Starting phenix.real_space_refine
on Mon Jul 28 23:54:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kaq_22780/07_2025/7kaq_22780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kaq_22780/07_2025/7kaq_22780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kaq_22780/07_2025/7kaq_22780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kaq_22780/07_2025/7kaq_22780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kaq_22780/07_2025/7kaq_22780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kaq_22780/07_2025/7kaq_22780.cif"
  }
  resolution = 4.0
  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=   0.008 sd=   0.064
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      39      5.16       5
     C    7008      2.51       5
     N    1812      2.21       5
     O    1894      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10753
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3345
          Classifications: {'peptide': 439}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 19, 'TRANS': 419}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 69
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 435
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "B"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 229
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 3864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3864
          Classifications: {'peptide': 492}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 28, 'TRANS': 463}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 86
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1129
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "F"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1471
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "G"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 280
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'TRANS': 55}
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 168
          Unresolved non-hydrogen dihedrals: 56
          Planarities with less than four sites: {'UNK:plan-1': 56}
          Unresolved non-hydrogen planarities: 56
  Time building chain proxies: 6.29, per 1000 atoms: 0.58
  Number of scatterers: 10753
  At special positions: 0
  Unit cell: (108.1, 125.35, 135.7, 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      39     16.00
     O    1894      8.00
     N    1812      7.00
     C    7008      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: 2.78
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2650

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 6 sheets defined
      71.3% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 47
    Processing helix  chain 'A' and resid 64 through 70
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 109 through 137
      removed outlier: 3.651A  pdb=" N   ILE A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.838A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 214 through 225
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 3.946A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ARG A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.560A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLY A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 314
      removed outlier: 3.722A  pdb=" N   ILE A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 341 through 346
    Processing helix  chain 'A' and resid 351 through 358
    Processing helix  chain 'A' and resid 358 through 384
      removed outlier: 3.696A  pdb=" N   THR A 367 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 409 through 416
    Processing helix  chain 'A' and resid 417 through 440
    Processing helix  chain 'A' and resid 444 through 466
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 3.576A  pdb=" N   HIS C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'B' and resid 53 through 82
    Processing helix  chain 'D' and resid 13 through 36
      removed outlier: 3.588A  pdb=" N   VAL D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      Proline residue:  D  28  - end of helix
    Processing helix  chain 'D' and resid 58 through 65
      removed outlier: 4.239A  pdb=" N   LEU D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   GLU D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU D  65 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 94 through 112
    Processing helix  chain 'D' and resid 212 through 217
    Processing helix  chain 'D' and resid 219 through 233
      removed outlier: 3.777A  pdb=" N   VAL D 224 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 248
    Processing helix  chain 'D' and resid 255 through 268
    Processing helix  chain 'D' and resid 276 through 285
      removed outlier: 3.645A  pdb=" N   ILE D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 294
      removed outlier: 3.855A  pdb=" N   LYS D 291 " --> pdb=" O   ALA D 287 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN D 292 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE D 293 " --> pdb=" O   GLU D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 4.325A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 362
      removed outlier: 3.756A  pdb=" N   ALA D 349 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 4.066A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
      removed outlier: 3.517A  pdb=" N   LEU D 395 " --> pdb=" O   THR D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.606A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.079A  pdb=" N   GLU D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 466 through 470
    Processing helix  chain 'D' and resid 480 through 486
      removed outlier: 4.248A  pdb=" N   ASP D 486 " --> pdb=" O   GLU D 482 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 490 through 494
      removed outlier: 3.590A  pdb=" N   LYS D 493 " --> pdb=" O   MET D 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 545
      removed outlier: 6.777A  pdb=" N   ASP D 542 " --> pdb=" O   ASN D 539 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP D 543 " --> pdb=" O   LEU D 540 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LYS D 544 " --> pdb=" O   ASN D 541 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP D 545 " --> pdb=" O   ASP D 542 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 554 through 558
      removed outlier: 3.534A  pdb=" N   HIS D 558 " --> pdb=" O   LEU D 555 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 86
      removed outlier: 3.595A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 123
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 3.513A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 182
      removed outlier: 3.513A  pdb=" N   VAL E 164 " --> pdb=" O   VAL E 160 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 4.123A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.589A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 41
    Processing helix  chain 'F' and resid 52 through 71
      removed outlier: 3.808A  pdb=" N   ASN F  68 " --> pdb=" O   SER F  64 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU F  69 " --> pdb=" O   GLY F  65 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLN F  70 " --> pdb=" O   MET F  66 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 91
    Processing helix  chain 'F' and resid 97 through 120
      Proline residue:  F 103  - end of helix
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.631A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 168
    Processing helix  chain 'F' and resid 174 through 192
      removed outlier: 3.619A  pdb=" N   ALA F 178 " --> pdb=" O   MET F 174 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 151 through 170
      removed outlier: 3.640A  pdb=" N   UNK G 170 " --> pdb=" O   UNK G 166 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 175 through 205
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211
    Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436
      removed outlier: 6.805A  pdb=" N   LYS D 454 " --> pdb=" O   ILE D 431 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ALA D 433 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   SER D 452 " --> pdb=" O   ALA D 433 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   PHE D 435 " --> pdb=" O   TYR D 450 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   TYR D 450 " --> pdb=" O   PHE D 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
    Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6

    705 hydrogen bonds defined for protein.
