 0.3648 r_free = 0.3648 target = 0.164065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.124573 restraints weight = 33368.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.129616 restraints weight = 14665.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.132907 restraints weight = 8108.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3300
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3300
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9703  Z= 0.138
  Angle     :  0.507   4.229  13309  Z= 0.270
  Chirality :  0.037   0.156   1443
  Planarity :  0.005   0.061   1599
  Dihedral  : 17.009  88.632   1610
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.74 %
    Favored  : 98.15 %
  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: -0.06 (0.26), residues: 1069
  helix:  1.44 (0.23), residues: 498
  sheet: -1.60 (0.44), residues: 137
  loop : -1.23 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 100 
 HIS   0.009   0.001   HIS A 282 
 PHE   0.016   0.001   PHE A  25 
 TYR   0.017   0.002   TYR C 234 
 ARG   0.009   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  445)
  hydrogen bonds       : angle       4.92714 ( 1255)
  covalent geometry    : bond        0.00316 ( 9703)
  covalent geometry    : angle       0.50683 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 264
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4535 (ttp) cc_final: 0.2998 (tmm)
REVERT: C   55 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7246 (ttm110)
REVERT: C   63 THR cc_start: 0.8473 (p) cc_final: 0.8172 (p)
REVERT: C  214 PHE cc_start: 0.7135 (t80) cc_final: 0.6775 (t80)
REVERT: D   89 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7167 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7639 (tt0) cc_final: 0.7422 (tt0)
REVERT: D  157 CYS cc_start: 0.8941 (m) cc_final: 0.8740 (m)
REVERT: D  214 PHE cc_start: 0.8113 (t80) cc_final: 0.7635 (t80)
REVERT: A   13 ASP cc_start: 0.8122 (p0) cc_final: 0.7570 (p0)
REVERT: A   28 ARG cc_start: 0.8635 (ttt90) cc_final: 0.8233 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9134 (tp) cc_final: 0.8903 (tp)
REVERT: A  196 ASP cc_start: 0.6803 (m-30) cc_final: 0.6457 (m-30)
REVERT: A  235 GLU cc_start: 0.8209 (tt0) cc_final: 0.7913 (tt0)
REVERT: B  162 ASP cc_start: 0.8074 (p0) cc_final: 0.7765 (p0)
REVERT: B  171 ARG cc_start: 0.8647 (ptp-110) cc_final: 0.8224 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8091 (t0) cc_final: 0.7868 (t0)
REVERT: B  258 LEU cc_start: 0.7921 (pt) cc_final: 0.7462 (mt)
REVERT: B  264 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7266 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 265
  average time/residue: 0.4809
  time to fit residues: 173.8334
Evaluate side-chains
  243 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0970
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
** B 272 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 = 0.3653 r_free = 0.3653 target = 0.165345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.123000 restraints weight = 38684.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.128603 restraints weight = 16416.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.132188 restraints weight = 8895.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9703  Z= 0.132
  Angle     :  0.516   4.825  13309  Z= 0.276
  Chirality :  0.037   0.137   1443
  Planarity :  0.005   0.058   1599
  Dihedral  : 16.900  88.632   1610
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.87 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1069
  helix:  1.47 (0.23), residues: 504
  sheet: -1.56 (0.44), residues: 142
  loop : -1.26 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A 282 
 PHE   0.014   0.001   PHE A  25 
 TYR   0.014   0.001   TYR A 238 
 ARG   0.008   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  445)
  hydrogen bonds       : angle       4.89526 ( 1255)
  covalent geometry    : bond        0.00303 ( 9703)
  covalent geometry    : angle       0.51566 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 262
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4552 (ttp) cc_final: 0.3056 (tmm)
REVERT: C   55 ARG cc_start: 0.7547 (mtm180) cc_final: 0.7212 (ttm110)
REVERT: C   63 THR cc_start: 0.8418 (p) cc_final: 0.8164 (p)
REVERT: C   75 GLN cc_start: 0.7055 (mt0) cc_final: 0.6726 (mt0)
REVERT: C  217 LYS cc_start: 0.7590 (mmtp) cc_final: 0.7188 (mtpt)
REVERT: D   89 ARG cc_start: 0.7460 (mmm160) cc_final: 0.7217 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7652 (tt0) cc_final: 0.7452 (tt0)
REVERT: D  214 PHE cc_start: 0.8104 (t80) cc_final: 0.7639 (t80)
REVERT: A   13 ASP cc_start: 0.8104 (p0) cc_final: 0.7558 (p0)
REVERT: A   28 ARG cc_start: 0.8626 (ttt90) cc_final: 0.8224 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9154 (tp) cc_final: 0.8939 (tp)
REVERT: A  196 ASP cc_start: 0.6745 (m-30) cc_final: 0.6429 (m-30)
REVERT: A  235 GLU cc_start: 0.8206 (tt0) cc_final: 0.7903 (tt0)
REVERT: A  272 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8116 (pp30)
