Starting phenix.real_space_refine
on Tue Apr 29 19:59:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv7_50791/04_2025/9fv7_50791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv7_50791/04_2025/9fv7_50791.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/9fv7_50791/04_2025/9fv7_50791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv7_50791/04_2025/9fv7_50791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv7_50791/04_2025/9fv7_50791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv7_50791/04_2025/9fv7_50791.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=   0.001 sd=   0.007
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 6.77, per 1000 atoms: 0.77
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (122.4, 114.92, 136.68, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      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: 2.17
  Conformation dependent library (CDL) restraints added in 993.4 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 6 sheets defined
      67.5% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 23 through 47
      removed outlier: 4.054A  pdb=" N   ALA B  39 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.800A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 107
      removed outlier: 3.522A  pdb=" N   TRP B  66 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.936A  pdb=" N   PHE B 115 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASP B 117 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 129
      removed outlier: 3.885A  pdb=" N   LEU B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   SER B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 164
    Processing helix  chain 'B' and resid 164 through 206
      Proline residue:  B 176  - end of helix
      removed outlier: 3.596A  pdb=" N   SER B 206 " --> pdb=" O   GLN B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 219
      removed outlier: 4.036A  pdb=" N   MET B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LYS B 215 " --> pdb=" O   LEU B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 250
    Processing helix  chain 'B' and resid 250 through 269
      removed outlier: 3.644A  pdb=" N   ILE B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA B 262 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 303
      removed outlier: 4.380A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.958A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 324
      removed outlier: 3.718A  pdb=" N   SER B 324 " --> pdb=" O   THR B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 389
      removed outlier: 4.105A  pdb=" N   ILE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 3.750A  pdb=" N   MET B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 472
      removed outlier: 3.513A  pdb=" N   ASP B 471 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR B 472 " --> pdb=" O   GLY B 469 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 468 through 472'
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 514 through 527
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 571 through 580
    Processing helix  chain 'A' and resid 16 through 21
    Processing helix  chain 'A' and resid 23 through 53
      removed outlier: 3.706A  pdb=" N   ALA A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASP A  41 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 62 through 111
      Proline residue:  A  68  - end of helix
      removed outlier: 4.103A  pdb=" N   GLY A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 116
      removed outlier: 3.690A  pdb=" N   PHE A 115 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 129
      removed outlier: 3.920A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 163
      removed outlier: 4.176A  pdb=" N   GLU A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 197
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 198 through 213
      removed outlier: 3.583A  pdb=" N   SER A 206 " --> pdb=" O   GLN A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 250
      removed outlier: 3.552A  pdb=" N   LYS A 232 " --> pdb=" O   LYS A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 271
      removed outlier: 3.633A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 295
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 303 through 323
      removed outlier: 3.683A  pdb=" N   GLY A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 389
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 458
      removed outlier: 3.631A  pdb=" N   MET A 456 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 482 through 498
      removed outlier: 3.529A  pdb=" N   ILE A 489 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA A 490 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 538 through 544
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'B' and resid 365 through 366
      removed outlier: 3.577A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 532 through 535
      removed outlier: 6.851A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 419 through 422
      removed outlier: 4.031A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ILE B 503 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL B 422 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 349
      removed outlier: 5.295A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ASN A 361 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 421
      removed outlier: 3.988A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 503 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)

    555 hydrogen bonds defined for protein.