    2070 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3404
        1.34 -     1.46: 2126
        1.46 -     1.57: 5370
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 10961
  Sorted by residual:
  bond pdb=" C   LYS D 493 "
       pdb=" N   GLN D 494 "
    ideal  model  delta    sigma   weight residual
    1.331  1.305  0.026 2.83e-02 1.25e+03 8.58e-01
  bond pdb=" CA  LEU F 102 "
       pdb=" C   LEU F 102 "
    ideal  model  delta    sigma   weight residual
    1.521  1.529 -0.008 1.14e-02 7.69e+03 5.47e-01
  bond pdb=" CA  LEU A 147 "
       pdb=" C   LEU A 147 "
    ideal  model  delta    sigma   weight residual
    1.525  1.540 -0.015 2.10e-02 2.27e+03 5.27e-01
  bond pdb=" C   GLU D  12 "
       pdb=" N   THR D  13 "
    ideal  model  delta    sigma   weight residual
    1.332  1.322  0.010 1.40e-02 5.10e+03 5.27e-01
  bond pdb=" CB  VAL C  54 "
       pdb=" CG1 VAL C  54 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.09e-01
  ... (remaining 10956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 14726
        1.91 -     3.81: 123
        3.81 -     5.72: 18
        5.72 -     7.63: 5
        7.63 -     9.53: 1
  Bond angle restraints: 14873
  Sorted by residual:
  angle pdb=" C   ILE A 417 "
        pdb=" N   ILE A 418 "
        pdb=" CA  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     120.33  122.46   -2.13 8.00e-01 1.56e+00 7.11e+00
  angle pdb=" N   PRO D 426 "
        pdb=" CA  PRO D 426 "
        pdb=" C   PRO D 426 "
      ideal   model   delta    sigma   weight residual
     110.55  114.48   -3.93 1.63e+00 3.76e-01 5.80e+00
  angle pdb=" C   ILE A 418 "
        pdb=" CA  ILE A 418 "
        pdb=" CB  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     114.00  110.93    3.07 1.31e+00 5.83e-01 5.48e+00
  angle pdb=" N   VAL D  25 "
        pdb=" CA  VAL D  25 "
        pdb=" C   VAL D  25 "
      ideal   model   delta    sigma   weight residual
     111.81  109.93    1.88 8.60e-01 1.35e+00 4.79e+00
  angle pdb=" C   PRO D 471 "
        pdb=" N   GLU D 472 "
        pdb=" CA  GLU D 472 "
      ideal   model   delta    sigma   weight residual
     121.54  125.52   -3.98 1.91e+00 2.74e-01 4.35e+00
  ... (remaining 14868 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 6189
       17.67 -    35.33: 338
       35.33 -    53.00: 54
       53.00 -    70.67: 5
       70.67 -    88.33: 9
  Dihedral angle restraints: 6595
    sinusoidal: 2518
      harmonic: 4077
  Sorted by residual:
  dihedral pdb=" CA  SER A 289 "
           pdb=" C   SER A 289 "
           pdb=" N   ASN A 290 "
           pdb=" CA  ASN A 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.74   16.26     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  GLU E 144 "
           pdb=" CG  GLU E 144 "
           pdb=" CD  GLU E 144 "
           pdb=" OE1 GLU E 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.33   88.33     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU F  63 "
           pdb=" CG  GLU F  63 "
           pdb=" CD  GLU F  63 "
           pdb=" OE1 GLU F  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.00   88.00     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 6592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1075
       0.027 -    0.054: 452
       0.054 -    0.080: 160
       0.080 -    0.107: 78
       0.107 -    0.134: 12
  Chirality restraints: 1777
  Sorted by residual:
  chirality pdb=" CA  ILE D 470 "
            pdb=" N   ILE D 470 "
            pdb=" C   ILE D 470 "
            pdb=" CB  ILE D 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CB  THR D 448 "
            pdb=" CA  THR D 448 "
            pdb=" OG1 THR D 448 "
            pdb=" CG2 THR D 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  SER A  83 "
            pdb=" N   SER A  83 "
            pdb=" C   SER A  83 "
            pdb=" CB  SER A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 1774 not shown)

  Planarity restraints: 1855
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO F  48 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 462 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO D 463 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO D 463 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D 463 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  93 "   -0.017 5.00e-02 4.00e+02   2.52e-02 1.01e+00
