Starting phenix.real_space_refine
on Tue Jul 29 01:29:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kam_22775/07_2025/7kam_22775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kam_22775/07_2025/7kam_22775.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kam_22775/07_2025/7kam_22775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kam_22775/07_2025/7kam_22775.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kam_22775/07_2025/7kam_22775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kam_22775/07_2025/7kam_22775.cif"
  }
  resolution = 3.8
  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=   0.005 sd=   0.059
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    7107      2.51       5
     N    1873      2.21       5
     O    1887      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10916
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3386
          Classifications: {'peptide': 452}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 22, 'TRANS': 429}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 70
    Chain: "C"
      Number of atoms: 440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 440
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 245
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 3678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3678
          Classifications: {'peptide': 476}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 31, 'TRANS': 444}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 71
    Chain: "E"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1359
          Classifications: {'peptide': 172}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 54
    Chain: "F"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1454
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 15, 'TRANS': 178}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 37
    Chain: "G"
      Number of atoms: 354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 354
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 145
          Unresolved non-hydrogen angles: 188
          Unresolved non-hydrogen dihedrals: 126
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 69
  Time building chain proxies: 11.67, per 1000 atoms: 1.07
  Number of scatterers: 10916
  At special positions: 0
  Unit cell: (107.16, 125.4, 139.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1887      8.00
     N    1873      7.00
     C    7107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.82
  Conformation dependent library (CDL) restraints added in 3.6 seconds
  

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2694

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      68.2% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 48
      removed outlier: 3.681A  pdb=" N   LEU A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE A  42 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE A  43 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 99
    Processing helix  chain 'A' and resid 107 through 136
    Processing helix  chain 'A' and resid 141 through 146
    Processing helix  chain 'A' and resid 148 through 173
      removed outlier: 3.711A  pdb=" N   LEU A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 160 " --> pdb=" O   GLN A 156 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLU A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LEU A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 185
      removed outlier: 3.685A  pdb=" N   ILE A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 198
      removed outlier: 3.879A  pdb=" N   ILE A 189 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   CYS A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 224
      removed outlier: 3.714A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 237
      removed outlier: 3.974A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ALA A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   TYR A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.732A  pdb=" N   LEU A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY A 262 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 312
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 340 through 346
    Processing helix  chain 'A' and resid 350 through 357
      removed outlier: 4.080A  pdb=" N   ASP A 357 " --> pdb=" O   GLU A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 383
      removed outlier: 3.663A  pdb=" N   THR A 361 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLU A 381 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL A 382 " --> pdb=" O   THR A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 398
      removed outlier: 3.925A  pdb=" N   LYS A 392 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 439
      removed outlier: 4.457A  pdb=" N   GLU A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      Proline residue:  A 418  - end of helix
      removed outlier: 4.015A  pdb=" N   ALA A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY A 439 " --> pdb=" O   SER A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 465
      removed outlier: 3.671A  pdb=" N   ILE A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 26
    Processing helix  chain 'C' and resid 30 through 67
      Proline residue:  C  61  - end of helix
    Processing helix  chain 'B' and resid 95 through 123
    Processing helix  chain 'D' and resid 14 through 28
      removed outlier: 3.541A  pdb=" N   PHE D  18 " --> pdb=" O   PHE D  14 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL D  26 " --> pdb=" O   LEU D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 35
      removed outlier: 3.985A  pdb=" N   LEU D  34 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 68
      removed outlier: 4.116A  pdb=" N   LEU D  68 " --> pdb=" O   LYS D  64 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 98