    1626 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.21

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2007
        1.33 -     1.46: 1868
        1.46 -     1.58: 4971
        1.58 -     1.70: 0
        1.70 -     1.83: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   GLU B 506 "
       pdb=" CA  GLU B 506 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.15e-02 7.56e+03 1.04e+01
  bond pdb=" N   LEU B 504 "
       pdb=" CA  LEU B 504 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.24e-02 6.50e+03 1.00e+01
  bond pdb=" N   LYS B  49 "
       pdb=" CA  LYS B  49 "
    ideal  model  delta    sigma   weight residual
    1.463  1.484 -0.021 6.90e-03 2.10e+04 8.84e+00
  bond pdb=" N   VAL A 375 "
       pdb=" CA  VAL A 375 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.29e-02 6.01e+03 8.58e+00
  bond pdb=" N   VAL A 372 "
       pdb=" CA  VAL A 372 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.20e-02 6.94e+03 8.54e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 11613
        2.62 -     5.25: 373
        5.25 -     7.87: 80
        7.87 -    10.49: 20
       10.49 -    13.11: 6
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   SER A 278 "
        pdb=" CA  SER A 278 "
        pdb=" C   SER A 278 "
      ideal   model   delta    sigma   weight residual
     114.56  102.49   12.07 1.27e+00 6.20e-01 9.04e+01
  angle pdb=" CA  GLU B 525 "
        pdb=" CB  GLU B 525 "
        pdb=" CG  GLU B 525 "
      ideal   model   delta    sigma   weight residual
     114.10  123.72   -9.62 2.00e+00 2.50e-01 2.32e+01
  angle pdb=" N   ALA A 293 "
        pdb=" CA  ALA A 293 "
        pdb=" C   ALA A 293 "
      ideal   model   delta    sigma   weight residual
     112.45  106.05    6.40 1.39e+00 5.18e-01 2.12e+01
  angle pdb=" CB  GLN B 134 "
        pdb=" CG  GLN B 134 "
        pdb=" CD  GLN B 134 "
      ideal   model   delta    sigma   weight residual
     112.60  120.29   -7.69 1.70e+00 3.46e-01 2.05e+01
  angle pdb=" CA  MET A 276 "
        pdb=" C   MET A 276 "
        pdb=" O   MET A 276 "
      ideal   model   delta    sigma   weight residual
     121.99  116.95    5.04 1.14e+00 7.69e-01 1.95e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 4601
       17.51 -    35.01: 672
       35.01 -    52.51: 147
       52.51 -    70.02: 29
       70.02 -    87.52: 5
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  THR B  19 "
           pdb=" C   THR B  19 "
           pdb=" N   ILE B  20 "
           pdb=" CA  ILE B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.30   27.70     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CA  LEU B  36 "
           pdb=" C   LEU B  36 "
           pdb=" N   ASN B  37 "
           pdb=" CA  ASN B  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.55  -25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ARG B  14 "
           pdb=" C   ARG B  14 "
           pdb=" N   ARG B  15 "
           pdb=" CA  ARG B  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.28   22.72     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1270
       0.095 -    0.190: 154
       0.190 -    0.284: 14
       0.284 -    0.379: 1
       0.379 -    0.474: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CB  ILE A 491 "
            pdb=" CA  ILE A 491 "
            pdb=" CG1 ILE A 491 "
            pdb=" CG2 ILE A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.47 2.00e-01 2.50e+01 5.62e+00
  chirality pdb=" CB  ILE A 170 "
            pdb=" CA  ILE A 170 "
            pdb=" CG1 ILE A 170 "
            pdb=" CG2 ILE A 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  LEU A 374 "
            pdb=" N   LEU A 374 "
            pdb=" C   LEU A 374 "
            pdb=" CB  LEU A 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 275 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.90e+00
        pdb=" C   VAL A 275 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   VAL A 275 "    0.019 2.00e-02 2.50e+03
        pdb=" N   MET A 276 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 133 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.74e+00
        pdb=" CD  GLU A 133 "   -0.048 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 133 "    0.018 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 133 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 213 "   -0.013 2.00e-02 2.50e+03   2.70e-02 7.28e+00
        pdb=" C   GLY B 213 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLY B 213 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   HIS B 214 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1748