        pdb=" N   PRO F  94 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO F  94 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO F  94 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1852 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 287
        2.71 -     3.25: 11487
        3.25 -     3.80: 17396
        3.80 -     4.35: 20289
        4.35 -     4.90: 34815
  Nonbonded interactions: 84274
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 287 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER A  72 "
            pdb=" O   LEU A  78 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" NH1 ARG F  92 "
            pdb=" OE1 GLU F  96 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   THR D 444 "
            pdb=" OG  SER D 447 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   PHE A 198 "
            pdb=" OH  TYR C  66 "
     model   vdw
     2.252 3.040
  ... (remaining 84269 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:             0.830
  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:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     26.180
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
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   0.026  10961  Z= 0.134
  Angle     :  0.521   9.533  14873  Z= 0.290
  Chirality :  0.037   0.134   1777
  Planarity :  0.003   0.041   1855
  Dihedral  : 11.528  88.332   3945
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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 (0.22), residues: 1322
  helix:  0.29 (0.17), residues: 833
  sheet: -2.85 (0.44), residues: 84
  loop : -2.05 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.012   0.001   PHE A  92 
 TYR   0.011   0.001   TYR F 190 
 ARG   0.002   0.000   ARG F 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13071 (  705)
  hydrogen bonds       : angle       4.94118 ( 2070)
  covalent geometry    : bond        0.00257 (10961)
  covalent geometry    : angle       0.52142 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.7945 (m-90) cc_final: 0.7212 (t-100)
REVERT: A  131 LEU cc_start: 0.9711 (mm) cc_final: 0.9365 (pp)
REVERT: A  158 MET cc_start: 0.9212 (ppp) cc_final: 0.9004 (ppp)
REVERT: A  191 GLU cc_start: 0.9306 (tt0) cc_final: 0.9081 (pp20)
REVERT: A  400 MET cc_start: 0.9222 (mmm) cc_final: 0.8813 (tpp)
REVERT: C   43 ASP cc_start: 0.9311 (p0) cc_final: 0.9044 (p0)
REVERT: C   46 GLU cc_start: 0.9278 (tt0) cc_final: 0.8797 (pt0)
REVERT: E   81 MET cc_start: 0.8987 (ttm) cc_final: 0.8682 (tpp)
REVERT: E  121 TYR cc_start: 0.8786 (t80) cc_final: 0.8499 (t80)
REVERT: E  141 ILE cc_start: 0.9618 (mm) cc_final: 0.9387 (tp)
REVERT: F   66 MET cc_start: 0.9593 (mmm) cc_final: 0.9334 (mmm)
REVERT: F   87 MET cc_start: 0.9481 (ttp) cc_final: 0.9064 (tmm)
REVERT: F  101 GLN cc_start: 0.8733 (tt0) cc_final: 0.8382 (mt0)
REVERT: F  107 PHE cc_start: 0.8621 (t80) cc_final: 0.8220 (t80)
REVERT: F  128 ASP cc_start: 0.9128 (m-30) cc_final: 0.8846 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2243
  time to fit residues: 43.4139
Evaluate side-chains
  81 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 124 optimal weight:    1.9990
   overall best weight:    6.3992

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
A 290 ASN
A 347 GLN
A 394 GLN
A 398 GLN
D 288 HIS
D 307 GLN
D 334 HIS
D 494 GLN
D 558 HIS
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  68 ASN
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.045913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.034712 restraints weight = 79094.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.035687 restraints weight = 43582.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.036374 restraints weight = 29321.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  10961  Z= 0.327
  Angle     :  0.741  14.574  14873  Z= 0.366
  Chirality :  0.043   0.181   1777
  Planarity :  0.004   0.035   1855
  Dihedral  :  3.697  18.633   1480
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.51 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.23), residues: 1322
  helix:  1.35 (0.18), residues: 827
  sheet: -2.35 (0.45), residues: 90
  loop : -1.41 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 513 
