Starting phenix.real_space_refine
on Fri Feb 14 11:58:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kei_37159/02_2025/8kei_37159.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kei_37159/02_2025/8kei_37159.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kei_37159/02_2025/8kei_37159.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kei_37159/02_2025/8kei_37159.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kei_37159/02_2025/8kei_37159.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kei_37159/02_2025/8kei_37159.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       2      5.49       5
     S      49      5.16       5
     C    6606      2.51       5
     N    1689      2.21       5
     O    1861      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10209
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1035
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 4, 'TRANS': 128}
    Chain: "B"
      Number of atoms: 4318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 534, 4318
          Classifications: {'peptide': 534}
          Link IDs: {'PTRANS': 22, 'TRANS': 511}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1648
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 12, 'TRANS': 211}
    Chain: "D"
      Number of atoms: 1304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1304
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 2, 'TRANS': 161}
    Chain: "E"
      Number of atoms: 1652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1652
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 10, 'TRANS': 206}
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 148
          Unusual residues: {'HEM': 2, 'LBN': 1, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.73, per 1000 atoms: 0.76
  Number of scatterers: 10209
  At special positions: 0
  Unit cell: (73.1, 102.85, 204, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      2     26.01
     S      49     16.00
     P       2     15.00
     O    1861      8.00
     N    1689      7.00
     C    6606      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 244 " - pdb=" SG  CYS B 257 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  51 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 149 " - pdb=" SG  CYS C 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 138 " - pdb=" SG  CYS E 198 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG B 603 " - " ASN B 132 "
      " NAG F   1 " - " ASN B 240 "
      " NAG G   1 " - " ASN B 149 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.75
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 18 sheets defined
      34.4% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 36 through 53
      removed outlier: 3.687A  pdb=" N   GLU A  53 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 78
      removed outlier: 3.533A  pdb=" N   THR A  74 " --> pdb=" O   GLN A  70 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   VAL A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A  78 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 98
      removed outlier: 3.537A  pdb=" N   SER A  98 " --> pdb=" O   HIS A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 103
      removed outlier: 4.144A  pdb=" N   PHE A 103 " --> pdb=" O   PRO A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 128
      removed outlier: 4.065A  pdb=" N   ALA A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 35
    Processing helix  chain 'B' and resid 36 through 39
      removed outlier: 3.543A  pdb=" N   PHE B  39 " --> pdb=" O   PRO B  36 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 36 through 39'
    Processing helix  chain 'B' and resid 40 through 47
    Processing helix  chain 'B' and resid 48 through 81
      removed outlier: 3.691A  pdb=" N   LEU B  52 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
      Proline residue:  B  56  - end of helix
      removed outlier: 3.707A  pdb=" N   PHE B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      Proline residue:  B  70  - end of helix
    Processing helix  chain 'B' and resid 96 through 131
      removed outlier: 3.667A  pdb=" N   GLU B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TRP B 125 " --> pdb=" O   PHE B 121 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG B 130 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   VAL B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 143
    Processing helix  chain 'B' and resid 164 through 173
    Processing helix  chain 'B' and resid 176 through 193
    Processing helix  chain 'B' and resid 207 through 210
    Processing helix  chain 'B' and resid 211 through 223
      removed outlier: 3.672A  pdb=" N   GLY B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 240
      removed outlier: 3.830A  pdb=" N   ALA B 237 " --> pdb=" O   ALA B 233 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 4.113A  pdb=" N   TRP B 251 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 291
    Processing helix  chain 'B' and resid 361 through 366
    Processing helix  chain 'B' and resid 413 through 430
      removed outlier: 3.755A  pdb=" N   ALA B 417 " --> pdb=" O   VAL B 413 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   SER B 418 " --> pdb=" O   THR B 414 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE B 419 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TRP B 424 " --> pdb=" O   LEU B 420 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   TYR B 425 " --> pdb=" O   LYS B 421 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS B 426 " --> pdb=" O   SER B 422 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TYR B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 463
      removed outlier: 3.729A  pdb=" N   ALA B 455 " --> pdb=" O   PHE B 451 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU B 457 " --> pdb=" O   TRP B 453 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN B 459 " --> pdb=" O   ALA B 455 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   SER B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 469