REVERT: A  289 MET cc_start: 0.8718 (ttt) cc_final: 0.8420 (ttp)
REVERT: A  291 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7388 (tp30)
REVERT: B  162 ASP cc_start: 0.8128 (p0) cc_final: 0.7689 (p0)
REVERT: B  197 ASP cc_start: 0.7984 (t0) cc_final: 0.7772 (t0)
REVERT: B  258 LEU cc_start: 0.7914 (pt) cc_final: 0.7449 (mt)
REVERT: B  264 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7281 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 262
  average time/residue: 0.4756
  time to fit residues: 170.1323
Evaluate side-chains
  242 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   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 272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.164521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.123383 restraints weight = 32216.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.128494 restraints weight = 14528.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.131894 restraints weight = 8190.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9703  Z= 0.145
  Angle     :  0.527   6.356  13309  Z= 0.281
  Chirality :  0.037   0.137   1443
  Planarity :  0.005   0.057   1599
  Dihedral  : 16.830  85.650   1610
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.26), residues: 1069
  helix:  1.42 (0.23), residues: 509
  sheet: -1.60 (0.44), residues: 143
  loop : -1.27 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 100 
 HIS   0.006   0.001   HIS A  71 
 PHE   0.015   0.001   PHE A  25 
 TYR   0.022   0.002   TYR B 167 
 ARG   0.009   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  445)
  hydrogen bonds       : angle       4.87914 ( 1255)
  covalent geometry    : bond        0.00328 ( 9703)
  covalent geometry    : angle       0.52699 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4579 (ttp) cc_final: 0.3064 (tmm)
REVERT: C   55 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7252 (ttm110)
REVERT: C   63 THR cc_start: 0.8382 (p) cc_final: 0.8135 (p)
REVERT: C  217 LYS cc_start: 0.7575 (mmtp) cc_final: 0.7178 (mtpt)
REVERT: D   55 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.6996 (tmm-80)
REVERT: D   89 ARG cc_start: 0.7459 (mmm160) cc_final: 0.7204 (mmm-85)
REVERT: D  141 GLN cc_start: 0.7525 (mp10) cc_final: 0.7278 (mp10)
REVERT: D  147 GLU cc_start: 0.7623 (tt0) cc_final: 0.7416 (tt0)
REVERT: D  214 PHE cc_start: 0.8107 (t80) cc_final: 0.7650 (t80)
REVERT: A   13 ASP cc_start: 0.8106 (p0) cc_final: 0.7583 (p0)
REVERT: A   28 ARG cc_start: 0.8601 (ttt90) cc_final: 0.8325 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9143 (tp) cc_final: 0.8916 (tp)
REVERT: A  196 ASP cc_start: 0.6800 (m-30) cc_final: 0.6449 (m-30)
REVERT: A  235 GLU cc_start: 0.8209 (tt0) cc_final: 0.7913 (tt0)
REVERT: B  162 ASP cc_start: 0.7952 (p0) cc_final: 0.7624 (p0)
REVERT: B  197 ASP cc_start: 0.8214 (t0) cc_final: 0.7976 (t0)
REVERT: B  258 LEU cc_start: 0.8033 (pt) cc_final: 0.7457 (mt)
REVERT: B  264 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7249 (tt0)
REVERT: B  286 MET cc_start: 0.8640 (mpp) cc_final: 0.8422 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.4860
  time to fit residues: 175.5062
Evaluate side-chains
  236 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 53 optimal weight:    0.3980
   chunk 105 optimal weight:   20.0000
   chunk 3 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 43 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C 109 ASN
C 140 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.165064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.123127 restraints weight = 37571.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.128594 restraints weight = 16055.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.132145 restraints weight = 8755.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9703  Z= 0.141
  Angle     :  0.526   4.647  13309  Z= 0.280
  Chirality :  0.037   0.138   1443
  Planarity :  0.005   0.057   1599
  Dihedral  : 16.780  85.439   1610
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1069
  helix:  1.47 (0.23), residues: 509
  sheet: -1.67 (0.43), residues: 145
  loop : -1.18 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  68 
 HIS   0.013   0.001   HIS B 282 
 PHE   0.014   0.001   PHE D  40 
 TYR   0.023   0.002   TYR D  77 
 ARG   0.009   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  445)
  hydrogen bonds       : angle       4.87064 ( 1255)
  covalent geometry    : bond        0.00325 ( 9703)
  covalent geometry    : angle       0.52573 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4762 (ttp) cc_final: 0.3246 (tmm)
REVERT: C   55 ARG cc_start: 0.7571 (mtm180) cc_final: 0.7250 (ttm110)
REVERT: C   63 THR cc_start: 0.8399 (p) cc_final: 0.8138 (p)
REVERT: C  140 GLN cc_start: 0.7326 (mm110) cc_final: 0.7014 (tt0)
REVERT: C  217 LYS cc_start: 0.7533 (mmtp) cc_final: 0.7244 (mtpt)
REVERT: D   55 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.6976 (tmm-80)
