Starting phenix.real_space_refine
on Sun Sep 13 07:34:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dq1_27646/09_2026/8dq1_27646_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dq1_27646/09_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_27646/09_2026/8dq1_27646_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dq1_27646/09_2026/8dq1_27646_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dq1_27646/09_2026/8dq1_27646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dq1_27646/09_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-2.2.1-6174/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: 4.65, 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: 1.51
  Conformation dependent library (CDL) restraints added in 540.8 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: 3.42
  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: 2.11 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:             0.740
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     22.580
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.480
-------------------------------------------------------------------------------
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= 0.596
  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       1.09638 /  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  : 0.453 
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: 0.7599 (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: 0.7539 (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: 0.8740 (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: 0.2052
  time to fit residues: 86.7693
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  : 0.408 
-------------------------------------------------------------------------------
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  86 ASN
A  98 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.167927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.127005 restraints weight = 38076.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.132539 restraints weight = 16229.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.135918 restraints weight = 8801.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.138399 restraints weight = 5766.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.139732 restraints weight = 4400.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    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 = 0.3360 r_free = 0.3360    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: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.1584

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= 0.157
  Angle     :  0.641   6.096  13309  Z= 0.344
  Chirality :  0.040   0.151   1443
  Planarity :  0.006   0.065   1599
  Dihedral  : 18.602  88.789   1610
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  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:  0.41 (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   0.008   0.001   ARG B 122 
 TYR   0.032   0.002   TYR C  72 
 PHE   0.013   0.001   PHE B 166 
 TRP   0.019   0.001   TRP A 100 
 HIS   0.008   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.16 ( 9703)
  covalent geometry    : angle       0.64088 /  0.34 (13309)
  hydrogen bonds       : bond        0.05723 /  3.81 (  445)
  hydrogen bonds       : angle       5.67803 /  4.14 ( 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
  282 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.441 
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: 0.7745 (mtm180) cc_final: 0.7384 (ttm110)
REVERT: C   75 GLN cc_start: 0.7348 (mt0) cc_final: 0.6962 (mt0)
REVERT: C  105 ARG cc_start: 0.6397 (mtt-85) cc_final: 0.5769 (mtt-85)
REVERT: C  109 ASN cc_start: 0.8123 (m110) cc_final: 0.7827 (m-40)
REVERT: D   32 GLU cc_start: 0.6816 (tt0) cc_final: 0.6470 (tt0)
REVERT: D   74 MET cc_start: 0.7227 (mmt) cc_final: 0.6931 (mmm)
REVERT: D   77 TYR cc_start: 0.8005 (m-80) cc_final: 0.7441 (m-80)
REVERT: D   89 ARG cc_start: 0.7719 (mmm160) cc_final: 0.7428 (mmm-85)
REVERT: D  147 GLU cc_start: 0.7680 (tt0) cc_final: 0.7364 (tt0)
REVERT: D  214 PHE cc_start: 0.7989 (t80) cc_final: 0.7316 (t80)
REVERT: A   13 ASP cc_start: 0.8253 (p0) cc_final: 0.7727 (p0)
REVERT: A   87 ASN cc_start: 0.8865 (p0) cc_final: 0.8618 (p0)
REVERT: A  161 ASP cc_start: 0.7784 (m-30) cc_final: 0.7551 (m-30)
REVERT: A  196 ASP cc_start: 0.6995 (m-30) cc_final: 0.6777 (m-30)