      removed outlier: 3.567A  pdb=" N   ARG B 468 " --> pdb=" O   MET B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 525
      removed outlier: 3.668A  pdb=" N   THR B 522 " --> pdb=" O   ASN B 518 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE B 523 " --> pdb=" O   GLU B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 554
      removed outlier: 3.927A  pdb=" N   SER B 547 " --> pdb=" O   ALA B 543 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   GLN B 549 " --> pdb=" O   THR B 545 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER B 550 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE B 551 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   SER B 552 " --> pdb=" O   LYS B 548 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 66
      removed outlier: 3.695A  pdb=" N   LYS C  66 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 200
      removed outlier: 3.526A  pdb=" N   GLY C 199 " --> pdb=" O   SER C 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 40
      removed outlier: 3.566A  pdb=" N   TRP D  24 " --> pdb=" O   GLY D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 62
      removed outlier: 3.895A  pdb=" N   PHE D  50 " --> pdb=" O   GLY D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 91
    Processing helix  chain 'D' and resid 92 through 94
      No H-bonds generated for 'chain 'D' and resid 92 through 94'
    Processing helix  chain 'D' and resid 146 through 162
    Processing helix  chain 'E' and resid 125 through 131
    Processing helix  chain 'E' and resid 186 through 191
      removed outlier: 4.679A  pdb=" N   GLU E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 229 through 231
    Processing sheet with id=AA2, first strand: chain 'B' and resid 296 through 301
      removed outlier: 5.731A  pdb=" N   ILE B 297 " --> pdb=" O   LYS B 313 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LYS B 313 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU B 310 " --> pdb=" O   ILE B 353 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 387
      removed outlier: 5.984A  pdb=" N   TRP B 337 " --> pdb=" O   VAL D 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 404 through 407
      removed outlier: 3.910A  pdb=" N   VAL B 407 " --> pdb=" O   PHE B 535 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ILE B 532 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 443 through 445
      removed outlier: 6.123A  pdb=" N   TRP B 443 " --> pdb=" O   TYR B 479 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 53
      removed outlier: 7.359A  pdb=" N   TRP C  37 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   CYS C  51 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   MET C  35 " --> pdb=" O   CYS C  51 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG C  98 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 144 through 151
    Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 151
    Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 163
      removed outlier: 3.787A  pdb=" N   THR C 160 " --> pdb=" O   ASN C 208 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASN C 206 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 5
    Processing sheet with id=AB3, first strand: chain 'D' and resid 107 through 116
      removed outlier: 3.829A  pdb=" N   ASP D 109 " --> pdb=" O   ARG D 129 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET D 125 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 116
      removed outlier: 3.829A  pdb=" N   ASP D 109 " --> pdb=" O   ARG D 129 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET D 125 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 5 through 7
      removed outlier: 3.638A  pdb=" N   VAL E  20 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 15
      removed outlier: 6.690A  pdb=" N   ALA E  14 " --> pdb=" O   LYS E 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'E' and resid 46 through 50
      removed outlier: 6.679A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   TYR E  50 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 118 through 122
      removed outlier: 6.181A  pdb=" N   TYR E 177 " --> pdb=" O   ASN E 142 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 157 through 158
      removed outlier: 3.663A  pdb=" N   PHE E 213 " --> pdb=" O   TYR E 196 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1134 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 3.10 seconds

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

  Histogram of bond lengths:
        1.20 -     1.37: 3238
        1.37 -     1.54: 6988
        1.54 -     1.71: 171
        1.71 -     1.88: 67
        1.88 -     2.05: 8
  Bond restraints: 10472
  Sorted by residual:
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.623 -0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" CA  VAL B 413 "
       pdb=" C   VAL B 413 "
    ideal  model  delta    sigma   weight residual
    1.523  1.461  0.061 1.31e-02 5.83e+03 2.19e+01
  bond pdb=" CA  THR B 414 "
       pdb=" C   THR B 414 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.052 1.26e-02 6.30e+03 1.72e+01
  bond pdb=" CA  ILE B 411 "
       pdb=" C   ILE B 411 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 1.26e-02 6.30e+03 1.48e+01
  bond pdb=" CA  ARG B 287 "
       pdb=" C   ARG B 287 "
    ideal  model  delta    sigma   weight residual
    1.523  1.470  0.053 1.37e-02 5.33e+03 1.48e+01
  ... (remaining 10467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 13913
        2.09 -     4.18: 241
        4.18 -     6.27: 57
        6.27 -     8.36: 16
        8.36 -    10.45: 7
  Bond angle restraints: 14234
  Sorted by residual:
  angle pdb=" N   VAL B 413 "
        pdb=" CA  VAL B 413 "
        pdb=" C   VAL B 413 "
      ideal   model   delta    sigma   weight residual
     112.17  105.08    7.09 9.50e-01 1.11e+00 5.57e+01