 HIS   0.012   0.002   HIS D 334 
 PHE   0.026   0.002   PHE B  64 
 TYR   0.016   0.002   TYR A 139 
 ARG   0.004   0.001   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03703 (  705)
  hydrogen bonds       : angle       4.41910 ( 2070)
  covalent geometry    : bond        0.00692 (10961)
  covalent geometry    : angle       0.74134 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 2.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8308 (m-90) cc_final: 0.7305 (t-100)
REVERT: A  158 MET cc_start: 0.9100 (ppp) cc_final: 0.8868 (ppp)
REVERT: A  290 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8252 (t0)
REVERT: A  337 MET cc_start: 0.8833 (mpp) cc_final: 0.8615 (pmm)
REVERT: B   58 LEU cc_start: 0.8971 (tt) cc_final: 0.8763 (tt)
REVERT: B   59 PHE cc_start: 0.8632 (m-10) cc_final: 0.7479 (t80)
REVERT: D  491 MET cc_start: 0.8982 (tmm) cc_final: 0.8458 (tpp)
REVERT: D  608 MET cc_start: 0.9522 (mtm) cc_final: 0.9191 (mtm)
REVERT: E  121 TYR cc_start: 0.9107 (t80) cc_final: 0.8759 (t80)
REVERT: E  165 MET cc_start: 0.8725 (ttp) cc_final: 0.8393 (ppp)
REVERT: E  200 ASN cc_start: 0.9592 (t0) cc_final: 0.9355 (t0)
REVERT: F   66 MET cc_start: 0.9665 (mmm) cc_final: 0.9416 (mmm)
REVERT: F   87 MET cc_start: 0.9371 (ttp) cc_final: 0.8955 (tmm)
REVERT: F  114 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8996 (p0)
  outliers start: 14
  outliers final: 7
  residues processed: 84
  average time/residue: 0.2465
  time to fit residues: 33.0297
Evaluate side-chains
  72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 2.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  114 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 135 optimal weight:   40.0000
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 127 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
A 290 ASN
D 282 HIS
D 330 HIS
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.047402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.036130 restraints weight = 76968.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.037156 restraints weight = 42108.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.037874 restraints weight = 28307.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10961  Z= 0.114
  Angle     :  0.556  13.527  14873  Z= 0.267
  Chirality :  0.039   0.213   1777
  Planarity :  0.003   0.036   1855
  Dihedral  :  3.362  18.378   1480
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.03 %
    Favored  : 84.54 %
  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:  1.01 (0.24), residues: 1322
  helix:  1.78 (0.18), residues: 841
  sheet: -1.95 (0.47), residues: 90
  loop : -1.13 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 309 
 PHE   0.018   0.001   PHE B  66 
 TYR   0.011   0.001   TYR F 190 
 ARG   0.002   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03258 (  705)
  hydrogen bonds       : angle       3.88574 ( 2070)
  covalent geometry    : bond        0.00246 (10961)
  covalent geometry    : angle       0.55558 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 3.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8324 (m-90) cc_final: 0.7311 (t-100)
REVERT: A  158 MET cc_start: 0.9115 (ppp) cc_final: 0.8880 (ppp)
REVERT: A  337 MET cc_start: 0.8811 (mpp) cc_final: 0.8565 (pmm)
REVERT: E  121 TYR cc_start: 0.8970 (t80) cc_final: 0.8665 (t80)
REVERT: F   66 MET cc_start: 0.9630 (mmm) cc_final: 0.9367 (mmp)
REVERT: F   87 MET cc_start: 0.9341 (ttp) cc_final: 0.8898 (tmm)
  outliers start: 16
  outliers final: 8
  residues processed: 88
  average time/residue: 0.2817
  time to fit residues: 42.0351
Evaluate side-chains
  72 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 83 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 114 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 106 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.047084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.035868 restraints weight = 77016.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.036893 restraints weight = 42475.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.037607 restraints weight = 28473.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10961  Z= 0.138
  Angle     :  0.565  12.494  14873  Z= 0.271
  Chirality :  0.039   0.220   1777
  Planarity :  0.003   0.038   1855