        2.77 -     3.31: 8818
        3.31 -     3.84: 15106
        3.84 -     4.37: 17143
        4.37 -     4.90: 27918
  Nonbonded interactions: 70733
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 245 "
            pdb=" OG  SER B 249 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   SER A  86 "
            pdb=" OG  SER A  90 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   GLY A 141 "
            pdb=" OG1 THR A 145 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   SER B 248 "
            pdb=" OG  SER B 251 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   GLY B 141 "
            pdb=" OG1 THR B 145 "
     model   vdw
     2.313 3.040
  ... (remaining 70728 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             90.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.220
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  117.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
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      :  0.006   0.091   8950  Z= 0.356
  Angle     :  1.185  13.114  12092  Z= 0.662
  Chirality :  0.062   0.474   1440
  Planarity :  0.007   0.058   1532
  Dihedral  : 16.984  87.524   3326
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.14 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 30.89 %
    Favored  : 68.18 %
  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: -2.26 (0.22), residues: 1134
  helix: -1.41 (0.16), residues: 752
  sheet: -0.83 (0.75), residues: 48
  loop : -1.32 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 165 
 HIS   0.025   0.003   HIS A 576 
 PHE   0.021   0.002   PHE B 429 
 TYR   0.018   0.002   TYR B  83 
 ARG   0.006   0.000   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14476 (  555)
  hydrogen bonds       : angle       7.10912 ( 1626)
  covalent geometry    : bond        0.00608 ( 8950)
  covalent geometry    : angle       1.18477 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.8457 (tpt) cc_final: 0.7785 (tpt)
REVERT: B  133 GLU cc_start: 0.8894 (pt0) cc_final: 0.8383 (tm-30)
REVERT: B  134 GLN cc_start: 0.9246 (tp40) cc_final: 0.9039 (tp40)
REVERT: B  244 MET cc_start: 0.9008 (ttm) cc_final: 0.8751 (mtt)
REVERT: A   75 MET cc_start: 0.9065 (mmm) cc_final: 0.8840 (mmm)
REVERT: A  276 MET cc_start: 0.8414 (ttt) cc_final: 0.8068 (ttm)
REVERT: A  295 MET cc_start: 0.7965 (tpp) cc_final: 0.6932 (tpt)
REVERT: A  312 MET cc_start: 0.8107 (mmt) cc_final: 0.7797 (mmt)
REVERT: A  456 MET cc_start: 0.9236 (mpp) cc_final: 0.8915 (pmm)
REVERT: A  460 MET cc_start: 0.8790 (tpt) cc_final: 0.8120 (mtt)
REVERT: A  503 ILE cc_start: 0.9081 (mm) cc_final: 0.8769 (pt)
REVERT: A  504 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9109 (tt)
REVERT: A  578 MET cc_start: 0.9492 (mtt) cc_final: 0.8876 (tmm)
  outliers start: 9
  outliers final: 2
  residues processed: 150
  average time/residue: 0.1815
  time to fit residues: 39.4430
Evaluate side-chains
  131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 128
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0270
   chunk 57 optimal weight:    0.0470
   chunk 45 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0370
   chunk 65 optimal weight:    0.6980
   chunk 101 optimal weight:    0.2980
   overall best weight:    0.1814

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

Flipped N/Q/H residues before XYZ refinement:
B 427 HIS
A  37 ASN
A 405 HIS
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.084839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.067193 restraints weight = 37757.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.069303 restraints weight = 20733.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.070691 restraints weight = 13968.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8950  Z= 0.131
  Angle     :  0.626  10.895  12092  Z= 0.324
  Chirality :  0.041   0.171   1440
  Planarity :  0.004   0.045   1532
  Dihedral  :  5.275  46.260   1242
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 29.34 %
    Favored  : 67.77 %
  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: -0.55 (0.24), residues: 1134
  helix:  0.04 (0.18), residues: 746
  sheet: -0.24 (0.77), residues: 48
  loop : -1.04 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  66 
 HIS   0.005   0.001   HIS A 576 
 PHE   0.014   0.001   PHE B 429 
 TYR   0.014   0.001   TYR B 439 