      removed outlier: 4.570A  pdb=" N   ILE D  78 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   ALA D  79 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 228
      removed outlier: 4.672A  pdb=" N   LEU D 217 " --> pdb=" O   LEU D 213 " (cutoff:3.500A)
      Proline residue:  D 218  - end of helix
    Processing helix  chain 'D' and resid 237 through 247
      removed outlier: 3.827A  pdb=" N   ARG D 246 " --> pdb=" O   GLY D 242 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLU D 247 " --> pdb=" O   ASN D 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 262
      removed outlier: 4.025A  pdb=" N   VAL D 258 " --> pdb=" O   GLY D 254 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ASN D 259 " --> pdb=" O   GLY D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 271
      removed outlier: 3.923A  pdb=" N   GLU D 269 " --> pdb=" O   GLU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 276
      removed outlier: 3.752A  pdb=" N   LYS D 275 " --> pdb=" O   SER D 272 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ALA D 276 " --> pdb=" O   GLY D 273 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 272 through 276'
    Processing helix  chain 'D' and resid 279 through 291
      removed outlier: 3.763A  pdb=" N   ASP D 291 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 306
      removed outlier: 4.070A  pdb=" N   VAL D 302 " --> pdb=" O   LYS D 298 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE D 306 " --> pdb=" O   VAL D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 324
    Processing helix  chain 'D' and resid 331 through 358
      removed outlier: 4.296A  pdb=" N   GLU D 335 " --> pdb=" O   VAL D 331 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER D 341 " --> pdb=" O   TYR D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 360 through 376
      removed outlier: 3.587A  pdb=" N   ARG D 368 " --> pdb=" O   ILE D 364 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 382 through 387
      removed outlier: 3.694A  pdb=" N   LEU D 385 " --> pdb=" O   SER D 382 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN D 386 " --> pdb=" O   PRO D 383 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU D 387 " --> pdb=" O   LEU D 384 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 382 through 387'
    Processing helix  chain 'D' and resid 391 through 399
      removed outlier: 3.516A  pdb=" N   GLU D 399 " --> pdb=" O   VAL D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 414
    Processing helix  chain 'D' and resid 418 through 424
    Processing helix  chain 'D' and resid 431 through 443
      removed outlier: 3.988A  pdb=" N   SER D 437 " --> pdb=" O   ASP D 433 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 37
      Proline residue:  E   9  - end of helix
      removed outlier: 3.648A  pdb=" N   LEU E  26 " --> pdb=" O   THR E  22 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 60
    Processing helix  chain 'E' and resid 71 through 106
      removed outlier: 4.503A  pdb=" N   GLN E  97 " --> pdb=" O   ARG E  93 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLN E 104 " --> pdb=" O   ALA E 100 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ARG E 105 " --> pdb=" O   LEU E 101 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY E 106 " --> pdb=" O   LEU E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 138
      removed outlier: 4.149A  pdb=" N   TRP E 113 " --> pdb=" O   GLY E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 167
    Processing helix  chain 'E' and resid 168 through 180
    Processing helix  chain 'F' and resid 31 through 56
      removed outlier: 3.858A  pdb=" N   ASP F  56 " --> pdb=" O   LEU F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 68 through 89
      removed outlier: 4.384A  pdb=" N   SER F  72 " --> pdb=" O   ASN F  68 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY F  89 " --> pdb=" O   ALA F  85 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 107
      removed outlier: 3.501A  pdb=" N   GLY F 107 " --> pdb=" O   GLU F 103 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 113 through 134
      removed outlier: 4.268A  pdb=" N   ALA F 117 " --> pdb=" O   PRO F 113 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 137 through 152
    Processing helix  chain 'F' and resid 156 through 171
    Processing helix  chain 'F' and resid 172 through 187
    Processing helix  chain 'F' and resid 192 through 203
    Processing helix  chain 'G' and resid 245 through 266
      removed outlier: 3.711A  pdb=" N   LEU G 266 " --> pdb=" O   PHE G 262 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 267 through 270
    Processing helix  chain 'G' and resid 274 through 305
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20
      removed outlier: 7.047A  pdb=" N   GLU A  19 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211
      removed outlier: 3.781A  pdb=" N   GLU A 210 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER D 187 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
      removed outlier: 3.792A  pdb=" N   VAL A 325 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 452 through 457
      removed outlier: 3.651A  pdb=" N   LYS D 452 " --> pdb=" O   LYS D 474 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL D 472 " --> pdb=" O   PHE D 454 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 560
      removed outlier: 3.617A  pdb=" N   VAL D 560 " --> pdb=" O   LEU D 550 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   LEU D 550 " --> pdb=" O   VAL D 560 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE D 549 " --> pdb=" O   HIS D 604 " (cutoff:3.500A)

    712 hydrogen bonds defined for protein.
    2124 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: 3.54

  Time building geometry restraints manager: 5.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3459
        1.34 -     1.46: 1604
        1.46 -     1.57: 6009
        1.57 -     1.69: 0
        1.69 -     1.81: 85