  Dihedral  :  3.301  19.223   1480
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.66 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.24), residues: 1322
  helix:  2.00 (0.18), residues: 841
  sheet: -1.51 (0.48), residues: 88
  loop : -0.86 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 309 
 PHE   0.022   0.001   PHE B  64 
 TYR   0.012   0.001   TYR F 190 
 ARG   0.004   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03120 (  705)
  hydrogen bonds       : angle       3.81140 ( 2070)
  covalent geometry    : bond        0.00303 (10961)
  covalent geometry    : angle       0.56502 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8306 (m-90) cc_final: 0.7322 (t-100)
REVERT: A  131 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9322 (pp)
REVERT: A  158 MET cc_start: 0.9122 (ppp) cc_final: 0.8890 (ppp)
REVERT: A  337 MET cc_start: 0.8841 (mpp) cc_final: 0.8579 (pmm)
REVERT: A  400 MET cc_start: 0.9050 (tpp) cc_final: 0.8806 (tpp)
REVERT: A  450 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9262 (mp)
REVERT: E   81 MET cc_start: 0.8817 (ttt) cc_final: 0.8613 (tpp)
REVERT: E  121 TYR cc_start: 0.8998 (t80) cc_final: 0.8671 (t80)
REVERT: E  165 MET cc_start: 0.8726 (ttp) cc_final: 0.8421 (ppp)
REVERT: F   66 MET cc_start: 0.9630 (mmm) cc_final: 0.9384 (mmp)
REVERT: F   87 MET cc_start: 0.9399 (ttp) cc_final: 0.8973 (tmm)
REVERT: F  108 MET cc_start: 0.9302 (mpp) cc_final: 0.8969 (mpp)
REVERT: F  128 ASP cc_start: 0.9184 (m-30) cc_final: 0.8955 (m-30)
  outliers start: 20
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1700
  time to fit residues: 23.1367
Evaluate side-chains
  78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 90 optimal weight:    9.9990
   chunk 123 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 61 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 130 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.047171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.035964 restraints weight = 77506.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.036980 restraints weight = 42726.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.037693 restraints weight = 28642.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10961  Z= 0.124
  Angle     :  0.551  12.090  14873  Z= 0.263
  Chirality :  0.039   0.233   1777
  Planarity :  0.003   0.036   1855
  Dihedral  :  3.250  18.947   1480
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.10 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.24), residues: 1322
  helix:  2.11 (0.18), residues: 842
  sheet: -1.04 (0.52), residues: 83
  loop : -0.75 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  95 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.016   0.001   PHE B  64 
 TYR   0.011   0.001   TYR F 190 
 ARG   0.004   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03021 (  705)
  hydrogen bonds       : angle       3.73914 ( 2070)
  covalent geometry    : bond        0.00271 (10961)
  covalent geometry    : angle       0.55138 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8416 (m-90) cc_final: 0.7391 (t-100)
REVERT: A  158 MET cc_start: 0.9172 (ppp) cc_final: 0.8923 (ppp)
REVERT: A  165 MET cc_start: 0.9486 (ppp) cc_final: 0.9111 (tmm)
REVERT: A  337 MET cc_start: 0.8849 (mpp) cc_final: 0.8578 (pmm)
REVERT: A  400 MET cc_start: 0.9001 (tpp) cc_final: 0.8626 (tpp)
REVERT: A  450 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9260 (mp)
REVERT: E   81 MET cc_start: 0.8894 (ttt) cc_final: 0.8649 (tpp)
REVERT: E  121 TYR cc_start: 0.8984 (t80) cc_final: 0.8656 (t80)
REVERT: E  165 MET cc_start: 0.8729 (ttp) cc_final: 0.8290 (tmm)
REVERT: E  186 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.9055 (ttm170)
REVERT: F   66 MET cc_start: 0.9633 (mmm) cc_final: 0.9396 (mmm)
REVERT: F   87 MET cc_start: 0.9313 (ttp) cc_final: 0.9009 (tmm)
REVERT: F  108 MET cc_start: 0.9322 (mpp) cc_final: 0.8899 (mmm)
REVERT: F  128 ASP cc_start: 0.9166 (m-30) cc_final: 0.8948 (m-30)
  outliers start: 28
  outliers final: 11
  residues processed: 90
  average time/residue: 0.2178
  time to fit residues: 30.9268
Evaluate side-chains
  76 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 1.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  186 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 58 optimal weight:   20.0000
