Starting phenix.real_space_refine
on Sat Jul  4 15:32:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dq1_27646/07_2026/8dq1_27646_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dq1_27646/07_2026/8dq1_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dq1_27646/07_2026/8dq1_27646_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dq1_27646/07_2026/8dq1_27646_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dq1_27646/07_2026/8dq1_27646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dq1_27646/07_2026/8dq1_27646.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 4.69, per 1000 atoms: 0.26
  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: 1.55
  Conformation dependent library (CDL) restraints added in 770.4 milliseconds
  

  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: 3.10
  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: 4.24

  Time building geometry restraints manager: 2.13 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: 31723
        3.26 -     6.52: 467
        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 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 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:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.110
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     22.740
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6668
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     :  1.096  11.602  13309  Z= 0.597
  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 : 14.75
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.033   0.001   ARG D  89 
 TYR   0.041   0.004   TYR B 201 
 PHE   0.037   0.003   PHE A  25 
 TRP   0.053   0.003   TRP A 100 
 HIS   0.020   0.003   HIS B  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01059 /  0.58 ( 9703)
  covalent geometry    : angle       1.09626 /  0.60 (13309)
  hydrogen bonds       : bond        0.17804 / 11.92 (  445)
  hydrogen bonds       : angle       6.81786 /  5.02 ( 1255)

*********************** 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  : 0.297 
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: C   41 ASP cc_start: 0.7948 (m-30) cc_final: 0.7589 (m-30)
REVERT: C   55 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7295 (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: 0.8096 (mt)
REVERT: C  109 ASN cc_start: 0.7980 (m110) cc_final: 0.7629 (m-40)
REVERT: C  142 ASN cc_start: 0.7395 (m110) cc_final: 0.7099 (t0)
REVERT: C  218 ASN cc_start: 0.7852 (m110) cc_final: 0.7600 (m110)
REVERT: D   32 GLU cc_start: 0.6368 (tt0) cc_final: 0.6168 (tt0)
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: 0.7255 (mmm)
REVERT: D   76 ASN cc_start: 0.8728 (t0) cc_final: 0.8407 (t0)
REVERT: D   77 TYR cc_start: 0.7363 (m-80) cc_final: 0.5796 (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: 0.7430 (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: 0.7592 (tt0)
REVERT: D  156 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6876 (ttm-80)
REVERT: D  214 PHE cc_start: 0.7954 (t80) cc_final: 0.7540 (t80)
REVERT: A   13 ASP cc_start: 0.8533 (p0) cc_final: 0.8094 (p0)
REVERT: A  118 ARG cc_start: 0.7923 (mpt-90) cc_final: 0.7523 (mmm160)
REVERT: A  122 ARG cc_start: 0.7441 (mpp80) cc_final: 0.7229 (mtt90)
REVERT: A  144 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: A  161 ASP cc_start: 0.8461 (m-30) cc_final: 0.8101 (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: 0.8739 (p90)
REVERT: A  289 MET cc_start: 0.8645 (ttt) cc_final: 0.8432 (ttp)
REVERT: B  167 TYR cc_start: 0.7656 (t80) cc_final: 0.7337 (t80)
REVERT: B  264 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6934 (tt0)
  outliers start: 8
  outliers final: 4
  residues processed: 305
  average time/residue: 0.2087
  time to fit residues: 87.4155
Evaluate side-chains
  262 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 257
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:   50.0000
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 129 ASN
C 164 GLN
C 215 HIS
D  19 GLN
D  86 ASN
A  98 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.167722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.126244 restraints weight = 38128.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.131996 restraints weight = 15862.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.135719 restraints weight = 8464.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.138118 restraints weight = 5462.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.139531 restraints weight = 4123.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.1564

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= 0.155
  Angle     :  0.640   5.536  13309  Z= 0.344
  Chirality :  0.040   0.147   1443
  Planarity :  0.006   0.065   1599
  Dihedral  : 18.631  89.150   1610
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.25), residues: 1069
  helix:  0.40 (0.23), residues: 486
  sheet: -1.81 (0.42), residues: 140
  loop : -1.50 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 122 
 TYR   0.032   0.002   TYR C  72 
 PHE   0.013   0.001   PHE A 276 
 TRP   0.020   0.001   TRP A 100 
 HIS   0.008   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.16 ( 9703)
  covalent geometry    : angle       0.63963 /  0.34 (13309)
  hydrogen bonds       : bond        0.05725 /  3.81 (  445)
  hydrogen bonds       : angle       5.68582 /  4.15 ( 1255)