  Bond restraints: 11157
  Sorted by residual:
  bond pdb=" C   GLY D 426 "
       pdb=" N   PRO D 427 "
    ideal  model  delta    sigma   weight residual
    1.332  1.351 -0.019 8.20e-03 1.49e+04 5.53e+00
  bond pdb=" N   GLY G 245 "
       pdb=" CA  GLY G 245 "
    ideal  model  delta    sigma   weight residual
    1.443  1.460 -0.017 1.37e-02 5.33e+03 1.54e+00
  bond pdb=" N   PRO G 246 "
       pdb=" CA  PRO G 246 "
    ideal  model  delta    sigma   weight residual
    1.471  1.458  0.013 1.29e-02 6.01e+03 1.08e+00
  bond pdb=" CA  ILE G 297 "
       pdb=" CB  ILE G 297 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.012 1.25e-02 6.40e+03 9.37e-01
  bond pdb=" CA  VAL G 278 "
       pdb=" CB  VAL G 278 "
    ideal  model  delta    sigma   weight residual
    1.540  1.527  0.012 1.29e-02 6.01e+03 9.12e-01
  ... (remaining 11152 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 15070
        2.58 -     5.17: 90
        5.17 -     7.75: 13
        7.75 -    10.33: 0
       10.33 -    12.92: 1
  Bond angle restraints: 15174
  Sorted by residual:
  angle pdb=" N   PRO G 246 "
        pdb=" CA  PRO G 246 "
        pdb=" CB  PRO G 246 "
      ideal   model   delta    sigma   weight residual
     103.44  110.18   -6.74 1.12e+00 7.97e-01 3.62e+01
  angle pdb=" N   VAL D 596 "
        pdb=" CA  VAL D 596 "
        pdb=" C   VAL D 596 "
      ideal   model   delta    sigma   weight residual
     113.71  109.41    4.30 9.50e-01 1.11e+00 2.05e+01
  angle pdb=" N   GLY D 426 "
        pdb=" CA  GLY D 426 "
        pdb=" C   GLY D 426 "
      ideal   model   delta    sigma   weight residual
     112.34  119.30   -6.96 2.04e+00 2.40e-01 1.16e+01
  angle pdb=" N   PRO D 427 "
        pdb=" CA  PRO D 427 "
        pdb=" C   PRO D 427 "
      ideal   model   delta    sigma   weight residual
     114.98  110.18    4.80 1.46e+00 4.69e-01 1.08e+01
  angle pdb=" CA  PRO D 427 "
        pdb=" C   PRO D 427 "
        pdb=" O   PRO D 427 "
      ideal   model   delta    sigma   weight residual
     118.38  121.74   -3.36 1.13e+00 7.83e-01 8.83e+00
  ... (remaining 15169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 6197
       17.89 -    35.78: 391
       35.78 -    53.67: 62
       53.67 -    71.56: 6
       71.56 -    89.45: 4
  Dihedral angle restraints: 6660
    sinusoidal: 2486
      harmonic: 4174
  Sorted by residual:
  dihedral pdb=" CA  GLY D 426 "
           pdb=" C   GLY D 426 "
           pdb=" N   PRO D 427 "
           pdb=" CA  PRO D 427 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.25   21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CB  GLU D 396 "
           pdb=" CG  GLU D 396 "
           pdb=" CD  GLU D 396 "
           pdb=" OE1 GLU D 396 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.45  -89.45     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" N   PRO G 246 "
           pdb=" C   PRO G 246 "
           pdb=" CA  PRO G 246 "
           pdb=" CB  PRO G 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  122.75   -7.65     0      2.50e+00 1.60e-01 9.37e+00
  ... (remaining 6657 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1429
       0.045 -    0.091: 294
       0.091 -    0.136: 49
       0.136 -    0.182: 1
       0.182 -    0.227: 1
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CA  PRO G 246 "
            pdb=" N   PRO G 246 "
            pdb=" C   PRO G 246 "
            pdb=" CB  PRO G 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  ILE D 478 "
            pdb=" CA  ILE D 478 "
            pdb=" CG1 ILE D 478 "
            pdb=" CG2 ILE D 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" CB  ILE D 473 "
            pdb=" CA  ILE D 473 "
            pdb=" CG1 ILE D 473 "
            pdb=" CG2 ILE D 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 1771 not shown)

  Planarity restraints: 1903
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 426 "   -0.038 5.00e-02 4.00e+02   5.81e-02 5.39e+00
        pdb=" N   PRO D 427 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO D 427 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 427 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 141 "    0.014 2.00e-02 2.50e+03   9.16e-03 2.10e+00
        pdb=" CG  TRP E 141 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 141 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 141 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 391 "    0.024 5.00e-02 4.00e+02   3.58e-02 2.05e+00
        pdb=" N   PRO D 392 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO D 392 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 392 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1900 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 187
        2.70 -     3.25: 11047
        3.25 -     3.80: 16763
        3.80 -     4.35: 19014
        4.35 -     4.90: 32652
  Nonbonded interactions: 79663
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 287 "
            pdb=" OG  SER A 385 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" NE2 GLN D 371 "
            pdb=" O   TYR D 610 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NE2 GLN D  63 "
            pdb=" OE2 GLU D 334 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" NE2 GLN D 386 "
            pdb=" O   MET D 611 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   ARG D 420 "
            pdb=" OG1 THR D 424 "
     model   vdw
     2.308 3.040
  ... (remaining 79658 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             46.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.060
  Set scattering table:                    0.110
  Process input model:                     45.780
  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:             0.010
  Load rotamer database and sin/cos tables:3.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   96.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
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      :  0.003   0.035  11157  Z= 0.128