REVERT: A  289 MET cc_start: 0.8648 (ttt) cc_final: 0.8293 (ttp)
REVERT: B   13 ASP cc_start: 0.7709 (p0) cc_final: 0.7454 (p0)
REVERT: B  162 ASP cc_start: 0.8210 (p0) cc_final: 0.8004 (p0)
REVERT: B  232 ASP cc_start: 0.8722 (p0) cc_final: 0.8064 (p0)
REVERT: B  264 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7214 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 282
  average time/residue: 0.2048
  time to fit residues: 80.2077
Evaluate side-chains
  253 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.166830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.124888 restraints weight = 40961.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.130700 restraints weight = 17182.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.134456 restraints weight = 9207.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.136904 restraints weight = 5923.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.138399 restraints weight = 4469.969|
|-----------------------------------------------------------------------------|
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:       16 |
|-----------------------------------------------------------------------------|
|-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:       16 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9703  Z= 0.174
  Angle     :  0.600   4.613  13309  Z= 0.323
  Chirality :  0.039   0.137   1443
  Planarity :  0.005   0.056   1599
  Dihedral  : 18.083  89.655   1610
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.84 (0.25), residues: 1069
  helix:  0.63 (0.23), residues: 492
  sheet: -1.78 (0.42), residues: 140
  loop : -1.45 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 122 
 TYR   0.018   0.002   TYR A 238 
 PHE   0.014   0.001   PHE B 166 
 TRP   0.035   0.002   TRP A 100 
 HIS   0.004   0.001   HIS A  74 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.17 ( 9703)
  covalent geometry    : angle       0.59973 /  0.32 (13309)
  hydrogen bonds       : bond        0.04909 /  3.29 (  445)
  hydrogen bonds       : angle       5.49751 /  4.01 ( 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
  274 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  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: C    1 MET cc_start: 0.4644 (ttp) cc_final: 0.4408 (ttp)
REVERT: C   55 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7355 (ttm110)
REVERT: C   75 GLN cc_start: 0.7148 (mt0) cc_final: 0.6740 (mt0)
REVERT: D   32 GLU cc_start: 0.6703 (tt0) cc_final: 0.6399 (tt0)
REVERT: D   74 MET cc_start: 0.7270 (mmt) cc_final: 0.6971 (mmm)
REVERT: D  147 GLU cc_start: 0.7721 (tt0) cc_final: 0.7469 (tt0)
REVERT: D  157 CYS cc_start: 0.9008 (m) cc_final: 0.8654 (m)
REVERT: D  214 PHE cc_start: 0.8008 (t80) cc_final: 0.7330 (t80)
REVERT: D  228 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7737 (mttp)
REVERT: A   13 ASP cc_start: 0.8225 (p0) cc_final: 0.7685 (p0)
REVERT: A  161 ASP cc_start: 0.7500 (m-30) cc_final: 0.7224 (m-30)
REVERT: A  187 GLU cc_start: 0.8454 (tp30) cc_final: 0.8253 (tp30)
REVERT: A  244 LEU cc_start: 0.8975 (tp) cc_final: 0.8704 (tp)
REVERT: A  289 MET cc_start: 0.8772 (ttt) cc_final: 0.8346 (ttp)
REVERT: B   13 ASP cc_start: 0.8238 (p0) cc_final: 0.7280 (p0)
REVERT: B  162 ASP cc_start: 0.8239 (p0) cc_final: 0.7965 (p0)
REVERT: B  171 ARG cc_start: 0.8317 (ptp-110) cc_final: 0.7998 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8836 (p0) cc_final: 0.8165 (p0)
REVERT: B  264 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7315 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.2048
  time to fit residues: 78.1879
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  : 0.426 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   chunk 101 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.168733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.127350 restraints weight = 39687.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.132982 restraints weight = 16959.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.136641 restraints weight = 9061.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.138709 restraints weight = 5934.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.140320 restraints weight = 4534.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    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 = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2410