*********************** 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
  279 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.370 
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: C   55 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7380 (ttm110)
REVERT: C   75 GLN cc_start: 0.7341 (mt0) cc_final: 0.6964 (mt0)
REVERT: C  105 ARG cc_start: 0.6356 (mtt-85) cc_final: 0.5715 (mtt-85)
REVERT: C  109 ASN cc_start: 0.8131 (m110) cc_final: 0.7841 (m-40)
REVERT: D   32 GLU cc_start: 0.6820 (tt0) cc_final: 0.6480 (tt0)
REVERT: D   74 MET cc_start: 0.7211 (mmt) cc_final: 0.6908 (mmm)
REVERT: D   89 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7407 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7665 (tt0) cc_final: 0.7460 (tt0)
REVERT: D  155 LEU cc_start: 0.8909 (mm) cc_final: 0.8702 (mm)
REVERT: D  214 PHE cc_start: 0.7988 (t80) cc_final: 0.7314 (t80)
REVERT: A   13 ASP cc_start: 0.8241 (p0) cc_final: 0.7868 (p0)
REVERT: A   87 ASN cc_start: 0.8860 (p0) cc_final: 0.8603 (p0)
REVERT: A  161 ASP cc_start: 0.7759 (m-30) cc_final: 0.7535 (m-30)
REVERT: A  196 ASP cc_start: 0.6980 (m-30) cc_final: 0.6764 (m-30)
REVERT: A  289 MET cc_start: 0.8630 (ttt) cc_final: 0.8271 (ttp)
REVERT: B   13 ASP cc_start: 0.7726 (p0) cc_final: 0.7401 (p0)
REVERT: B  232 ASP cc_start: 0.8705 (p0) cc_final: 0.8052 (p0)
REVERT: B  264 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7168 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1958
  time to fit residues: 75.4363
Evaluate side-chains
  252 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.1188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 164 GLN
D 220 GLN
A  98 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.166298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.123956 restraints weight = 41089.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.129820 restraints weight = 17256.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.133553 restraints weight = 9244.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.136047 restraints weight = 5957.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.137492 restraints weight = 4510.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9703  Z= 0.191
  Angle     :  0.599   4.584  13309  Z= 0.324
  Chirality :  0.040   0.144   1443
  Planarity :  0.005   0.057   1599
  Dihedral  : 18.087  89.509   1610
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.25), residues: 1069
  helix:  0.58 (0.23), residues: 492
  sheet: -1.82 (0.42), residues: 140
  loop : -1.43 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  54 
 TYR   0.018   0.002   TYR A 238 
 PHE   0.014   0.001   PHE B 166 
 TRP   0.037   0.002   TRP A 100 
 HIS   0.004   0.001   HIS A  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.19 ( 9703)
  covalent geometry    : angle       0.59875 /  0.32 (13309)
  hydrogen bonds       : bond        0.04954 /  3.32 (  445)
  hydrogen bonds       : angle       5.50799 /  4.02 ( 1255)

*********************** 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
  275 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 0.468 
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   55 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7399 (ttm110)
REVERT: C   75 GLN cc_start: 0.7175 (mt0) cc_final: 0.6774 (mt0)
REVERT: D   32 GLU cc_start: 0.6705 (tt0) cc_final: 0.6404 (tt0)
REVERT: D   34 GLU cc_start: 0.6964 (tp30) cc_final: 0.6531 (tp30)
REVERT: D   74 MET cc_start: 0.7273 (mmt) cc_final: 0.6976 (mmm)
REVERT: D  147 GLU cc_start: 0.7751 (tt0) cc_final: 0.7302 (tt0)
REVERT: D  157 CYS cc_start: 0.9011 (m) cc_final: 0.8694 (m)
REVERT: D  214 PHE cc_start: 0.8019 (t80) cc_final: 0.7340 (t80)
REVERT: D  228 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7752 (mttp)
REVERT: A   13 ASP cc_start: 0.8187 (p0) cc_final: 0.7657 (p0)
REVERT: A  161 ASP cc_start: 0.7516 (m-30) cc_final: 0.7256 (m-30)
REVERT: A  196 ASP cc_start: 0.6829 (m-30) cc_final: 0.6624 (m-30)
REVERT: A  244 LEU cc_start: 0.8978 (tp) cc_final: 0.8706 (tp)
REVERT: A  289 MET cc_start: 0.8787 (ttt) cc_final: 0.8356 (ttp)
REVERT: B   13 ASP cc_start: 0.8252 (p0) cc_final: 0.7323 (p0)
REVERT: B  162 ASP cc_start: 0.8272 (p0) cc_final: 0.7975 (p0)
REVERT: B  171 ARG cc_start: 0.8350 (ptp-110) cc_final: 0.8024 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8844 (p0) cc_final: 0.8203 (p0)
REVERT: B  264 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7321 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 275
  average time/residue: 0.1988
  time to fit residues: 75.8528
Evaluate side-chains
  247 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  61 HIS
A  98 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.166035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.125460 restraints weight = 39548.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.130960 restraints weight = 16630.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.134541 restraints weight = 8879.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.136820 restraints weight = 5724.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.138243 restraints weight = 4314.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2421