  angle pdb=" C   THR B 414 "
        pdb=" N   PRO B 415 "
        pdb=" CA  PRO B 415 "
      ideal   model   delta    sigma   weight residual
     119.56  113.36    6.20 1.01e+00 9.80e-01 3.76e+01
  angle pdb=" C   GLY B 275 "
        pdb=" N   PRO B 276 "
        pdb=" CA  PRO B 276 "
      ideal   model   delta    sigma   weight residual
     119.05  112.50    6.55 1.11e+00 8.12e-01 3.48e+01
  angle pdb=" N   SER B 291 "
        pdb=" CA  SER B 291 "
        pdb=" C   SER B 291 "
      ideal   model   delta    sigma   weight residual
     112.59  119.49   -6.90 1.22e+00 6.72e-01 3.20e+01
  angle pdb=" C   VAL B 286 "
        pdb=" CA  VAL B 286 "
        pdb=" CB  VAL B 286 "
      ideal   model   delta    sigma   weight residual
     112.16  104.02    8.14 1.55e+00 4.16e-01 2.76e+01
  ... (remaining 14229 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.23: 5879
       32.23 -    64.46: 285
       64.46 -    96.69: 32
       96.69 -   128.92: 7
      128.92 -   161.15: 1
  Dihedral angle restraints: 6204
    sinusoidal: 2533
      harmonic: 3671
  Sorted by residual:
  dihedral pdb=" CA  MET C  35 "
           pdb=" C   MET C  35 "
           pdb=" N   CYS C  36 "
           pdb=" CA  CYS C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.77  -24.23     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" O5  LBN B 604 "
           pdb=" C2  LBN B 604 "
           pdb=" C3  LBN B 604 "
           pdb=" O7  LBN B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67  -98.48  161.15     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" CA  ASP B  95 "
           pdb=" C   ASP B  95 "
           pdb=" N   ARG B  96 "
           pdb=" CA  ARG B  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.38   21.62     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 6201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1512
       0.090 -    0.180: 80
       0.180 -    0.270: 3
       0.270 -    0.361: 2
       0.361 -    0.451: 1
  Chirality restraints: 1598
  Sorted by residual:
  chirality pdb=" C1  NAG B 603 "
            pdb=" ND2 ASN B 132 "
            pdb=" C2  NAG B 603 "
            pdb=" O5  NAG B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.95   -0.45 2.00e-01 2.50e+01 5.08e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 240 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN B 149 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 1595 not shown)

  Planarity restraints: 1749
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 527 "   -0.069 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO B 528 "    0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO B 528 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 528 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 272 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   TRP B 272 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   TRP B 272 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 273 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  96 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   ARG B  96 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ARG B  96 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN B  97 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1746 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 328
        2.70 -     3.25: 9871
        3.25 -     3.80: 15524
        3.80 -     4.35: 18558
        4.35 -     4.90: 32103
  Nonbonded interactions: 76384
  Sorted by model distance:
  nonbonded pdb=" O   ARG B 559 "
            pdb=" NH1 ARG B 559 "
     model   vdw
     2.150 3.120
  nonbonded pdb=" O3  NAG G   2 "
            pdb=" O2  BMA G   3 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OE1 GLU A  53 "
            pdb=" OH  TYR A 121 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OH  TYR D   2 "
            pdb=" OG1 THR D 139 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OE2 GLU C   6 "
            pdb=" OG1 THR C 116 "
     model   vdw
     2.224 3.040
  ... (remaining 76379 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 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.320
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     26.310
  Find NCS groups from input model:        0.130
  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:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104  10472  Z= 0.279
  Angle     :  0.727  10.455  14234  Z= 0.380
  Chirality :  0.045   0.451   1598
  Planarity :  0.004   0.102   1746
  Dihedral  : 18.448 161.154   3834
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 32.96 %
    Favored  : 66.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.25), residues: 1258
  helix:  1.41 (0.28), residues: 386
  sheet:  0.19 (0.35), residues: 265
  loop : -1.48 (0.26), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  37 
 HIS   0.009   0.001   HIS B 119 
 PHE   0.019   0.001   PHE B 520 
 TYR   0.012   0.001   TYR A 121 
 ARG   0.019   0.001   ARG B  96 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
REVERT: B  465 MET cc_start: 0.7743 (ptm) cc_final: 0.7513 (ttp)
  outliers start: 5
  outliers final: 4
  residues processed: 140
  average time/residue: 0.2170
  time to fit residues: 43.9187
Evaluate side-chains
  131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain C residue   56 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0270
   overall best weight:    1.4044

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
B 338 HIS
B 477 ASN
B 518 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.139281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111476 restraints weight = 17178.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.111771 restraints weight = 12874.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.112727 restraints weight = 12916.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10472  Z= 0.294
  Angle     :  0.654   8.335  14234  Z= 0.323