  Angle     :  0.543  12.917  15174  Z= 0.295
  Chirality :  0.037   0.227   1774
  Planarity :  0.004   0.058   1903
  Dihedral  : 11.788  89.454   3966
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.04 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  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: -1.16 (0.22), residues: 1414
  helix:  0.23 (0.16), residues: 907
  sheet: -2.34 (0.51), residues: 81
  loop : -2.54 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP E 141 
 HIS   0.003   0.001   HIS B 114 
 PHE   0.013   0.001   PHE A 263 
 TYR   0.011   0.001   TYR A 237 
 ARG   0.002   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10402 (  712)
  hydrogen bonds       : angle       4.50465 ( 2124)
  covalent geometry    : bond        0.00269 (11157)
  covalent geometry    : angle       0.54292 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 MET cc_start: 0.8268 (tpp) cc_final: 0.7980 (ttt)
REVERT: C   18 ASP cc_start: 0.8178 (m-30) cc_final: 0.7944 (m-30)
REVERT: B  102 LEU cc_start: 0.8528 (tp) cc_final: 0.8108 (tp)
REVERT: D  270 MET cc_start: 0.7891 (tmm) cc_final: 0.7436 (tmm)
REVERT: E   92 ILE cc_start: 0.9544 (mt) cc_final: 0.9278 (mm)
REVERT: E  110 ASP cc_start: 0.6936 (t70) cc_final: 0.6482 (t70)
REVERT: E  151 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7836 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2817
  time to fit residues: 67.6749
Evaluate side-chains
  106 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 72 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 111 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 67 optimal weight:    0.3980
   chunk 82 optimal weight:    3.9990
   chunk 128 optimal weight:    8.9990
   overall best weight:    4.0788

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
A 220 HIS
A 290 ASN
D  61 GLN
D  63 GLN
D 386 GLN
D 470 GLN
D 604 HIS
E  56 HIS
E  95 GLN
E 114 GLN
E 166 GLN
F  34 GLN
F  43 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.066074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.051477 restraints weight = 56957.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.052772 restraints weight = 31118.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.053569 restraints weight = 21400.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11157  Z= 0.233
  Angle     :  0.656  13.633  15174  Z= 0.325
  Chirality :  0.039   0.145   1774
  Planarity :  0.005   0.049   1903
  Dihedral  :  3.464  19.643   1550
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.96 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.38 %
    Favored  : 85.06 %
  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:  0.15 (0.23), residues: 1414
  helix:  1.33 (0.17), residues: 920
  sheet: -2.31 (0.49), residues: 83
  loop : -2.26 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 141 
 HIS   0.003   0.001   HIS D 604 
 PHE   0.026   0.002   PHE D  15 
 TYR   0.014   0.001   TYR A 237 
 ARG   0.014   0.001   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04271 (  712)
  hydrogen bonds       : angle       4.03091 ( 2124)
  covalent geometry    : bond        0.00538 (11157)
  covalent geometry    : angle       0.65596 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 MET cc_start: 0.8620 (tpp) cc_final: 0.8317 (ttt)
REVERT: C   18 ASP cc_start: 0.8702 (m-30) cc_final: 0.8355 (m-30)
REVERT: D   90 MET cc_start: 0.8898 (mmm) cc_final: 0.8570 (mmp)
REVERT: E   92 ILE cc_start: 0.9510 (mt) cc_final: 0.9200 (mm)
REVERT: F   43 GLN cc_start: 0.8620 (mt0) cc_final: 0.8411 (pm20)
REVERT: F  137 MET cc_start: 0.7843 (mpp) cc_final: 0.7223 (mpp)
REVERT: F  186 ILE cc_start: 0.9139 (tp) cc_final: 0.8872 (tt)
  outliers start: 17
  outliers final: 12
  residues processed: 126
  average time/residue: 0.2378
  time to fit residues: 45.9303
Evaluate side-chains
  121 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  372 CYS
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:   40.0000
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 119 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0270
   chunk 52 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 136 optimal weight:   40.0000
   chunk 31 optimal weight:   20.0000
   chunk 69 optimal weight:    3.9990
   overall best weight:    3.0046

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

Flipped N/Q/H residues before XYZ refinement:
D 386 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.066007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.051465 restraints weight = 57787.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.052747 restraints weight = 31118.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.053659 restraints weight = 21210.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
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      :  0.004   0.040  11157  Z= 0.177
  Angle     :  0.600  14.552  15174  Z= 0.293
  Chirality :  0.038   0.142   1774
  Planarity :  0.004   0.047   1903
  Dihedral  :  3.408  15.432   1550
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.11 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.87 %
    Favored  : 81.30 %
  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:  0.65 (0.23), residues: 1414
  helix:  1.73 (0.17), residues: 933
  sheet: -2.14 (0.49), residues: 83
  loop : -2.23 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 141 
 HIS   0.003   0.001   HIS C  59 
 PHE   0.027   0.002   PHE D 563 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.006   0.000   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04034 (  712)
  hydrogen bonds       : angle       3.82892 ( 2124)
  covalent geometry    : bond        0.00408 (11157)
  covalent geometry    : angle       0.60006 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 3.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 MET cc_start: 0.9279 (mmp) cc_final: 0.8914 (mmt)