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= 0.160
  Angle     :  0.570   5.789  13309  Z= 0.306
  Chirality :  0.038   0.137   1443
  Planarity :  0.005   0.064   1599
  Dihedral  : 17.870  89.983   1610
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.80 (0.23), residues: 486
  sheet: -1.75 (0.42), residues: 138
  loop : -1.39 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 114 
 TYR   0.015   0.002   TYR C  72 
 PHE   0.013   0.001   PHE A  25 
 TRP   0.041   0.001   TRP A 100 
 HIS   0.009   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 ( 9703)
  covalent geometry    : angle       0.56995 /  0.31 (13309)
  hydrogen bonds       : bond        0.04421 /  2.96 (  445)
  hydrogen bonds       : angle       5.35260 /  3.90 ( 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  : 0.488 
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: 0.7681 (mtm180) cc_final: 0.7347 (ttm110)
REVERT: C   75 GLN cc_start: 0.7100 (mt0) cc_final: 0.6728 (mt0)
REVERT: D   32 GLU cc_start: 0.6625 (tt0) cc_final: 0.6360 (tt0)
REVERT: D   34 GLU cc_start: 0.7009 (tp30) cc_final: 0.6698 (tp30)
REVERT: D   74 MET cc_start: 0.7156 (mmt) cc_final: 0.6838 (mmm)
REVERT: D  147 GLU cc_start: 0.7643 (tt0) cc_final: 0.7435 (tt0)
REVERT: D  157 CYS cc_start: 0.9029 (m) cc_final: 0.8801 (m)
REVERT: D  214 PHE cc_start: 0.8025 (t80) cc_final: 0.7376 (t80)
REVERT: D  228 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7787 (mttp)
REVERT: A   13 ASP cc_start: 0.8191 (p0) cc_final: 0.7668 (p0)
REVERT: A  118 ARG cc_start: 0.7623 (mmt90) cc_final: 0.6795 (mmm160)
REVERT: A  196 ASP cc_start: 0.6766 (m-30) cc_final: 0.6548 (m-30)
REVERT: A  244 LEU cc_start: 0.9004 (tp) cc_final: 0.8755 (tp)
REVERT: A  289 MET cc_start: 0.8762 (ttt) cc_final: 0.8370 (ttp)
REVERT: B   13 ASP cc_start: 0.8163 (p0) cc_final: 0.7284 (p0)
REVERT: B  162 ASP cc_start: 0.8090 (p0) cc_final: 0.7845 (p0)
REVERT: B  171 ARG cc_start: 0.8373 (ptp-110) cc_final: 0.8051 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8753 (p0) cc_final: 0.8036 (p0)
REVERT: B  264 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7372 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.2060
  time to fit residues: 76.7984
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  : 0.458 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.7982

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.166008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.125211 restraints weight = 40261.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.130807 restraints weight = 16858.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.134421 restraints weight = 8925.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.136681 restraints weight = 5770.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.137918 restraints weight = 4388.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3346
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    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: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9703  Z= 0.151
  Angle     :  0.551   5.296  13309  Z= 0.296
  Chirality :  0.038   0.138   1443
  Planarity :  0.005   0.050   1599
  Dihedral  : 17.625  89.965   1610
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  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: -0.60 (0.26), residues: 1069
  helix:  0.91 (0.23), residues: 492
  sheet: -1.79 (0.42), residues: 140
  loop : -1.39 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 122 
 TYR   0.017   0.002   TYR D  72 
 PHE   0.014   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        0.00334 /  0.15 ( 9703)
  covalent geometry    : angle       0.55072 /  0.30 (13309)
  hydrogen bonds       : bond        0.04195 /  2.83 (  445)
  hydrogen bonds       : angle       5.25927 /  3.83 ( 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
  263 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   55 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7353 (ttm110)
REVERT: C   75 GLN cc_start: 0.7147 (mt0) cc_final: 0.6757 (mt0)
REVERT: D   32 GLU cc_start: 0.6643 (tt0) cc_final: 0.6378 (tt0)
REVERT: D  147 GLU cc_start: 0.7612 (tt0) cc_final: 0.7393 (tt0)
REVERT: D  157 CYS cc_start: 0.9001 (m) cc_final: 0.8769 (m)
REVERT: D  214 PHE cc_start: 0.8050 (t80) cc_final: 0.7419 (t80)
REVERT: A   13 ASP cc_start: 0.8200 (p0) cc_final: 0.7668 (p0)
REVERT: A   28 ARG cc_start: 0.8606 (ttt-90) cc_final: 0.8393 (ttt-90)