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= 0.148
  Angle     :  0.565   6.057  13309  Z= 0.303
  Chirality :  0.038   0.138   1443
  Planarity :  0.005   0.066   1599
  Dihedral  : 17.916  89.964   1610
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.26), residues: 1069
  helix:  0.83 (0.23), residues: 486
  sheet: -1.76 (0.42), residues: 138
  loop : -1.42 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 114 
 TYR   0.013   0.002   TYR A 238 
 PHE   0.014   0.001   PHE A  25 
 TRP   0.041   0.002   TRP A 100 
 HIS   0.012   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 9703)
  covalent geometry    : angle       0.56523 /  0.30 (13309)
  hydrogen bonds       : bond        0.04410 /  2.95 (  445)
  hydrogen bonds       : angle       5.34129 /  3.89 ( 1255)

*********************** 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
  267 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.429 
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: 0.6398 (ttm) cc_final: 0.5890 (ttm)
REVERT: C   55 ARG cc_start: 0.7663 (mtm180) cc_final: 0.7326 (ttm110)
REVERT: C   75 GLN cc_start: 0.7100 (mt0) cc_final: 0.6725 (mt0)
REVERT: D   32 GLU cc_start: 0.6603 (tt0) cc_final: 0.6355 (tt0)
REVERT: D   34 GLU cc_start: 0.6985 (tp30) cc_final: 0.6645 (tp30)
REVERT: D   74 MET cc_start: 0.7167 (mmt) cc_final: 0.6836 (mmm)
REVERT: D  157 CYS cc_start: 0.9019 (m) cc_final: 0.8788 (m)
REVERT: D  214 PHE cc_start: 0.8024 (t80) cc_final: 0.7370 (t80)
REVERT: D  228 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7799 (mttp)
REVERT: A   13 ASP cc_start: 0.8187 (p0) cc_final: 0.7672 (p0)
REVERT: A  244 LEU cc_start: 0.8996 (tp) cc_final: 0.8746 (tp)
REVERT: A  289 MET cc_start: 0.8703 (ttt) cc_final: 0.8309 (ttp)
REVERT: B   13 ASP cc_start: 0.8083 (p0) cc_final: 0.7138 (p0)
REVERT: B  162 ASP cc_start: 0.8070 (p0) cc_final: 0.7837 (p0)
REVERT: B  171 ARG cc_start: 0.8373 (ptp-110) cc_final: 0.8054 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8748 (p0) cc_final: 0.8017 (p0)
REVERT: B  264 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7417 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1974
  time to fit residues: 73.3075
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  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0870
   chunk 73 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 72 optimal weight:    0.3980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.4358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.167133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.126362 restraints weight = 40297.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.131891 restraints weight = 16836.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.135522 restraints weight = 8976.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.137854 restraints weight = 5755.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.139209 restraints weight = 4343.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.2549

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= 0.124
  Angle     :  0.534   5.679  13309  Z= 0.287
  Chirality :  0.037   0.140   1443
  Planarity :  0.005   0.051   1599
  Dihedral  : 17.800  89.961   1610
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.52
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.26), residues: 1069
  helix:  0.98 (0.24), residues: 492
  sheet: -1.74 (0.42), residues: 140
  loop : -1.39 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 122 
 TYR   0.018   0.002   TYR D  72 
 PHE   0.013   0.001   PHE A  25 
 TRP   0.042   0.001   TRP A 100 
 HIS   0.015   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 9703)
  covalent geometry    : angle       0.53370 /  0.29 (13309)
  hydrogen bonds       : bond        0.04111 /  2.77 (  445)
  hydrogen bonds       : angle       5.21112 /  3.79 ( 1255)