REVERT: C   18 ASP cc_start: 0.8705 (m-30) cc_final: 0.8370 (m-30)
REVERT: D   90 MET cc_start: 0.8842 (mmm) cc_final: 0.8513 (mmm)
REVERT: E   87 LYS cc_start: 0.9612 (ttmm) cc_final: 0.9309 (ttmm)
REVERT: E   92 ILE cc_start: 0.9489 (mt) cc_final: 0.9187 (mm)
REVERT: E  121 LYS cc_start: 0.9181 (pttp) cc_final: 0.8863 (ptpp)
REVERT: F   34 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9059 (pt0)
REVERT: F  137 MET cc_start: 0.8306 (mpp) cc_final: 0.7630 (mpp)
REVERT: F  186 ILE cc_start: 0.9198 (tp) cc_final: 0.8921 (tt)
REVERT: G  266 LEU cc_start: 0.8401 (mp) cc_final: 0.8138 (mp)
  outliers start: 20
  outliers final: 14
  residues processed: 135
  average time/residue: 0.3970
  time to fit residues: 82.7338
Evaluate side-chains
  125 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 2.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  372 CYS
Chi-restraints excluded: chain D residue  429 LEU
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain F residue   34 GLN
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   78 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 58 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0870
   chunk 32 optimal weight:   20.0000
   chunk 76 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 127 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.0760

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
D  61 GLN
F  49 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.067103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.052694 restraints weight = 56174.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.054031 restraints weight = 30228.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.054904 restraints weight = 20567.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11157  Z= 0.113
  Angle     :  0.573  14.594  15174  Z= 0.274
  Chirality :  0.037   0.145   1774
  Planarity :  0.004   0.050   1903
  Dihedral  :  3.282  15.072   1550
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.97 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.88 %
    Favored  : 79.47 %
  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:  1.00 (0.23), residues: 1414
  helix:  1.98 (0.17), residues: 930
  sheet: -1.98 (0.49), residues: 83
  loop : -2.00 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 138 
 HIS   0.002   0.001   HIS C  59 
 PHE   0.021   0.001   PHE D  15 
 TYR   0.011   0.001   TYR A 237 
 ARG   0.004   0.000   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  712)
  hydrogen bonds       : angle       3.57400 ( 2124)
  covalent geometry    : bond        0.00252 (11157)
  covalent geometry    : angle       0.57316 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 2.535 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8467 (tt)
REVERT: C   18 ASP cc_start: 0.8660 (m-30) cc_final: 0.8322 (m-30)
REVERT: D   90 MET cc_start: 0.8816 (mmm) cc_final: 0.8469 (mmm)
REVERT: D  270 MET cc_start: 0.8251 (tmm) cc_final: 0.7983 (tmm)
REVERT: E   92 ILE cc_start: 0.9491 (mt) cc_final: 0.9191 (mm)
REVERT: E  151 GLU cc_start: 0.8731 (mm-30) cc_final: 0.7604 (mm-30)
REVERT: E  165 TYR cc_start: 0.8888 (m-10) cc_final: 0.8629 (m-80)
REVERT: F  137 MET cc_start: 0.8210 (mpp) cc_final: 0.7577 (mpp)
REVERT: F  146 LYS cc_start: 0.9255 (tttt) cc_final: 0.8763 (tptp)
REVERT: F  186 ILE cc_start: 0.9210 (tp) cc_final: 0.8906 (tt)
  outliers start: 18
  outliers final: 11
  residues processed: 132
  average time/residue: 0.3019
  time to fit residues: 65.6414
Evaluate side-chains
  125 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   15 PHE
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  327 LEU
Chi-restraints excluded: chain D residue  372 CYS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain F residue   60 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 123 optimal weight:   10.0000
   chunk 138 optimal weight:   10.0000
   chunk 125 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 85 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 114 HIS
D 386 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.066374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.052376 restraints weight = 55207.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.053751 restraints weight = 29935.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.054585 restraints weight = 20444.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11157  Z= 0.234
  Angle     :  0.648  14.683  15174  Z= 0.315
  Chirality :  0.039   0.175   1774
  Planarity :  0.004   0.053   1903
  Dihedral  :  3.404  15.364   1550
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.75 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.16 %
    Favored  : 76.90 %
  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:  1.02 (0.23), residues: 1414
  helix:  2.01 (0.17), residues: 933
  sheet: -2.01 (0.50), residues: 83
  loop : -2.08 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 141 
 HIS   0.003   0.001   HIS C  59 
 PHE   0.028   0.002   PHE D 563 
 TYR   0.014   0.001   TYR A 237 
 ARG   0.003   0.000   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  712)
  hydrogen bonds       : angle       3.87244 ( 2124)
  covalent geometry    : bond        0.00539 (11157)
  covalent geometry    : angle       0.64753 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 2.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8467 (tt)
REVERT: A  345 MET cc_start: 0.9342 (mmp) cc_final: 0.9032 (mmp)
REVERT: C   18 ASP cc_start: 0.8813 (m-30) cc_final: 0.8453 (m-30)
REVERT: D   90 MET cc_start: 0.8896 (mmm) cc_final: 0.8503 (mmm)
REVERT: D  415 MET cc_start: 0.7081 (tmm) cc_final: 0.6849 (tmm)
REVERT: E   87 LYS cc_start: 0.9660 (ttmm) cc_final: 0.9378 (ttmm)
REVERT: E   92 ILE cc_start: 0.9441 (mt) cc_final: 0.9122 (mm)
REVERT: E  121 LYS cc_start: 0.9216 (pttp) cc_final: 0.8656 (ptpp)
REVERT: E  151 GLU cc_start: 0.8746 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: F  137 MET cc_start: 0.8330 (mpp) cc_final: 0.7645 (mpp)