REVERT: A  244 LEU cc_start: 0.8991 (tp) cc_final: 0.8740 (tp)
REVERT: A  289 MET cc_start: 0.8717 (ttt) cc_final: 0.8318 (ttp)
REVERT: B   13 ASP cc_start: 0.8089 (p0) cc_final: 0.7258 (p0)
REVERT: B  162 ASP cc_start: 0.8099 (p0) cc_final: 0.7802 (p0)
REVERT: B  171 ARG cc_start: 0.8390 (ptp-110) cc_final: 0.8089 (ptp-110)
REVERT: B  232 ASP cc_start: 0.8782 (p0) cc_final: 0.8076 (p0)
REVERT: B  264 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7400 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.2084
  time to fit residues: 77.0752
Evaluate side-chains
  240 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0060
   chunk 77 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
B 272 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.166475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.125292 restraints weight = 40934.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.130918 restraints weight = 17070.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.134565 restraints weight = 9070.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.136851 restraints weight = 5851.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.138118 restraints weight = 4418.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    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 = 0.3350 r_free = 0.3350    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 (8 function evaluations)
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9703  Z= 0.134
  Angle     :  0.527   5.236  13309  Z= 0.283
  Chirality :  0.037   0.140   1443
  Planarity :  0.004   0.049   1599
  Dihedral  : 17.516  89.788   1610
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  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: -0.45 (0.26), residues: 1069
  helix:  1.06 (0.23), residues: 492
  sheet: -1.75 (0.42), residues: 140
  loop : -1.34 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 122 
 TYR   0.013   0.002   TYR A 238 
 PHE   0.014   0.001   PHE A  25 
 TRP   0.028   0.001   TRP A 100 
 HIS   0.010   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 9703)
  covalent geometry    : angle       0.52694 /  0.28 (13309)
  hydrogen bonds       : bond        0.03960 /  2.67 (  445)
  hydrogen bonds       : angle       5.11972 /  3.72 ( 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
  260 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.4704 (ttp) cc_final: 0.2727 (tmm)
REVERT: C   55 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7313 (ttm110)
REVERT: C   63 THR cc_start: 0.8514 (p) cc_final: 0.8279 (p)
REVERT: C   75 GLN cc_start: 0.7136 (mt0) cc_final: 0.6767 (mt0)
REVERT: D   32 GLU cc_start: 0.6610 (tt0) cc_final: 0.6362 (tt0)
REVERT: D   37 ARG cc_start: 0.6064 (tmt170) cc_final: 0.5842 (ttt-90)
REVERT: D  147 GLU cc_start: 0.7638 (tt0) cc_final: 0.7387 (tt0)
REVERT: D  214 PHE cc_start: 0.8039 (t80) cc_final: 0.7410 (t80)
REVERT: A   13 ASP cc_start: 0.8180 (p0) cc_final: 0.7645 (p0)
REVERT: A   77 LEU cc_start: 0.9159 (tp) cc_final: 0.8932 (tp)
REVERT: A  244 LEU cc_start: 0.8967 (tp) cc_final: 0.8747 (tp)
REVERT: A  289 MET cc_start: 0.8756 (ttt) cc_final: 0.8331 (ttp)
REVERT: A  291 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7232 (tp30)
REVERT: B   13 ASP cc_start: 0.7997 (p0) cc_final: 0.7155 (p0)
REVERT: B  162 ASP cc_start: 0.8063 (p0) cc_final: 0.7742 (p0)
REVERT: B  171 ARG cc_start: 0.8386 (ptp-110) cc_final: 0.8119 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8280 (t0) cc_final: 0.8019 (t0)
REVERT: B  232 ASP cc_start: 0.8782 (p0) cc_final: 0.8083 (p0)
REVERT: B  264 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7387 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1927
  time to fit residues: 70.8939
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  : 0.585 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.166009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.124746 restraints weight = 40691.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.130426 restraints weight = 16958.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.134034 restraints weight = 8981.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.136404 restraints weight = 5777.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.137397 restraints weight = 4356.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    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 = 0.3347 r_free = 0.3347    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 (10 function evaluations)