   chunk 110 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:    8.9990
   chunk 87 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 128 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.047639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.036424 restraints weight = 76944.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.037475 restraints weight = 41216.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.038203 restraints weight = 27269.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10961  Z= 0.101
  Angle     :  0.545  10.953  14873  Z= 0.260
  Chirality :  0.039   0.246   1777
  Planarity :  0.003   0.036   1855
  Dihedral  :  3.179  19.146   1480
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.26 %
    Favored  : 81.86 %
  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:  1.74 (0.24), residues: 1322
  helix:  2.18 (0.18), residues: 844
  sheet: -1.07 (0.51), residues: 88
  loop : -0.58 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  95 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.022   0.001   PHE B  64 
 TYR   0.020   0.001   TYR C  66 
 ARG   0.005   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02925 (  705)
  hydrogen bonds       : angle       3.60830 ( 2070)
  covalent geometry    : bond        0.00218 (10961)
  covalent geometry    : angle       0.54458 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8510 (m-90) cc_final: 0.7398 (t-100)
REVERT: A  158 MET cc_start: 0.9176 (ppp) cc_final: 0.8914 (ppp)
REVERT: A  165 MET cc_start: 0.9489 (ppp) cc_final: 0.9104 (tmm)
REVERT: A  244 MET cc_start: 0.8408 (mtm) cc_final: 0.8036 (pmm)
REVERT: A  337 MET cc_start: 0.8870 (mpp) cc_final: 0.8537 (pmm)
REVERT: A  400 MET cc_start: 0.9066 (tpp) cc_final: 0.8702 (tpp)
REVERT: E  121 TYR cc_start: 0.8924 (t80) cc_final: 0.8631 (t80)
REVERT: E  165 MET cc_start: 0.8745 (ttp) cc_final: 0.8333 (tmm)
REVERT: F   66 MET cc_start: 0.9619 (mmm) cc_final: 0.9394 (mmm)
REVERT: F   87 MET cc_start: 0.9393 (ttp) cc_final: 0.8993 (tmm)
REVERT: F  108 MET cc_start: 0.9332 (mpp) cc_final: 0.8918 (mmm)
  outliers start: 21
  outliers final: 11
  residues processed: 84
  average time/residue: 0.1987
  time to fit residues: 26.1643
Evaluate side-chains
  78 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain E residue  171 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.046434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.035391 restraints weight = 78589.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.036344 restraints weight = 43179.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.037047 restraints weight = 29279.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10961  Z= 0.181
  Angle     :  0.609  11.417  14873  Z= 0.293
  Chirality :  0.040   0.248   1777
  Planarity :  0.003   0.035   1855
  Dihedral  :  3.315  19.011   1480
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.53 %
    Favored  : 81.14 %
  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:  1.75 (0.24), residues: 1322
  helix:  2.16 (0.18), residues: 848
  sheet: -1.00 (0.53), residues: 88
  loop : -0.55 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  95 
 HIS   0.004   0.001   HIS D 390 
 PHE   0.019   0.001   PHE B  64 
 TYR   0.019   0.001   TYR C  66 
 ARG   0.003   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03093 (  705)
  hydrogen bonds       : angle       3.79982 ( 2070)
  covalent geometry    : bond        0.00394 (10961)
  covalent geometry    : angle       0.60899 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 69
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8463 (m-90) cc_final: 0.7547 (t-100)
REVERT: A  158 MET cc_start: 0.9177 (ppp) cc_final: 0.8972 (ppp)
REVERT: A  165 MET cc_start: 0.9522 (ppp) cc_final: 0.9181 (ppp)
REVERT: A  244 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8022 (pmm)
REVERT: A  337 MET cc_start: 0.8890 (mpp) cc_final: 0.8673 (pmm)
REVERT: B   59 PHE cc_start: 0.8596 (m-10) cc_final: 0.7372 (t80)
REVERT: E  121 TYR cc_start: 0.8991 (t80) cc_final: 0.8641 (t80)
REVERT: F  108 MET cc_start: 0.9343 (mpp) cc_final: 0.8958 (mmm)
REVERT: F  113 ILE cc_start: 0.9662 (OUTLIER) cc_final: 0.9222 (mt)
REVERT: F  128 ASP cc_start: 0.9031 (m-30) cc_final: 0.8682 (p0)
  outliers start: 26