  Chirality :  0.043   0.374   1598
  Planarity :  0.004   0.067   1746
  Dihedral  : 10.405 150.149   1599
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 30.28 %
    Favored  : 65.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.25), residues: 1258
  helix:  1.32 (0.28), residues: 389
  sheet: -0.01 (0.34), residues: 277
  loop : -1.33 (0.27), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  37 
 HIS   0.008   0.001   HIS B 119 
 PHE   0.018   0.001   PHE B  62 
 TYR   0.012   0.001   TYR E 144 
 ARG   0.004   0.000   ARG B 559 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 142
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  465 MET cc_start: 0.7501 (ptm) cc_final: 0.7289 (ttp)
REVERT: D  122 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8137 (ttpp)
REVERT: E  102 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7411 (t80)
  outliers start: 50
  outliers final: 32
  residues processed: 186
  average time/residue: 0.1991
  time to fit residues: 54.0520
Evaluate side-chains
  166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  154 VAL
Chi-restraints excluded: chain E residue  180 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0040
   chunk 50 optimal weight:    0.7980
   chunk 79 optimal weight:    8.9990
   chunk 98 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 GLN
C 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.140767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.113513 restraints weight = 17266.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112957 restraints weight = 12457.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.114345 restraints weight = 10767.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10472  Z= 0.192
  Angle     :  0.597   8.552  14234  Z= 0.292
  Chirality :  0.042   0.324   1598
  Planarity :  0.004   0.063   1746
  Dihedral  :  9.046 144.431   1597
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 29.44 %
    Favored  : 65.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1258
  helix:  1.48 (0.28), residues: 388
  sheet:  0.01 (0.34), residues: 274
  loop : -1.33 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 163 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.012   0.001   PHE B 570 
 TYR   0.014   0.001   TYR D  86 
 ARG   0.004   0.000   ARG D 129 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 138
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 LEU cc_start: 0.8483 (tt) cc_final: 0.8140 (tt)
REVERT: B  465 MET cc_start: 0.7590 (ptm) cc_final: 0.7366 (ttp)
REVERT: D  122 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8114 (ttpp)
REVERT: E  102 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7456 (t80)
  outliers start: 54
  outliers final: 32
  residues processed: 182
  average time/residue: 0.1924
  time to fit residues: 51.7634
Evaluate side-chains
  164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   94 HIS
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  154 VAL
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0670
   chunk 85 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 114 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.7122

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.146418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.119367 restraints weight = 16897.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.119111 restraints weight = 13735.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120470 restraints weight = 13868.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10472  Z= 0.199
  Angle     :  0.588   8.022  14234  Z= 0.287
  Chirality :  0.041   0.306   1598
  Planarity :  0.004   0.061   1746
  Dihedral  :  8.481 140.266   1596
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 29.35 %
    Favored  : 65.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.25), residues: 1258
  helix:  1.54 (0.28), residues: 389
  sheet: -0.00 (0.34), residues: 274
  loop : -1.32 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 163 
 HIS   0.005   0.001   HIS B 119 
 PHE   0.011   0.001   PHE B  62 
 TYR   0.011   0.001   TYR B 427 
 ARG   0.003   0.000   ARG D 129 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 137
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8128 (tt)
REVERT: B  465 MET cc_start: 0.7614 (ptm) cc_final: 0.7375 (ttp)
REVERT: D  114 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7753 (mm-30)
REVERT: D  122 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8143 (ttpp)
REVERT: E  102 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7446 (t80)
REVERT: E  128 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6516 (tp-100)
  outliers start: 61
  outliers final: 45
  residues processed: 186
  average time/residue: 0.2057
  time to fit residues: 56.7015
Evaluate side-chains
  183 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 134
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   94 HIS
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 ASN
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  154 VAL
Chi-restraints excluded: chain E residue  196 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 115 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.146976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.118787 restraints weight = 16792.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.118278 restraints weight = 12314.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.119530 restraints weight = 12195.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10472  Z= 0.238
  Angle     :  0.602   9.232  14234  Z= 0.294
  Chirality :  0.041   0.290   1598
  Planarity :  0.004   0.068   1746
  Dihedral  :  8.262 135.558   1596
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 29.35 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1258
  helix:  1.48 (0.27), residues: 395
  sheet: -0.06 (0.34), residues: 276
  loop : -1.33 (0.27), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 163 