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9703  Z= 0.151
  Angle     :  0.543   7.308  13309  Z= 0.292
  Chirality :  0.038   0.146   1443
  Planarity :  0.005   0.082   1599
  Dihedral  : 17.456  89.813   1610
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.31 %
    Favored  : 98.59 %
  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: -0.48 (0.26), residues: 1069
  helix:  1.02 (0.23), residues: 492
  sheet: -1.77 (0.42), residues: 140
  loop : -1.32 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 156 
 TYR   0.014   0.002   TYR A 238 
 PHE   0.013   0.001   PHE A  25 
 TRP   0.048   0.001   TRP A 100 
 HIS   0.009   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 ( 9703)
  covalent geometry    : angle       0.54285 /  0.29 (13309)
  hydrogen bonds       : bond        0.03918 /  2.65 (  445)
  hydrogen bonds       : angle       5.13888 /  3.73 ( 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
  259 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 258
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   55 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7320 (ttm110)
REVERT: C   63 THR cc_start: 0.8514 (p) cc_final: 0.8285 (p)
REVERT: C   75 GLN cc_start: 0.7126 (mt0) cc_final: 0.6829 (mt0)
REVERT: D   32 GLU cc_start: 0.6686 (tt0) cc_final: 0.6399 (tt0)
REVERT: D  214 PHE cc_start: 0.8004 (t80) cc_final: 0.7390 (t80)
REVERT: A   13 ASP cc_start: 0.8166 (p0) cc_final: 0.7642 (p0)
REVERT: A   77 LEU cc_start: 0.9142 (tp) cc_final: 0.8895 (tp)
REVERT: A  244 LEU cc_start: 0.8989 (tp) cc_final: 0.8748 (tp)
REVERT: A  289 MET cc_start: 0.8807 (ttt) cc_final: 0.8424 (ttp)
REVERT: B   13 ASP cc_start: 0.8062 (p0) cc_final: 0.7269 (p0)
REVERT: B  162 ASP cc_start: 0.8070 (p0) cc_final: 0.7737 (p0)
REVERT: B  171 ARG cc_start: 0.8418 (ptp-110) cc_final: 0.8129 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8288 (t0) cc_final: 0.8024 (t0)
REVERT: B  232 ASP cc_start: 0.8784 (p0) cc_final: 0.8106 (p0)
REVERT: B  264 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7367 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 258
  average time/residue: 0.2013
  time to fit residues: 72.7935
Evaluate side-chains
  238 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  89 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.163415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.122655 restraints weight = 36661.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.127924 restraints weight = 15830.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.131366 restraints weight = 8657.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.133547 restraints weight = 5682.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.134730 restraints weight = 4366.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.123   9703  Z= 0.202
  Angle     :  0.568   5.115  13309  Z= 0.305
  Chirality :  0.039   0.138   1443
  Planarity :  0.005   0.077   1599
  Dihedral  : 17.477  89.825   1610
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.66 (0.25), residues: 1069
  helix:  0.85 (0.23), residues: 504
  sheet: -1.81 (0.42), residues: 137
  loop : -1.48 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 122 
 TYR   0.016   0.002   TYR A 238 
 PHE   0.014   0.001   PHE A  25 
 TRP   0.037   0.002   TRP A 100 
 HIS   0.009   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00465 /  0.20 ( 9703)
  covalent geometry    : angle       0.56836 /  0.30 (13309)
  hydrogen bonds       : bond        0.04048 /  2.72 (  445)
  hydrogen bonds       : angle       5.14916 /  3.75 ( 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
  263 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.3989 (ttp) cc_final: 0.2616 (tmm)
REVERT: C   34 GLU cc_start: 0.7714 (tp30) cc_final: 0.7432 (tp30)
REVERT: C   55 ARG cc_start: 0.7664 (mtm180) cc_final: 0.7333 (ttm110)
REVERT: C   75 GLN cc_start: 0.7199 (mt0) cc_final: 0.6874 (mt0)
REVERT: C  218 ASN cc_start: 0.7606 (m110) cc_final: 0.7389 (m110)
REVERT: D   32 GLU cc_start: 0.6712 (tt0) cc_final: 0.6419 (tt0)
REVERT: D  141 GLN cc_start: 0.7643 (mp10) cc_final: 0.7372 (mp10)
REVERT: D  214 PHE cc_start: 0.8041 (t80) cc_final: 0.7433 (t80)
REVERT: A   13 ASP cc_start: 0.8200 (p0) cc_final: 0.7678 (p0)
REVERT: A   77 LEU cc_start: 0.9166 (tp) cc_final: 0.8927 (tp)