 ARG   0.002   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04842 (  555)
  hydrogen bonds       : angle       5.12988 ( 1626)
  covalent geometry    : bond        0.00246 ( 8950)
  covalent geometry    : angle       0.62553 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 CYS cc_start: 0.9073 (m) cc_final: 0.8814 (m)
REVERT: B   98 MET cc_start: 0.8482 (tpt) cc_final: 0.7857 (tpt)
REVERT: B  133 GLU cc_start: 0.8665 (pt0) cc_final: 0.8395 (tm-30)
REVERT: B  134 GLN cc_start: 0.9283 (tp40) cc_final: 0.9062 (tp40)
REVERT: B  312 MET cc_start: 0.7950 (mmm) cc_final: 0.7593 (mmm)
REVERT: A   23 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7884 (m-80)
REVERT: A   80 ILE cc_start: 0.9189 (mm) cc_final: 0.8965 (tp)
REVERT: A  149 GLU cc_start: 0.8655 (mp0) cc_final: 0.8315 (mp0)
REVERT: A  164 SER cc_start: 0.7962 (m) cc_final: 0.7625 (p)
REVERT: A  276 MET cc_start: 0.8004 (ttt) cc_final: 0.7662 (ttt)
REVERT: A  295 MET cc_start: 0.8194 (tpp) cc_final: 0.7351 (tpp)
REVERT: A  312 MET cc_start: 0.8246 (mmt) cc_final: 0.7928 (mmt)
REVERT: A  460 MET cc_start: 0.8670 (tpt) cc_final: 0.8064 (mtt)
REVERT: A  503 ILE cc_start: 0.8893 (mm) cc_final: 0.8658 (pt)
REVERT: A  504 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9021 (tt)
REVERT: A  578 MET cc_start: 0.9451 (mtt) cc_final: 0.8882 (tmm)
  outliers start: 28
  outliers final: 16
  residues processed: 159
  average time/residue: 0.2169
  time to fit residues: 51.1548
Evaluate side-chains
  150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   56 PHE
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 52 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A 487 GLN
A 527 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.082296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.064534 restraints weight = 38461.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.066608 restraints weight = 20967.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.067970 restraints weight = 14121.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8950  Z= 0.140
  Angle     :  0.587   7.374  12092  Z= 0.306
  Chirality :  0.041   0.156   1440
  Planarity :  0.003   0.049   1532
  Dihedral  :  4.721  36.467   1241
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 27.27 %
    Favored  : 66.84 %
  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 (0.25), residues: 1134
  helix:  0.81 (0.19), residues: 750
  sheet:  0.08 (0.78), residues: 48
  loop : -0.88 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 576 
 PHE   0.017   0.001   PHE B 429 
 TYR   0.016   0.001   TYR B 439 
 ARG   0.004   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  555)
  hydrogen bonds       : angle       4.70444 ( 1626)
  covalent geometry    : bond        0.00282 ( 8950)
  covalent geometry    : angle       0.58730 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 134
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6974 (m-80)
REVERT: B   47 LEU cc_start: 0.9121 (tp) cc_final: 0.8817 (tp)
REVERT: B   80 ILE cc_start: 0.9290 (mm) cc_final: 0.9043 (tp)
REVERT: B   98 MET cc_start: 0.8479 (tpt) cc_final: 0.7873 (tpt)
REVERT: B  133 GLU cc_start: 0.8672 (pt0) cc_final: 0.8414 (tm-30)
REVERT: B  385 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9132 (tt)
REVERT: B  450 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9269 (tt)
REVERT: B  534 VAL cc_start: 0.9471 (t) cc_final: 0.9072 (p)
REVERT: A   13 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6746 (m-10)
REVERT: A   23 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7592 (m-80)
REVERT: A   80 ILE cc_start: 0.9249 (mm) cc_final: 0.9037 (tp)
REVERT: A  149 GLU cc_start: 0.8574 (mp0) cc_final: 0.8259 (mp0)
REVERT: A  276 MET cc_start: 0.7864 (ttt) cc_final: 0.7583 (ttm)
REVERT: A  295 MET cc_start: 0.8357 (tpp) cc_final: 0.7624 (tpp)
REVERT: A  312 MET cc_start: 0.8337 (mmt) cc_final: 0.8019 (mmt)
REVERT: A  392 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8644 (m-10)
REVERT: A  460 MET cc_start: 0.8687 (tpt) cc_final: 0.8085 (mtt)
REVERT: A  487 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8842 (tp-100)
REVERT: A  504 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9004 (tt)
REVERT: A  578 MET cc_start: 0.9431 (mtt) cc_final: 0.8856 (tmm)
  outliers start: 57
  outliers final: 35
  residues processed: 174
  average time/residue: 0.1678
  time to fit residues: 43.7149
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 126
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 92 optimal weight:   10.0000