*********************** 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
  262 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.454 
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: 0.6326 (ttm) cc_final: 0.6035 (ttm)
REVERT: C   55 ARG cc_start: 0.7639 (mtm180) cc_final: 0.7303 (ttm110)
REVERT: C   75 GLN cc_start: 0.7115 (mt0) cc_final: 0.6747 (mt0)
REVERT: D   32 GLU cc_start: 0.6637 (tt0) cc_final: 0.6380 (tt0)
REVERT: D   34 GLU cc_start: 0.7158 (tp30) cc_final: 0.6952 (tp30)
REVERT: D   96 TRP cc_start: 0.8342 (m-10) cc_final: 0.8123 (m-10)
REVERT: D  157 CYS cc_start: 0.8959 (m) cc_final: 0.8752 (m)
REVERT: D  214 PHE cc_start: 0.8023 (t80) cc_final: 0.7375 (t80)
REVERT: A   13 ASP cc_start: 0.8173 (p0) cc_final: 0.7631 (p0)
REVERT: A   28 ARG cc_start: 0.8606 (ttt-90) cc_final: 0.8380 (ttt-90)
REVERT: A   77 LEU cc_start: 0.9152 (tp) cc_final: 0.8886 (tp)
REVERT: A  289 MET cc_start: 0.8684 (ttt) cc_final: 0.8225 (ttp)
REVERT: A  291 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7107 (tp30)
REVERT: B   13 ASP cc_start: 0.7982 (p0) cc_final: 0.7141 (p0)
REVERT: B  162 ASP cc_start: 0.8029 (p0) cc_final: 0.7754 (p0)
REVERT: B  171 ARG cc_start: 0.8338 (ptp-110) cc_final: 0.8065 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8729 (p0) cc_final: 0.8022 (p0)
REVERT: B  264 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7445 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.1887
  time to fit residues: 69.5471
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  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 113 ASN
B 272 GLN

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 = 0.165080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.124113 restraints weight = 40979.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.129682 restraints weight = 17111.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.133249 restraints weight = 9021.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.135607 restraints weight = 5758.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.137030 restraints weight = 4313.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9703  Z= 0.159
  Angle     :  0.542   5.795  13309  Z= 0.290
  Chirality :  0.038   0.140   1443
  Planarity :  0.005   0.048   1599
  Dihedral  : 17.740  89.714   1610
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.26), residues: 1069
  helix:  1.05 (0.23), residues: 492
  sheet: -1.74 (0.42), residues: 140
  loop : -1.37 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 122 
 TYR   0.014   0.002   TYR A 238 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.026   0.001   TRP A 100 
 HIS   0.011   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.16 ( 9703)
  covalent geometry    : angle       0.54229 /  0.29 (13309)
  hydrogen bonds       : bond        0.04030 /  2.72 (  445)
  hydrogen bonds       : angle       5.12125 /  3.73 ( 1255)

*********************** 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: 0
    poor density    : 265
  time to evaluate  : 0.425 
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   55 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7298 (ttm110)
REVERT: C   75 GLN cc_start: 0.7185 (mt0) cc_final: 0.6798 (mt0)
REVERT: D   32 GLU cc_start: 0.6604 (tt0) cc_final: 0.6352 (tt0)
REVERT: D   37 ARG cc_start: 0.6140 (tmt170) cc_final: 0.5900 (ttt-90)
REVERT: D   96 TRP cc_start: 0.8376 (m-10) cc_final: 0.8141 (m-10)
REVERT: D  214 PHE cc_start: 0.8044 (t80) cc_final: 0.7400 (t80)
REVERT: A   13 ASP cc_start: 0.8208 (p0) cc_final: 0.7669 (p0)
REVERT: A  244 LEU cc_start: 0.8972 (tp) cc_final: 0.8768 (tp)
REVERT: A  289 MET cc_start: 0.8790 (ttt) cc_final: 0.8402 (ttp)
REVERT: B   13 ASP cc_start: 0.8004 (p0) cc_final: 0.7166 (p0)
REVERT: B  162 ASP cc_start: 0.8070 (p0) cc_final: 0.7757 (p0)
REVERT: B  171 ARG cc_start: 0.8431 (ptp-110) cc_final: 0.8142 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8290 (t0) cc_final: 0.8021 (t0)
REVERT: B  232 ASP cc_start: 0.8782 (p0) cc_final: 0.8087 (p0)
REVERT: B  264 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7492 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.1807
  time to fit residues: 67.1272
Evaluate side-chains
  234 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 95 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:    0.3980
   chunk 72 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.166031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.124483 restraints weight = 40630.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.130124 restraints weight = 17223.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.133762 restraints weight = 9170.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.136191 restraints weight = 5896.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.137595 restraints weight = 4437.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3343
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.2886