REVERT: A  122 ARG cc_start: 0.7314 (mtt90) cc_final: 0.7088 (mtm110)
REVERT: A  291 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7325 (tp30)
REVERT: B   13 ASP cc_start: 0.8110 (p0) cc_final: 0.7290 (p0)
REVERT: B  162 ASP cc_start: 0.8125 (p0) cc_final: 0.7751 (p0)
REVERT: B  171 ARG cc_start: 0.8513 (ptp-110) cc_final: 0.8182 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8292 (t0) cc_final: 0.8061 (t0)
REVERT: B  232 ASP cc_start: 0.8844 (p0) cc_final: 0.8171 (p0)
REVERT: B  264 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7398 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.1972
  time to fit residues: 73.3541
Evaluate side-chains
  243 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 71 optimal weight:    0.4980
   chunk 87 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   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 = 0.165031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.124519 restraints weight = 37290.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.129831 restraints weight = 15971.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.133323 restraints weight = 8693.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.135500 restraints weight = 5687.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.136845 restraints weight = 4349.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9703  Z= 0.131
  Angle     :  0.533   5.243  13309  Z= 0.287
  Chirality :  0.038   0.139   1443
  Planarity :  0.005   0.072   1599
  Dihedral  : 17.447  88.804   1610
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.33 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.26), residues: 1069
  helix:  1.04 (0.23), residues: 498
  sheet: -1.74 (0.43), residues: 137
  loop : -1.33 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 122 
 TYR   0.013   0.002   TYR A 238 
 PHE   0.016   0.001   PHE A  25 
 TRP   0.043   0.002   TRP A 100 
 HIS   0.008   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 9703)
  covalent geometry    : angle       0.53318 /  0.29 (13309)
  hydrogen bonds       : bond        0.03867 /  2.60 (  445)
  hydrogen bonds       : angle       5.08553 /  3.70 ( 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
  258 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 257
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.3938 (ttp) cc_final: 0.2636 (tmm)
REVERT: C   55 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7294 (ttm110)
REVERT: C   63 THR cc_start: 0.8375 (p) cc_final: 0.8131 (p)
REVERT: D   89 ARG cc_start: 0.7329 (mmm160) cc_final: 0.7073 (mmm-85)
REVERT: D  141 GLN cc_start: 0.7580 (mp10) cc_final: 0.7331 (mp10)
REVERT: D  214 PHE cc_start: 0.8040 (t80) cc_final: 0.7439 (t80)
REVERT: D  222 LYS cc_start: 0.6789 (tptt) cc_final: 0.6355 (tttp)
REVERT: A   13 ASP cc_start: 0.8151 (p0) cc_final: 0.7630 (p0)
REVERT: A   77 LEU cc_start: 0.9139 (tp) cc_final: 0.8909 (tp)
REVERT: A  291 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7316 (tp30)
REVERT: B   13 ASP cc_start: 0.8119 (p0) cc_final: 0.7359 (p0)
REVERT: B  162 ASP cc_start: 0.8136 (p0) cc_final: 0.7765 (p0)
REVERT: B  171 ARG cc_start: 0.8490 (ptp-110) cc_final: 0.8170 (ptp-110)
REVERT: B  197 ASP cc_start: 0.8232 (t0) cc_final: 0.7998 (t0)
REVERT: B  232 ASP cc_start: 0.8801 (p0) cc_final: 0.8147 (p0)
REVERT: B  264 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7390 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 258
  average time/residue: 0.2045
  time to fit residues: 74.3150
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  : 0.480 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 25 optimal weight:    0.4980
   chunk 12 optimal weight:    0.5980
   chunk 68 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 = 0.3655 r_free = 0.3655 target = 0.164903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.124232 restraints weight = 36411.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.129512 restraints weight = 15725.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.132923 restraints weight = 8564.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.135080 restraints weight = 5640.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.136355 restraints weight = 4347.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    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 = 0.3328 r_free = 0.3328    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: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9703  Z= 0.133