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1787
  time to fit residues: 25.4054
Evaluate side-chains
  82 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  474 ASN
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain F residue  113 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 6 optimal weight:    0.4980
   chunk 105 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   chunk 120 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.046731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.035967 restraints weight = 75767.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.036878 restraints weight = 42812.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.037535 restraints weight = 29313.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10961  Z= 0.155
  Angle     :  0.639  14.021  14873  Z= 0.298
  Chirality :  0.040   0.301   1777
  Planarity :  0.003   0.037   1855
  Dihedral  :  3.314  17.606   1480
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.16 %
    Favored  : 81.23 %
  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:  1.76 (0.24), residues: 1322
  helix:  2.13 (0.18), residues: 850
  sheet: -0.91 (0.53), residues: 88
  loop : -0.49 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.018   0.001   PHE B  64 
 TYR   0.018   0.001   TYR C  66 
 ARG   0.004   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03101 (  705)
  hydrogen bonds       : angle       3.78266 ( 2070)
  covalent geometry    : bond        0.00344 (10961)
  covalent geometry    : angle       0.63892 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8385 (m-90) cc_final: 0.7502 (t-100)
REVERT: A  165 MET cc_start: 0.9445 (ppp) cc_final: 0.9053 (ppp)
REVERT: A  337 MET cc_start: 0.8847 (mpp) cc_final: 0.8487 (pmm)
REVERT: B   59 PHE cc_start: 0.8559 (m-10) cc_final: 0.7380 (t80)
REVERT: E  121 TYR cc_start: 0.8894 (t80) cc_final: 0.8672 (t80)
REVERT: E  165 MET cc_start: 0.8806 (ttp) cc_final: 0.8327 (ppp)
REVERT: F   66 MET cc_start: 0.9012 (mmm) cc_final: 0.8766 (mmm)
REVERT: F  108 MET cc_start: 0.9249 (mpp) cc_final: 0.8922 (mmm)
REVERT: F  113 ILE cc_start: 0.9620 (OUTLIER) cc_final: 0.9186 (mt)
REVERT: F  128 ASP cc_start: 0.8915 (m-30) cc_final: 0.8678 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 79
  average time/residue: 0.1651
  time to fit residues: 21.7175
Evaluate side-chains
  82 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  443 VAL
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  113 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 107 optimal weight:    9.9990
   chunk 73 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   chunk 108 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 101 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.047277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.036160 restraints weight = 77305.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.037188 restraints weight = 42353.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.037879 restraints weight = 28324.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10961  Z= 0.114
  Angle     :  0.626  12.979  14873  Z= 0.290
  Chirality :  0.040   0.321   1777
  Planarity :  0.003   0.038   1855
  Dihedral  :  3.242  19.673   1480
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.61 %
    Favored  : 81.14 %
  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:  1.85 (0.24), residues: 1322
  helix:  2.17 (0.18), residues: 849
  sheet: -0.76 (0.54), residues: 88
  loop : -0.41 (0.34), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.030   0.001   PHE B  64 
 TYR   0.018   0.001   TYR C  66 
 ARG   0.004   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  705)
  hydrogen bonds       : angle       3.64582 ( 2070)
  covalent geometry    : bond        0.00253 (10961)
  covalent geometry    : angle       0.62596 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8487 (m-90) cc_final: 0.7480 (t-100)
REVERT: A  165 MET cc_start: 0.9508 (ppp) cc_final: 0.9115 (ppp)
REVERT: A  337 MET cc_start: 0.8917 (mpp) cc_final: 0.8558 (pmm)
REVERT: A  400 MET cc_start: 0.9061 (tpp) cc_final: 0.8741 (tpp)
REVERT: A  450 LEU cc_start: 0.9561 (mp) cc_final: 0.9318 (mm)
REVERT: E  121 TYR cc_start: 0.8960 (t80) cc_final: 0.8664 (t80)
REVERT: E  165 MET cc_start: 0.8834 (ttp) cc_final: 0.8613 (ppp)