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= 0.145
  Angle     :  0.536   5.015  13309  Z= 0.288
  Chirality :  0.038   0.146   1443
  Planarity :  0.006   0.112   1599
  Dihedral  : 17.709  89.724   1610
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.98 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.26), residues: 1069
  helix:  1.07 (0.23), residues: 492
  sheet: -1.66 (0.44), residues: 133
  loop : -1.36 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG C 156 
 TYR   0.014   0.002   TYR A 238 
 PHE   0.014   0.001   PHE A  25 
 TRP   0.044   0.001   TRP A 100 
 HIS   0.012   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 9703)
  covalent geometry    : angle       0.53623 /  0.29 (13309)
  hydrogen bonds       : bond        0.03933 /  2.65 (  445)
  hydrogen bonds       : angle       5.11809 /  3.72 ( 1255)

*********************** 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
  254 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 253
  time to evaluate  : 0.439 
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   55 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7253 (ttm110)
REVERT: C   63 THR cc_start: 0.8524 (p) cc_final: 0.8261 (p)
REVERT: C   75 GLN cc_start: 0.7127 (mt0) cc_final: 0.6819 (mt0)
REVERT: D   32 GLU cc_start: 0.6663 (tt0) cc_final: 0.6382 (tt0)
REVERT: D   96 TRP cc_start: 0.8374 (m-10) cc_final: 0.8137 (m-10)
REVERT: D  214 PHE cc_start: 0.8013 (t80) cc_final: 0.7500 (t80)
REVERT: A   13 ASP cc_start: 0.8170 (p0) cc_final: 0.7634 (p0)
REVERT: A   77 LEU cc_start: 0.9133 (tp) cc_final: 0.8855 (tp)
REVERT: A  244 LEU cc_start: 0.8978 (tp) cc_final: 0.8752 (tp)
REVERT: A  289 MET cc_start: 0.8814 (ttt) cc_final: 0.8397 (ttp)
REVERT: A  291 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7281 (tp30)
REVERT: B   13 ASP cc_start: 0.7977 (p0) cc_final: 0.7161 (p0)
REVERT: B   58 ASP cc_start: 0.8182 (t70) cc_final: 0.7886 (t0)
REVERT: B  162 ASP cc_start: 0.8039 (p0) cc_final: 0.7713 (p0)
REVERT: B  171 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.8159 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8272 (t0) cc_final: 0.8020 (t0)
REVERT: B  232 ASP cc_start: 0.8789 (p0) cc_final: 0.8113 (p0)
REVERT: B  264 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7367 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 254
  average time/residue: 0.1833
  time to fit residues: 65.3746
Evaluate side-chains
  232 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.164759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.123573 restraints weight = 36452.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.128859 restraints weight = 15818.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.132337 restraints weight = 8735.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.134516 restraints weight = 5764.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.135936 restraints weight = 4415.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9703  Z= 0.159
  Angle     :  0.546   5.538  13309  Z= 0.294
  Chirality :  0.038   0.139   1443
  Planarity :  0.006   0.097   1599
  Dihedral  : 17.725  89.942   1610
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.44 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.26), residues: 1069
  helix:  1.05 (0.23), residues: 492
  sheet: -1.75 (0.43), residues: 137
  loop : -1.33 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 156 
 TYR   0.015   0.002   TYR A 238 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.036   0.002   TRP A 100 
 HIS   0.020   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 9703)
  covalent geometry    : angle       0.54647 /  0.29 (13309)
  hydrogen bonds       : bond        0.03982 /  2.68 (  445)
  hydrogen bonds       : angle       5.09171 /  3.70 ( 1255)