 HIS   0.008   0.001   HIS B 119 
 PHE   0.014   0.001   PHE B  62 
 TYR   0.016   0.001   TYR D  86 
 ARG   0.004   0.000   ARG D 129 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 137
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8554 (mt0)
REVERT: B   60 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8087 (tt)
REVERT: B  161 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7066 (ttpp)
REVERT: D  122 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8115 (ttpp)
REVERT: E    3 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7616 (tt)
REVERT: E  102 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.7425 (t80)
REVERT: E  128 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6655 (tp-100)
  outliers start: 68
  outliers final: 48
  residues processed: 192
  average time/residue: 0.2111
  time to fit residues: 58.5236
Evaluate side-chains
  191 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 136
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 ASN
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 119 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.148028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.119791 restraints weight = 16939.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.119741 restraints weight = 11412.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121079 restraints weight = 11641.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10472  Z= 0.202
  Angle     :  0.601   8.440  14234  Z= 0.292
  Chirality :  0.041   0.278   1598
  Planarity :  0.004   0.066   1746
  Dihedral  :  8.100 132.021   1596
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 29.72 %
    Favored  : 63.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.25), residues: 1258
  helix:  1.52 (0.27), residues: 398
  sheet: -0.02 (0.34), residues: 274
  loop : -1.33 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 163 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.037   0.001   PHE C 131 
 TYR   0.014   0.001   TYR B 427 
 ARG   0.005   0.000   ARG D 129 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 135
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8548 (mt0)
REVERT: B   60 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8080 (tt)
REVERT: B  161 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7017 (ttpp)
REVERT: D  114 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7921 (mm-30)
REVERT: D  122 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8123 (ttpp)
REVERT: E    3 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7613 (tt)
REVERT: E  102 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.7421 (t80)
  outliers start: 68
  outliers final: 49
  residues processed: 191
  average time/residue: 0.1985
  time to fit residues: 55.1790
Evaluate side-chains
  183 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 128
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  358 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  150 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0980
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.148995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121122 restraints weight = 17117.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.120883 restraints weight = 11380.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.122192 restraints weight = 11055.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10472  Z= 0.182
  Angle     :  0.594   8.810  14234  Z= 0.286
  Chirality :  0.040   0.265   1598
  Planarity :  0.004   0.069   1746
  Dihedral  :  7.903 127.761   1596
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 30.19 %
    Favored  : 63.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.25), residues: 1258
  helix:  1.58 (0.28), residues: 400
  sheet: -0.09 (0.33), residues: 281
  loop : -1.32 (0.27), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 163 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.028   0.001   PHE C 131 
 TYR   0.018   0.001   TYR D  86 
 ARG   0.005   0.000   ARG D 129 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 137
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8560 (mt0)
REVERT: B   60 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8053 (tt)
REVERT: B  161 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7020 (ttpp)
REVERT: B  268 MET cc_start: 0.8750 (ppp) cc_final: 0.8450 (ppp)
REVERT: C  157 GLU cc_start: 0.8468 (mp0) cc_final: 0.8044 (mp0)
REVERT: D  151 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8029 (mm-30)
REVERT: E    3 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7591 (tt)
REVERT: E  102 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.7477 (t80)
  outliers start: 64
  outliers final: 48
  residues processed: 194
  average time/residue: 0.1917
  time to fit residues: 54.9900
Evaluate side-chains
  186 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 133
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   94 HIS
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 123 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0170
   chunk 83 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.9022

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.147223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.118732 restraints weight = 17088.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.118724 restraints weight = 11149.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.119807 restraints weight = 11586.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10472  Z= 0.224
  Angle     :  0.616   9.915  14234  Z= 0.297
  Chirality :  0.041   0.262   1598
  Planarity :  0.004   0.069   1746
  Dihedral  :  7.866 124.208   1596
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 29.91 %
    Favored  : 64.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1258
  helix:  1.56 (0.27), residues: 400
  sheet: -0.06 (0.33), residues: 286