   chunk 99 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.3182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.080970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.063044 restraints weight = 38473.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.065103 restraints weight = 20900.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.066466 restraints weight = 14047.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8950  Z= 0.149
  Angle     :  0.591   9.444  12092  Z= 0.306
  Chirality :  0.041   0.165   1440
  Planarity :  0.003   0.050   1532
  Dihedral  :  4.595  29.142   1241
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 26.86 %
    Favored  : 66.32 %
  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:  0.70 (0.25), residues: 1134
  helix:  1.10 (0.19), residues: 744
  sheet:  0.30 (0.81), residues: 44
  loop : -0.79 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 537 
 PHE   0.016   0.001   PHE B 429 
 TYR   0.015   0.001   TYR B 439 
 ARG   0.005   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04261 (  555)
  hydrogen bonds       : angle       4.58225 ( 1626)
  covalent geometry    : bond        0.00308 ( 8950)
  covalent geometry    : angle       0.59115 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 131
  time to evaluate  : 1.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7132 (m-80)
REVERT: B   47 LEU cc_start: 0.9121 (tp) cc_final: 0.8851 (tp)
REVERT: B   80 ILE cc_start: 0.9301 (mm) cc_final: 0.9079 (tp)
REVERT: B   98 MET cc_start: 0.8426 (tpt) cc_final: 0.7856 (tpt)
REVERT: B  133 GLU cc_start: 0.8671 (pt0) cc_final: 0.8390 (tm-30)
REVERT: B  385 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9130 (tt)
REVERT: B  534 VAL cc_start: 0.9493 (t) cc_final: 0.9135 (p)
REVERT: B  543 GLU cc_start: 0.9260 (mm-30) cc_final: 0.9019 (mm-30)
REVERT: A   13 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6842 (m-10)
REVERT: A   23 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7474 (m-80)
REVERT: A   80 ILE cc_start: 0.9285 (mm) cc_final: 0.9082 (tp)
REVERT: A  291 MET cc_start: 0.9408 (mmm) cc_final: 0.9070 (mpp)
REVERT: A  295 MET cc_start: 0.8357 (tpp) cc_final: 0.8098 (tpp)
REVERT: A  312 MET cc_start: 0.8436 (mmt) cc_final: 0.8178 (mmt)
REVERT: A  504 LEU cc_start: 0.9358 (tp) cc_final: 0.8975 (tp)
REVERT: A  574 GLN cc_start: 0.9554 (OUTLIER) cc_final: 0.9230 (pm20)
REVERT: A  578 MET cc_start: 0.9421 (mtt) cc_final: 0.8828 (tmm)
  outliers start: 66
  outliers final: 49
  residues processed: 180
  average time/residue: 0.2436
  time to fit residues: 66.3005
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 125
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  574 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 89 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 487 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.079119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.061032 restraints weight = 38553.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.063054 restraints weight = 20812.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.064397 restraints weight = 13974.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8950  Z= 0.184
  Angle     :  0.634   9.330  12092  Z= 0.327
  Chirality :  0.042   0.160   1440
  Planarity :  0.003   0.052   1532
  Dihedral  :  4.543  22.087   1239
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 27.89 %
    Favored  : 65.39 %
  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:  0.77 (0.25), residues: 1134
  helix:  1.09 (0.19), residues: 750
  sheet:  0.68 (0.82), residues: 42
  loop : -0.70 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.017   0.002   PHE B 429 
 TYR   0.021   0.001   TYR B 439 
 ARG   0.006   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04405 (  555)
  hydrogen bonds       : angle       4.59537 ( 1626)
  covalent geometry    : bond        0.00384 ( 8950)
  covalent geometry    : angle       0.63447 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 126
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8310 (m-80) cc_final: 0.8086 (t80)
REVERT: B   98 MET cc_start: 0.8385 (tpt) cc_final: 0.7820 (tpt)
REVERT: B  133 GLU cc_start: 0.8671 (pt0) cc_final: 0.8381 (tm-30)
REVERT: B  245 VAL cc_start: 0.9204 (t) cc_final: 0.8937 (p)
REVERT: B  276 MET cc_start: 0.8193 (tpp) cc_final: 0.7911 (mmm)
REVERT: B  534 VAL cc_start: 0.9543 (t) cc_final: 0.9208 (p)
REVERT: B  543 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9091 (mm-30)