*********************** 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
  251 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 0.353 
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   55 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7264 (ttm110)
REVERT: C   75 GLN cc_start: 0.7189 (mt0) cc_final: 0.6850 (mt0)
REVERT: D   32 GLU cc_start: 0.6652 (tt0) cc_final: 0.6382 (tt0)
REVERT: D  214 PHE cc_start: 0.8019 (t80) cc_final: 0.7416 (t80)
REVERT: A   13 ASP cc_start: 0.8178 (p0) cc_final: 0.7652 (p0)
REVERT: A   77 LEU cc_start: 0.9127 (tp) cc_final: 0.8861 (tp)
REVERT: A  196 ASP cc_start: 0.6850 (m-30) cc_final: 0.6570 (m-30)
REVERT: B   13 ASP cc_start: 0.8074 (p0) cc_final: 0.7267 (p0)
REVERT: B  162 ASP cc_start: 0.8052 (p0) cc_final: 0.7716 (p0)
REVERT: B  171 ARG cc_start: 0.8501 (ptp-110) cc_final: 0.8179 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8244 (t0) cc_final: 0.7986 (t0)
REVERT: B  232 ASP cc_start: 0.8801 (p0) cc_final: 0.8120 (p0)
REVERT: B  264 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7370 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 251
  average time/residue: 0.1874
  time to fit residues: 66.2658
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  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.165456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.124408 restraints weight = 37504.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.129762 restraints weight = 16222.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.133325 restraints weight = 8891.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.135596 restraints weight = 5824.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.136721 restraints weight = 4461.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.3073

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= 0.138
  Angle     :  0.540   5.668  13309  Z= 0.290
  Chirality :  0.038   0.140   1443
  Planarity :  0.005   0.075   1599
  Dihedral  : 17.706  89.804   1610
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.26), residues: 1069
  helix:  1.09 (0.23), residues: 504
  sheet: -1.73 (0.43), residues: 137
  loop : -1.43 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 156 
 TYR   0.014   0.002   TYR C 234 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.044   0.002   TRP A 100 
 HIS   0.016   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 9703)
  covalent geometry    : angle       0.54037 /  0.29 (13309)
  hydrogen bonds       : bond        0.03880 /  2.60 (  445)
  hydrogen bonds       : angle       5.05291 /  3.67 ( 1255)

*********************** 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
  257 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 256
  time to evaluate  : 0.388 
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   55 ARG cc_start: 0.7567 (mtm180) cc_final: 0.7243 (ttm110)
REVERT: D   32 GLU cc_start: 0.6632 (tt0) cc_final: 0.6352 (tt0)
REVERT: D   89 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7056 (mmm-85)
REVERT: D   96 TRP cc_start: 0.8404 (m-10) cc_final: 0.8074 (m-10)
REVERT: D  214 PHE cc_start: 0.8031 (t80) cc_final: 0.7542 (t80)
REVERT: D  222 LYS cc_start: 0.6776 (tptt) cc_final: 0.6318 (tmtt)
REVERT: A   13 ASP cc_start: 0.8145 (p0) cc_final: 0.7619 (p0)
REVERT: A   77 LEU cc_start: 0.9118 (tp) cc_final: 0.8851 (tp)
REVERT: A  196 ASP cc_start: 0.6826 (m-30) cc_final: 0.6541 (m-30)
REVERT: A  291 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7294 (tp30)
REVERT: B   13 ASP cc_start: 0.8151 (p0) cc_final: 0.7392 (p0)
REVERT: B   58 ASP cc_start: 0.8051 (t70) cc_final: 0.7838 (t0)
REVERT: B  162 ASP cc_start: 0.8155 (p0) cc_final: 0.7779 (p0)
REVERT: B  171 ARG cc_start: 0.8493 (ptp-110) cc_final: 0.8196 (ptp-110)
REVERT: B  191 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7761 (tpp80)
REVERT: B  197 ASP cc_start: 0.8216 (t0) cc_final: 0.8015 (t0)
REVERT: B  232 ASP cc_start: 0.8780 (p0) cc_final: 0.8129 (p0)
REVERT: B  264 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7356 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 257
  average time/residue: 0.1876
  time to fit residues: 68.2172
Evaluate side-chains
  242 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.164695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.123850 restraints weight = 36265.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.129175 restraints weight = 15697.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.132653 restraints weight = 8600.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.134811 restraints weight = 5668.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.136219 restraints weight = 4330.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3175