REVERT: F  186 ILE cc_start: 0.9218 (tp) cc_final: 0.8916 (tt)
  outliers start: 32
  outliers final: 26
  residues processed: 135
  average time/residue: 0.3010
  time to fit residues: 63.0691
Evaluate side-chains
  134 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain D residue   15 PHE
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  327 LEU
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  372 CYS
Chi-restraints excluded: chain D residue  429 LEU
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain E residue  107 SER
Chi-restraints excluded: chain F residue   60 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 111 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
D 386 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.068471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.054042 restraints weight = 56398.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.055523 restraints weight = 29329.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.056276 restraints weight = 19508.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11157  Z= 0.109
  Angle     :  0.580  14.826  15174  Z= 0.274
  Chirality :  0.037   0.176   1774
  Planarity :  0.004   0.055   1903
  Dihedral  :  3.263  15.222   1550
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.62 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.17 %
    Favored  : 76.81 %
  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:  1.34 (0.23), residues: 1414
  helix:  2.24 (0.17), residues: 927
  sheet: -1.78 (0.50), residues: 81
  loop : -1.84 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 138 
 HIS   0.002   0.000   HIS C  59 
 PHE   0.022   0.001   PHE D 563 
 TYR   0.011   0.001   TYR E 158 
 ARG   0.003   0.000   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  712)
  hydrogen bonds       : angle       3.48612 ( 2124)
  covalent geometry    : bond        0.00239 (11157)
  covalent geometry    : angle       0.57987 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8519 (tt)
REVERT: A  345 MET cc_start: 0.9299 (mmp) cc_final: 0.8963 (mmp)
REVERT: C   16 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8646 (tt)
REVERT: C   18 ASP cc_start: 0.8757 (m-30) cc_final: 0.8400 (m-30)
REVERT: C   59 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.8028 (t-90)
REVERT: D  415 MET cc_start: 0.7173 (tmm) cc_final: 0.6888 (tmm)
REVERT: E   87 LYS cc_start: 0.9634 (ttmm) cc_final: 0.9322 (ttmm)
REVERT: E   92 ILE cc_start: 0.9448 (mt) cc_final: 0.9143 (mm)
REVERT: E  121 LYS cc_start: 0.9158 (pttp) cc_final: 0.8826 (pttp)
REVERT: E  125 ASP cc_start: 0.8868 (m-30) cc_final: 0.8663 (p0)
REVERT: E  151 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7528 (mm-30)
REVERT: F  137 MET cc_start: 0.8240 (mpp) cc_final: 0.7637 (mpp)
REVERT: F  186 ILE cc_start: 0.9184 (tp) cc_final: 0.8862 (tt)
  outliers start: 22
  outliers final: 13
  residues processed: 138
  average time/residue: 0.1761
  time to fit residues: 38.2700
Evaluate side-chains
  126 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   59 HIS
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   15 PHE
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  327 LEU
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  596 VAL
Chi-restraints excluded: chain E residue  107 SER
Chi-restraints excluded: chain F residue   60 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    6.9990
   chunk 101 optimal weight:    9.9990
   chunk 102 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 112 optimal weight:    7.9990
   chunk 105 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 81 optimal weight:    3.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
D 386 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.065814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.051346 restraints weight = 56736.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.052726 restraints weight = 30936.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.053452 restraints weight = 21277.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  11157  Z= 0.268
  Angle     :  0.688  15.134  15174  Z= 0.335
  Chirality :  0.040   0.210   1774
  Planarity :  0.004   0.055   1903
  Dihedral  :  3.479  15.592   1550
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.17 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.45 %
    Favored  : 75.16 %
  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:  1.21 (0.23), residues: 1414
  helix:  2.14 (0.17), residues: 933
  sheet: -1.92 (0.49), residues: 81
  loop : -1.95 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 225 
 HIS   0.004   0.001   HIS C  59 
 PHE   0.024   0.002   PHE D 581 
 TYR   0.014   0.002   TYR A 237 
 ARG   0.003   0.000   ARG E  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04293 (  712)
  hydrogen bonds       : angle       3.98101 ( 2124)
  covalent geometry    : bond        0.00613 (11157)
  covalent geometry    : angle       0.68757 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 112
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8543 (tt)
REVERT: A  345 MET cc_start: 0.9359 (mmp) cc_final: 0.9071 (tpp)
REVERT: C   16 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8734 (tt)
REVERT: C   18 ASP cc_start: 0.8828 (m-30) cc_final: 0.8470 (m-30)
REVERT: C   59 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8140 (t-90)
REVERT: D  270 MET cc_start: 0.8434 (tmm) cc_final: 0.8077 (tmm)
REVERT: D  415 MET cc_start: 0.7313 (tmm) cc_final: 0.6959 (tmm)
REVERT: D  429 LEU cc_start: 0.8068 (mp) cc_final: 0.7737 (mp)
REVERT: E   87 LYS cc_start: 0.9667 (ttmm) cc_final: 0.9375 (ttmm)
REVERT: E   92 ILE cc_start: 0.9434 (mt) cc_final: 0.9109 (mm)
REVERT: F  137 MET cc_start: 0.8381 (mpp) cc_final: 0.7699 (mpp)
REVERT: F  186 ILE cc_start: 0.9202 (tp) cc_final: 0.8892 (tt)
  outliers start: 37
  outliers final: 24
  residues processed: 142