REVERT: A   13 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7012 (m-10)
REVERT: A   23 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7547 (m-80)
REVERT: A   48 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9228 (tt)
REVERT: A   98 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8115 (tpt)
REVERT: A  149 GLU cc_start: 0.8795 (mp0) cc_final: 0.8323 (mp0)
REVERT: A  291 MET cc_start: 0.9412 (mmm) cc_final: 0.9036 (mpp)
REVERT: A  295 MET cc_start: 0.8464 (tpp) cc_final: 0.8130 (tpp)
REVERT: A  312 MET cc_start: 0.8607 (mmt) cc_final: 0.8395 (mmt)
REVERT: A  487 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8827 (tp-100)
REVERT: A  504 LEU cc_start: 0.9394 (tp) cc_final: 0.9006 (tp)
REVERT: A  578 MET cc_start: 0.9369 (mtt) cc_final: 0.9156 (tmm)
  outliers start: 65
  outliers final: 52
  residues processed: 175
  average time/residue: 0.1583
  time to fit residues: 42.1093
Evaluate side-chains
  176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 119
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  374 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 55 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.079508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.061594 restraints weight = 38249.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.063600 restraints weight = 20451.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.064964 restraints weight = 13727.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8950  Z= 0.156
  Angle     :  0.622   9.857  12092  Z= 0.319
  Chirality :  0.042   0.208   1440
  Planarity :  0.003   0.053   1532
  Dihedral  :  4.519  21.204   1239
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 29.44 %
    Favored  : 64.88 %
  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:  0.79 (0.25), residues: 1134
  helix:  1.13 (0.19), residues: 746
  sheet:  0.54 (0.84), residues: 44
  loop : -0.72 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.012   0.001   PHE A 116 
 TYR   0.018   0.001   TYR B 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04271 (  555)
  hydrogen bonds       : angle       4.56284 ( 1626)
  covalent geometry    : bond        0.00332 ( 8950)
  covalent geometry    : angle       0.62239 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 124
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8293 (m-80) cc_final: 0.8082 (t80)
REVERT: B   98 MET cc_start: 0.8348 (tpt) cc_final: 0.7782 (tpt)
REVERT: B  111 MET cc_start: 0.9121 (tmm) cc_final: 0.8152 (tmm)
REVERT: B  133 GLU cc_start: 0.8659 (pt0) cc_final: 0.8367 (tm-30)
REVERT: B  245 VAL cc_start: 0.9223 (t) cc_final: 0.8958 (p)
REVERT: B  534 VAL cc_start: 0.9536 (t) cc_final: 0.9206 (p)
REVERT: B  543 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9086 (mm-30)
REVERT: A   13 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6988 (m-10)
REVERT: A   23 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7578 (m-80)
REVERT: A   48 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9251 (tt)
REVERT: A   98 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8055 (tpt)
REVERT: A  149 GLU cc_start: 0.8820 (mp0) cc_final: 0.8285 (mp0)
REVERT: A  291 MET cc_start: 0.9448 (mmm) cc_final: 0.9078 (mpp)
REVERT: A  295 MET cc_start: 0.8465 (tpp) cc_final: 0.8144 (tpp)
REVERT: A  312 MET cc_start: 0.8599 (mmt) cc_final: 0.8397 (mmt)
REVERT: A  504 LEU cc_start: 0.9395 (tp) cc_final: 0.9031 (tp)
REVERT: A  574 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.9378 (pm20)
REVERT: A  578 MET cc_start: 0.9336 (mtt) cc_final: 0.9029 (tmm)
  outliers start: 55
  outliers final: 43
  residues processed: 164
  average time/residue: 0.1801
  time to fit residues: 44.8426
Evaluate side-chains
  167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 119
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  574 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 104 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN
A 487 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.080555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062853 restraints weight = 38355.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.064880 restraints weight = 20300.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.066277 restraints weight = 13529.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8950  Z= 0.130
  Angle     :  0.613   9.634  12092  Z= 0.310
  Chirality :  0.041   0.175   1440
  Planarity :  0.003   0.053   1532
  Dihedral  :  4.435  22.942   1239