  Angle     :  0.537   4.817  13309  Z= 0.290
  Chirality :  0.038   0.137   1443
  Planarity :  0.005   0.069   1599
  Dihedral  : 17.425  88.301   1610
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  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: -0.38 (0.26), residues: 1069
  helix:  1.10 (0.23), residues: 498
  sheet: -1.73 (0.43), residues: 137
  loop : -1.31 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 122 
 TYR   0.014   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 B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 9703)
  covalent geometry    : angle       0.53675 /  0.29 (13309)
  hydrogen bonds       : bond        0.03822 /  2.58 (  445)
  hydrogen bonds       : angle       5.05054 /  3.67 ( 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
  256 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 255
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.3990 (ttp) cc_final: 0.2806 (tmm)
REVERT: C   55 ARG cc_start: 0.7601 (mtm180) cc_final: 0.7251 (ttm110)
REVERT: C   63 THR cc_start: 0.8433 (p) cc_final: 0.8144 (p)
REVERT: C   75 GLN cc_start: 0.7112 (mt0) cc_final: 0.6577 (mt0)
REVERT: D   32 GLU cc_start: 0.6645 (tt0) cc_final: 0.6431 (tt0)
REVERT: D   89 ARG cc_start: 0.7326 (mmm160) cc_final: 0.7081 (mmm-85)
REVERT: D  141 GLN cc_start: 0.7570 (mp10) cc_final: 0.7280 (mp10)
REVERT: D  214 PHE cc_start: 0.8037 (t80) cc_final: 0.7445 (t80)
REVERT: D  222 LYS cc_start: 0.6656 (tptt) cc_final: 0.6341 (tttp)
REVERT: A   13 ASP cc_start: 0.8138 (p0) cc_final: 0.7615 (p0)
REVERT: A   38 GLU cc_start: 0.8600 (tp30) cc_final: 0.8368 (tp30)
REVERT: A   77 LEU cc_start: 0.9136 (tp) cc_final: 0.8923 (tp)
REVERT: A  235 GLU cc_start: 0.8103 (tt0) cc_final: 0.7789 (tt0)
REVERT: A  291 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7302 (tp30)
REVERT: B   13 ASP cc_start: 0.8121 (p0) cc_final: 0.7370 (p0)
REVERT: B  162 ASP cc_start: 0.8107 (p0) cc_final: 0.7765 (p0)
REVERT: B  171 ARG cc_start: 0.8496 (ptp-110) cc_final: 0.8214 (ptp-110)
REVERT: B  191 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7869 (tpp80)
REVERT: B  197 ASP cc_start: 0.8112 (t0) cc_final: 0.7892 (t0)
REVERT: B  232 ASP cc_start: 0.8791 (p0) cc_final: 0.8107 (p0)
REVERT: B  264 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7257 (tt0)
REVERT: B  269 TRP cc_start: 0.7937 (m-10) cc_final: 0.7714 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 256
  average time/residue: 0.2086
  time to fit residues: 74.2843
Evaluate side-chains
  239 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0570
   chunk 89 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.4076

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.166141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.124421 restraints weight = 43072.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.130147 restraints weight = 17758.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.133816 restraints weight = 9357.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.136155 restraints weight = 6019.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.137584 restraints weight = 4529.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3346
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    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 = 0.3346 r_free = 0.3346    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: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9703  Z= 0.116
  Angle     :  0.526   5.398  13309  Z= 0.283
  Chirality :  0.037   0.140   1443
  Planarity :  0.005   0.067   1599
  Dihedral  : 17.406  86.832   1610
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  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: -0.23 (0.26), residues: 1069
  helix:  1.22 (0.24), residues: 498
  sheet: -1.65 (0.43), residues: 137
  loop : -1.24 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  55 
 TYR   0.013   0.001   TYR A 238 
 PHE   0.015   0.001   PHE A  25 
 TRP   0.040   0.002   TRP A 100 
 HIS   0.019   0.001   HIS B 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 ( 9703)
  covalent geometry    : angle       0.52596 /  0.28 (13309)
  hydrogen bonds       : bond        0.03739 /  2.54 (  445)
  hydrogen bonds       : angle       5.00479 /  3.64 ( 1255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3438.82 seconds
wall clock time: 59 minutes 38.07 seconds (3578.07 seconds total)