  average time/residue: 0.1986
  time to fit residues: 44.1351
Evaluate side-chains
  136 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   59 HIS
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain D residue   15 PHE
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  327 LEU
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  372 CYS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  596 VAL
Chi-restraints excluded: chain E residue  107 SER
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain F residue   60 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 117 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
D 386 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.065904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.051366 restraints weight = 55972.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.052740 restraints weight = 29845.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.053571 restraints weight = 20144.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11157  Z= 0.122
  Angle     :  0.610  15.629  15174  Z= 0.286
  Chirality :  0.038   0.209   1774
  Planarity :  0.004   0.054   1903
  Dihedral  :  3.344  15.508   1550
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.76 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.91 %
    Favored  : 74.70 %
  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:  1.48 (0.24), residues: 1414
  helix:  2.32 (0.17), residues: 929
  sheet: -1.86 (0.49), residues: 81
  loop : -1.70 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  84 
 HIS   0.003   0.000   HIS C  59 
 PHE   0.021   0.001   PHE D  15 
 TYR   0.010   0.001   TYR A 237 
 ARG   0.003   0.000   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  712)
  hydrogen bonds       : angle       3.60668 ( 2124)
  covalent geometry    : bond        0.00275 (11157)
  covalent geometry    : angle       0.60951 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8812 (mm)
REVERT: A  153 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8476 (tt)
REVERT: A  345 MET cc_start: 0.9275 (mmp) cc_final: 0.8913 (mmp)
REVERT: C   16 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8621 (tt)
REVERT: C   18 ASP cc_start: 0.8731 (m-30) cc_final: 0.8380 (m-30)
REVERT: C   59 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.8040 (t-90)
REVERT: D  270 MET cc_start: 0.8322 (tmm) cc_final: 0.7951 (tmm)
REVERT: D  415 MET cc_start: 0.7322 (tmm) cc_final: 0.6955 (tmm)
REVERT: D  599 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7467 (p90)
REVERT: E   92 ILE cc_start: 0.9463 (mt) cc_final: 0.9159 (mm)
REVERT: E  121 LYS cc_start: 0.9168 (pptt) cc_final: 0.8765 (ptpp)
REVERT: E  151 GLU cc_start: 0.8758 (mm-30) cc_final: 0.7574 (mm-30)
REVERT: E  162 MET cc_start: 0.9088 (tpp) cc_final: 0.8466 (mpp)
REVERT: F  137 MET cc_start: 0.8177 (mpp) cc_final: 0.7691 (mpp)
REVERT: F  186 ILE cc_start: 0.9198 (tp) cc_final: 0.8867 (tt)
  outliers start: 26
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1837
  time to fit residues: 38.7175
Evaluate side-chains
  132 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   59 HIS
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain D residue   15 PHE
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  327 LEU
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  596 VAL
Chi-restraints excluded: chain D residue  599 PHE
Chi-restraints excluded: chain E residue  107 SER
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain F residue   60 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 101 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 116 optimal weight:    3.9990
   chunk 135 optimal weight:    9.9990
   chunk 133 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 140 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
D 386 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.064452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.050289 restraints weight = 57081.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.051618 restraints weight = 32429.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.052456 restraints weight = 20254.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11157  Z= 0.229
  Angle     :  0.681  15.434  15174  Z= 0.327
  Chirality :  0.040   0.213   1774
  Planarity :  0.004   0.056   1903
  Dihedral  :  3.499  17.845   1550
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.17 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.82 %
    Favored  : 74.52 %
  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:  1.34 (0.24), residues: 1414
  helix:  2.20 (0.17), residues: 935
  sheet: -1.87 (0.50), residues: 81
  loop : -1.79 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 141 
 HIS   0.004   0.001   HIS C  59 
 PHE   0.023   0.002   PHE E  23 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.003   0.000   ARG E  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04192 (  712)
  hydrogen bonds       : angle       3.90553 ( 2124)
  covalent geometry    : bond        0.00526 (11157)
  covalent geometry    : angle       0.68125 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8848 (mm)
REVERT: A  153 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8560 (tt)
REVERT: A  345 MET cc_start: 0.9268 (mmp) cc_final: 0.8915 (mmt)
REVERT: C   16 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8665 (tt)
REVERT: C   18 ASP cc_start: 0.8726 (m-30) cc_final: 0.8379 (m-30)
REVERT: C   59 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8160 (t-90)
REVERT: D  270 MET cc_start: 0.8330 (tmm) cc_final: 0.7997 (tmm)
REVERT: D  415 MET cc_start: 0.7403 (tmm) cc_final: 0.7048 (tmm)
REVERT: D  599 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7546 (p90)
REVERT: E   87 LYS cc_start: 0.9629 (ttmm) cc_final: 0.9372 (ttmm)
REVERT: E   92 ILE cc_start: 0.9488 (mt) cc_final: 0.9176 (mm)
REVERT: E  121 LYS cc_start: 0.9226 (pptt) cc_final: 0.8829 (ptpp)