REVERT: D   89 ARG cc_start: 0.7464 (mmm160) cc_final: 0.7225 (mmm-85)
REVERT: D  207 ILE cc_start: 0.7339 (tp) cc_final: 0.7127 (tp)
REVERT: D  214 PHE cc_start: 0.8157 (t80) cc_final: 0.7634 (t80)
REVERT: A   13 ASP cc_start: 0.8118 (p0) cc_final: 0.7587 (p0)
REVERT: A   28 ARG cc_start: 0.8619 (ttt90) cc_final: 0.8311 (ttt-90)
REVERT: A  196 ASP cc_start: 0.6796 (m-30) cc_final: 0.6424 (m-30)
REVERT: A  235 GLU cc_start: 0.8224 (tt0) cc_final: 0.7951 (tt0)
REVERT: A  291 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7377 (tp30)
REVERT: B  162 ASP cc_start: 0.8057 (p0) cc_final: 0.7621 (p0)
REVERT: B  258 LEU cc_start: 0.7928 (pt) cc_final: 0.7464 (mt)
REVERT: B  264 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7377 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.4685
  time to fit residues: 170.9314
Evaluate side-chains
  243 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0770
   chunk 106 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.163828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.121087 restraints weight = 42355.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.126817 restraints weight = 17454.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.130557 restraints weight = 9293.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9703  Z= 0.142
  Angle     :  0.532   4.770  13309  Z= 0.283
  Chirality :  0.037   0.142   1443
  Planarity :  0.005   0.056   1599
  Dihedral  : 16.762  86.340   1610
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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:  0.03 (0.26), residues: 1069
  helix:  1.48 (0.23), residues: 509
  sheet: -1.64 (0.44), residues: 145
  loop : -1.17 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C  68 
 HIS   0.008   0.001   HIS A  69 
 PHE   0.015   0.001   PHE A  25 
 TYR   0.022   0.002   TYR D  77 
 ARG   0.009   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  445)
  hydrogen bonds       : angle       4.85841 ( 1255)
  covalent geometry    : bond        0.00325 ( 9703)
  covalent geometry    : angle       0.53218 (13309)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4799 (ttp) cc_final: 0.3268 (tmm)
REVERT: C   55 ARG cc_start: 0.7533 (mtm180) cc_final: 0.7204 (ttm110)
REVERT: C   63 THR cc_start: 0.8453 (p) cc_final: 0.8123 (p)
REVERT: C  217 LYS cc_start: 0.7572 (mmtp) cc_final: 0.7327 (mtpt)
REVERT: D   55 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.6985 (tmm-80)
REVERT: D   89 ARG cc_start: 0.7496 (mmm160) cc_final: 0.7234 (mmm-85)
REVERT: D  141 GLN cc_start: 0.7419 (mp10) cc_final: 0.7043 (mp10)
REVERT: D  207 ILE cc_start: 0.7342 (tp) cc_final: 0.7128 (tp)
REVERT: D  214 PHE cc_start: 0.8173 (t80) cc_final: 0.7653 (t80)
REVERT: A   13 ASP cc_start: 0.8112 (p0) cc_final: 0.7588 (p0)
REVERT: A   28 ARG cc_start: 0.8606 (ttt90) cc_final: 0.8312 (ttt-90)
REVERT: A   38 GLU cc_start: 0.8540 (tp30) cc_final: 0.8334 (tp30)
REVERT: A  196 ASP cc_start: 0.6766 (m-30) cc_final: 0.6404 (m-30)
REVERT: A  235 GLU cc_start: 0.8238 (tt0) cc_final: 0.7947 (tt0)
REVERT: A  291 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7355 (tp30)
REVERT: B   84 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7297 (ttp-110)
REVERT: B  162 ASP cc_start: 0.7901 (p0) cc_final: 0.7584 (p0)
REVERT: B  258 LEU cc_start: 0.8040 (pt) cc_final: 0.7449 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.4628
  time to fit residues: 165.7960
Evaluate side-chains
  243 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0970
   chunk 70 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 105 optimal weight:   20.0000
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
C 109 ASN
C 220 GLN
D 216 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.164526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.122568 restraints weight = 37146.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.128038 restraints weight = 15948.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.131591 restraints weight = 8655.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.3824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9703  Z= 0.133
  Angle     :  0.519   4.763  13309  Z= 0.277
  Chirality :  0.037   0.141   1443
  Planarity :  0.005   0.055   1599
  Dihedral  : 16.732  86.421   1610
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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:  0.11 (0.26), residues: 1069
  helix:  1.54 (0.23), residues: 509
  sheet: -1.61 (0.44), residues: 145
  loop : -1.12 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C  68 
 HIS   0.008   0.001   HIS A  69 
 PHE   0.014   0.001   PHE A  25 
 TYR   0.018   0.002   TYR D  77 
 ARG   0.009   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03488 (  445)
  hydrogen bonds       : angle       4.80189 ( 1255)
  covalent geometry    : bond        0.00304 ( 9703)
  covalent geometry    : angle       0.51937 (13309)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6824.66 seconds
wall clock time: 117 minutes 8.79 seconds (7028.79 seconds total)