  loop : -1.36 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 163 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.028   0.001   PHE C 131 
 TYR   0.015   0.001   TYR B 427 
 ARG   0.007   0.000   ARG D 118 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 132
  time to evaluate  : 1.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8495 (mt0)
REVERT: B   60 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8115 (tt)
REVERT: B  161 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7106 (ttpp)
REVERT: B  268 MET cc_start: 0.8779 (ppp) cc_final: 0.8497 (ppp)
REVERT: E    3 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7583 (tt)
REVERT: E  102 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.7469 (t80)
  outliers start: 64
  outliers final: 53
  residues processed: 186
  average time/residue: 0.1938
  time to fit residues: 52.8841
Evaluate side-chains
  189 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 131
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  150 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 87 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.148566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.120912 restraints weight = 16901.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.122083 restraints weight = 11927.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.122603 restraints weight = 10448.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10472  Z= 0.298
  Angle     :  0.673  10.954  14234  Z= 0.325
  Chirality :  0.042   0.263   1598
  Planarity :  0.005   0.091   1746
  Dihedral  :  7.981 120.591   1596
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 30.37 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1258
  helix:  1.54 (0.28), residues: 392
  sheet: -0.09 (0.33), residues: 283
  loop : -1.36 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 163 
 HIS   0.009   0.001   HIS B 119 
 PHE   0.026   0.001   PHE C 131 
 TYR   0.021   0.001   TYR D  86 
 ARG   0.007   0.000   ARG E  17 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 132
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8492 (mt0)
REVERT: B   60 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8144 (tt)
REVERT: B  161 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7170 (ttpp)
REVERT: E    3 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7668 (tt)
REVERT: E  102 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.7471 (t80)
  outliers start: 60
  outliers final: 52
  residues processed: 184
  average time/residue: 0.1947
  time to fit residues: 52.6706
Evaluate side-chains
  186 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 129
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  358 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 85 optimal weight:    0.3980
   chunk 61 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0770
   chunk 117 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 90 optimal weight:    0.2980
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.150383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.123315 restraints weight = 16766.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123115 restraints weight = 10690.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.124503 restraints weight = 8915.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10472  Z= 0.232
  Angle     :  0.649  11.828  14234  Z= 0.312
  Chirality :  0.041   0.260   1598
  Planarity :  0.004   0.076   1746
  Dihedral  :  7.871 116.745   1596
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 30.56 %
    Favored  : 63.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.25), residues: 1258
  helix:  1.55 (0.28), residues: 393
  sheet: -0.20 (0.33), residues: 282
  loop : -1.35 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 163 
 HIS   0.009   0.001   HIS B 119 
 PHE   0.025   0.001   PHE C 131 
 TYR   0.015   0.001   TYR B 427 
 ARG   0.006   0.000   ARG D 118 

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 132
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8542 (mt0)
REVERT: B   60 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: B  161 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7107 (ttpp)
REVERT: B  268 MET cc_start: 0.8777 (ppp) cc_final: 0.6786 (ppp)
REVERT: E    3 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7650 (tt)
REVERT: E  102 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.7487 (t80)
  outliers start: 60
  outliers final: 53
  residues processed: 183
  average time/residue: 0.2043
  time to fit residues: 54.6350
Evaluate side-chains
  188 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 130
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  358 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 110 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 111 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0370
   chunk 41 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.148934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.120806 restraints weight = 16923.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.120679 restraints weight = 11589.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.121889 restraints weight = 12000.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10472  Z= 0.179
  Angle     :  0.634  11.638  14234  Z= 0.306
  Chirality :  0.041   0.251   1598
  Planarity :  0.004   0.073   1746
  Dihedral  :  7.648 109.079   1596
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 31.11 %
    Favored  : 63.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.25), residues: 1258
  helix:  1.57 (0.28), residues: 400
  sheet: -0.25 (0.33), residues: 282
  loop : -1.30 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 337 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.028   0.001   PHE C 131 
 TYR   0.019   0.001   TYR A 121 
 ARG   0.008   0.000   ARG B 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3097.38 seconds
wall clock time: 56 minutes 52.69 seconds (3412.69 seconds total)