REVERT: F   66 MET cc_start: 0.9127 (mmm) cc_final: 0.8908 (mmp)
REVERT: F  108 MET cc_start: 0.9364 (mpp) cc_final: 0.8967 (mmm)
REVERT: F  113 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9187 (mt)
REVERT: F  128 ASP cc_start: 0.8951 (m-30) cc_final: 0.8641 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1887
  time to fit residues: 24.5702
Evaluate side-chains
  76 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 1.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain F residue  113 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 128 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.047109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.036004 restraints weight = 77402.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.037012 restraints weight = 42417.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.037708 restraints weight = 28462.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10961  Z= 0.128
  Angle     :  0.657  15.379  14873  Z= 0.301
  Chirality :  0.040   0.343   1777
  Planarity :  0.003   0.037   1855
  Dihedral  :  3.218  19.209   1480
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 17.87 %
    Favored  : 80.97 %
  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:  1.84 (0.24), residues: 1322
  helix:  2.16 (0.18), residues: 847
  sheet: -0.71 (0.54), residues: 88
  loop : -0.42 (0.34), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  95 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.027   0.001   PHE B  64 
 TYR   0.017   0.001   TYR C  66 
 ARG   0.004   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03034 (  705)
  hydrogen bonds       : angle       3.68257 ( 2070)
  covalent geometry    : bond        0.00290 (10961)
  covalent geometry    : angle       0.65723 (14873)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.8505 (m-90) cc_final: 0.7475 (t-100)
REVERT: A  165 MET cc_start: 0.9502 (ppp) cc_final: 0.9117 (ppp)
REVERT: A  337 MET cc_start: 0.8932 (mpp) cc_final: 0.8573 (pmm)
REVERT: A  400 MET cc_start: 0.9042 (tpp) cc_final: 0.8721 (tpp)
REVERT: A  450 LEU cc_start: 0.9571 (mp) cc_final: 0.9317 (mm)
REVERT: E  121 TYR cc_start: 0.8895 (t80) cc_final: 0.8619 (t80)
REVERT: E  165 MET cc_start: 0.8852 (ttp) cc_final: 0.8628 (ppp)
REVERT: F   66 MET cc_start: 0.9116 (mmm) cc_final: 0.8859 (mmp)
REVERT: F  108 MET cc_start: 0.9368 (mpp) cc_final: 0.8990 (mmm)
REVERT: F  113 ILE cc_start: 0.9650 (OUTLIER) cc_final: 0.9191 (mt)
REVERT: F  128 ASP cc_start: 0.8956 (m-30) cc_final: 0.8648 (p0)
  outliers start: 13
  outliers final: 10
  residues processed: 75
  average time/residue: 0.2077
  time to fit residues: 24.8649
Evaluate side-chains
  75 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  448 THR
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  599 THR
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  171 CYS
Chi-restraints excluded: chain F residue  113 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 120 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.047320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.036262 restraints weight = 76452.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.037288 restraints weight = 41866.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.037961 restraints weight = 28008.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10961  Z= 0.117
  Angle     :  0.640  14.911  14873  Z= 0.294
  Chirality :  0.040   0.339   1777
  Planarity :  0.003   0.038   1855
  Dihedral  :  3.177  19.161   1480
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.87 %
    Favored  : 80.61 %
  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:  1.90 (0.24), residues: 1322
  helix:  2.19 (0.18), residues: 848
  sheet: -0.61 (0.55), residues: 88
  loop : -0.37 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  14 
 HIS   0.003   0.001   HIS D 330 
 PHE   0.028   0.001   PHE B  64 
 TYR   0.018   0.001   TYR C  66 
 ARG   0.004   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02983 (  705)
  hydrogen bonds       : angle       3.65465 ( 2070)
  covalent geometry    : bond        0.00263 (10961)
  covalent geometry    : angle       0.63963 (14873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3946.01 seconds
wall clock time: 73 minutes 35.19 seconds (4415.19 seconds total)