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= 0.151
  Angle     :  0.541   5.597  13309  Z= 0.291
  Chirality :  0.038   0.137   1443
  Planarity :  0.005   0.069   1599
  Dihedral  : 17.674  89.222   1610
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.25), residues: 1069
  helix:  1.08 (0.23), residues: 504
  sheet: -1.71 (0.43), residues: 137
  loop : -1.45 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 156 
 TYR   0.015   0.002   TYR A 238 
 PHE   0.016   0.001   PHE A  25 
 TRP   0.041   0.002   TRP A 100 
 HIS   0.006   0.001   HIS A  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 ( 9703)
  covalent geometry    : angle       0.54056 /  0.29 (13309)
  hydrogen bonds       : bond        0.03861 /  2.60 (  445)
  hydrogen bonds       : angle       5.02795 /  3.66 ( 1255)

********************** 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
  255 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 0.437 
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   55 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7260 (ttm110)
REVERT: C   63 THR cc_start: 0.8355 (p) cc_final: 0.8118 (p)
REVERT: C  214 PHE cc_start: 0.7007 (t80) cc_final: 0.6609 (t80)
REVERT: D   12 ASP cc_start: 0.7728 (t0) cc_final: 0.7516 (t0)
REVERT: D   32 GLU cc_start: 0.6659 (tt0) cc_final: 0.6412 (tt0)
REVERT: D   89 ARG cc_start: 0.7331 (mmm160) cc_final: 0.7080 (mmm-85)
REVERT: D   96 TRP cc_start: 0.8429 (m-10) cc_final: 0.8180 (m-10)
REVERT: D  214 PHE cc_start: 0.8052 (t80) cc_final: 0.7457 (t80)
REVERT: D  222 LYS cc_start: 0.6620 (tptt) cc_final: 0.6321 (tttp)
REVERT: A   13 ASP cc_start: 0.8154 (p0) cc_final: 0.7614 (p0)
REVERT: A   38 GLU cc_start: 0.8593 (tp30) cc_final: 0.8369 (tp30)
REVERT: A   77 LEU cc_start: 0.9118 (tp) cc_final: 0.8855 (tp)
REVERT: A  196 ASP cc_start: 0.6824 (m-30) cc_final: 0.6519 (m-30)
REVERT: A  291 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7318 (tp30)
REVERT: B   13 ASP cc_start: 0.8128 (p0) cc_final: 0.7375 (p0)
REVERT: B  162 ASP cc_start: 0.8142 (p0) cc_final: 0.7791 (p0)
REVERT: B  171 ARG cc_start: 0.8526 (ptp-110) cc_final: 0.8231 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8086 (t0) cc_final: 0.7861 (t0)
REVERT: B  232 ASP cc_start: 0.8808 (p0) cc_final: 0.8113 (p0)
REVERT: B  264 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7506 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 255
  average time/residue: 0.1872
  time to fit residues: 66.8250
Evaluate side-chains
  235 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 97 optimal weight:    0.8980
   chunk 92 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 272 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.164972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.123028 restraints weight = 43480.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.128756 restraints weight = 17802.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.132434 restraints weight = 9356.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.134894 restraints weight = 6000.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.136363 restraints weight = 4507.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3234

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= 0.136
  Angle     :  0.544  10.394  13309  Z= 0.291
  Chirality :  0.038   0.137   1443
  Planarity :  0.005   0.097   1599
  Dihedral  : 17.647  88.513   1610
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.11 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.26), residues: 1069
  helix:  1.19 (0.23), residues: 504
  sheet: -1.68 (0.43), residues: 137
  loop : -1.41 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C 156 
 TYR   0.014   0.001   TYR A 238 
 PHE   0.016   0.001   PHE A  25 
 TRP   0.040   0.002   TRP A 100 
 HIS   0.007   0.001   HIS C 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 9703)
  covalent geometry    : angle       0.54356 /  0.29 (13309)
  hydrogen bonds       : bond        0.03828 /  2.59 (  445)
  hydrogen bonds       : angle       4.99495 /  3.63 ( 1255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3211.25 seconds
wall clock time: 55 minutes 19.26 seconds (3319.26 seconds total)