REVERT: E  151 GLU cc_start: 0.8869 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: F  137 MET cc_start: 0.8203 (mpp) cc_final: 0.7788 (mpp)
REVERT: F  186 ILE cc_start: 0.9158 (tp) cc_final: 0.8824 (tt)
  outliers start: 29
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1818
  time to fit residues: 37.8711
Evaluate side-chains
  134 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   59 HIS
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   15 PHE
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  327 LEU
Chi-restraints excluded: chain D residue  372 CYS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  581 PHE
Chi-restraints excluded: chain D residue  596 VAL
Chi-restraints excluded: chain D residue  599 PHE
Chi-restraints excluded: chain E residue  107 SER
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain F residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0020
   chunk 129 optimal weight:   10.0000
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
D 386 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.066055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.051549 restraints weight = 55960.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.052910 restraints weight = 29755.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.053741 restraints weight = 20145.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11157  Z= 0.118
  Angle     :  0.639  15.492  15174  Z= 0.298
  Chirality :  0.038   0.237   1774
  Planarity :  0.004   0.053   1903
  Dihedral  :  3.393  20.449   1550
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.76 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 23.56 %
    Favored  : 74.43 %
  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:  1.53 (0.23), residues: 1414
  helix:  2.33 (0.17), residues: 929
  sheet: -1.82 (0.50), residues: 81
  loop : -1.61 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 176 
 HIS   0.002   0.001   HIS F 132 
 PHE   0.022   0.001   PHE D  15 
 TYR   0.013   0.001   TYR E 158 
 ARG   0.003   0.000   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03841 (  712)
  hydrogen bonds       : angle       3.57233 ( 2124)
  covalent geometry    : bond        0.00260 (11157)
  covalent geometry    : angle       0.63876 (15174)

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

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

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2828 Ramachandran restraints generated.
    1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.7001 (tpp) cc_final: 0.6652 (tmm)
REVERT: A  135 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8798 (mm)
REVERT: A  153 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8453 (tt)
REVERT: A  345 MET cc_start: 0.9261 (mmp) cc_final: 0.8894 (mmp)
REVERT: C   16 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8607 (tt)
REVERT: C   18 ASP cc_start: 0.8721 (m-30) cc_final: 0.8371 (m-30)
REVERT: C   59 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.8038 (t-90)
REVERT: D  415 MET cc_start: 0.7403 (tmm) cc_final: 0.7033 (tmm)
REVERT: D  599 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.7606 (p90)
REVERT: E   87 LYS cc_start: 0.9623 (ttmm) cc_final: 0.9357 (ttmm)
REVERT: E   92 ILE cc_start: 0.9460 (mt) cc_final: 0.9165 (mm)
REVERT: E  121 LYS cc_start: 0.9233 (pptt) cc_final: 0.8773 (ptpp)
REVERT: E  151 GLU cc_start: 0.8717 (mm-30) cc_final: 0.7547 (mm-30)
REVERT: F  137 MET cc_start: 0.8139 (mpp) cc_final: 0.7811 (mpp)
REVERT: F  170 MET cc_start: 0.8524 (mtt) cc_final: 0.8059 (mmt)
REVERT: F  186 ILE cc_start: 0.9154 (tp) cc_final: 0.8813 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 132
  average time/residue: 0.1848
  time to fit residues: 37.9854
Evaluate side-chains
  128 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   59 HIS
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain D residue   15 PHE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  327 LEU
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  528 VAL
Chi-restraints excluded: chain D residue  596 VAL
Chi-restraints excluded: chain D residue  599 PHE
Chi-restraints excluded: chain E residue  107 SER
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain F residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 107 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0000
   chunk 112 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 134 optimal weight:    0.5980
   chunk 131 optimal weight:    0.0030
   chunk 95 optimal weight:    3.9990
   chunk 87 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.068344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.054530 restraints weight = 54814.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.055986 restraints weight = 28905.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.056807 restraints weight = 19499.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11157  Z= 0.115
  Angle     :  0.620  15.377  15174  Z= 0.292
  Chirality :  0.038   0.243   1774
  Planarity :  0.004   0.056   1903
  Dihedral  :  3.317  19.147   1550
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.90 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 23.56 %
    Favored  : 74.34 %
  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:  1.61 (0.23), residues: 1414
  helix:  2.38 (0.17), residues: 929
  sheet: -1.71 (0.50), residues: 81
  loop : -1.55 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 176 
 HIS   0.002   0.000   HIS F 132 
 PHE   0.026   0.001   PHE D 563 
 TYR   0.017   0.001   TYR E 158 
 ARG   0.003   0.000   ARG F  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  712)
  hydrogen bonds       : angle       3.50841 ( 2124)
  covalent geometry    : bond        0.00255 (11157)
  covalent geometry    : angle       0.62042 (15174)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4042.68 seconds
wall clock time: 76 minutes 38.20 seconds (4598.20 seconds total)