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 28.72 %
    Favored  : 65.39 %
  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:  0.91 (0.25), residues: 1134
  helix:  1.24 (0.19), residues: 742
  sheet:  0.76 (0.86), residues: 44
  loop : -0.70 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 537 
 PHE   0.011   0.001   PHE A 116 
 TYR   0.017   0.001   TYR B 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04064 (  555)
  hydrogen bonds       : angle       4.45358 ( 1626)
  covalent geometry    : bond        0.00274 ( 8950)
  covalent geometry    : angle       0.61348 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 127
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8279 (m-80) cc_final: 0.8076 (t80)
REVERT: B   98 MET cc_start: 0.8310 (tpt) cc_final: 0.7758 (tpt)
REVERT: B  111 MET cc_start: 0.9078 (tmm) cc_final: 0.8768 (tmm)
REVERT: B  133 GLU cc_start: 0.8682 (pt0) cc_final: 0.8354 (tm-30)
REVERT: B  200 MET cc_start: 0.8600 (mmp) cc_final: 0.7987 (mmm)
REVERT: B  244 MET cc_start: 0.8786 (ttm) cc_final: 0.8420 (ttp)
REVERT: B  276 MET cc_start: 0.8244 (tpp) cc_final: 0.7917 (tpp)
REVERT: B  385 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9164 (tt)
REVERT: B  534 VAL cc_start: 0.9513 (t) cc_final: 0.9195 (p)
REVERT: A   13 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6911 (m-10)
REVERT: A   23 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7560 (m-80)
REVERT: A  143 LEU cc_start: 0.9281 (tp) cc_final: 0.9049 (tt)
REVERT: A  149 GLU cc_start: 0.8735 (mp0) cc_final: 0.8249 (mp0)
REVERT: A  291 MET cc_start: 0.9454 (mmm) cc_final: 0.9059 (mpp)
REVERT: A  295 MET cc_start: 0.8434 (tpp) cc_final: 0.8103 (tpp)
REVERT: A  460 MET cc_start: 0.8664 (tpt) cc_final: 0.8007 (mtp)
REVERT: A  487 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8756 (tp40)
REVERT: A  504 LEU cc_start: 0.9342 (tp) cc_final: 0.8987 (tp)
  outliers start: 57
  outliers final: 44
  residues processed: 170
  average time/residue: 0.1549
  time to fit residues: 39.9066
Evaluate side-chains
  167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 119
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  534 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 99 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 487 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.079815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.061794 restraints weight = 39054.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.063852 restraints weight = 20991.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.065230 restraints weight = 14025.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8950  Z= 0.152
  Angle     :  0.647  10.213  12092  Z= 0.327
  Chirality :  0.041   0.139   1440
  Planarity :  0.003   0.052   1532
  Dihedral  :  4.472  21.755   1239
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 28.82 %
    Favored  : 65.08 %
  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:  0.87 (0.25), residues: 1134
  helix:  1.18 (0.19), residues: 744
  sheet:  0.78 (0.86), residues: 44
  loop : -0.67 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.013   0.001   PHE A 116 
 TYR   0.019   0.001   TYR B 439 
 ARG   0.006   0.000   ARG A 486 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04162 (  555)
  hydrogen bonds       : angle       4.48427 ( 1626)
  covalent geometry    : bond        0.00325 ( 8950)
  covalent geometry    : angle       0.64701 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 121
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8304 (m-80) cc_final: 0.8084 (t80)
REVERT: B   98 MET cc_start: 0.8304 (tpt) cc_final: 0.7749 (tpt)
REVERT: B  108 MET cc_start: 0.9272 (mmm) cc_final: 0.8994 (mmt)
REVERT: B  111 MET cc_start: 0.9147 (tmm) cc_final: 0.8754 (tmm)
REVERT: B  133 GLU cc_start: 0.8692 (pt0) cc_final: 0.8379 (tm-30)
REVERT: B  276 MET cc_start: 0.8292 (tpp) cc_final: 0.8012 (tpp)
REVERT: B  385 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9188 (tt)
REVERT: B  534 VAL cc_start: 0.9528 (t) cc_final: 0.9187 (p)
REVERT: A   13 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6954 (m-10)
REVERT: A   23 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7578 (m-80)
REVERT: A   98 MET cc_start: 0.8414 (tpt) cc_final: 0.7975 (tpt)
REVERT: A  143 LEU cc_start: 0.9295 (tp) cc_final: 0.9057 (tt)
REVERT: A  210 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8299 (tpp)
REVERT: A  295 MET cc_start: 0.8434 (tpp) cc_final: 0.8102 (tpp)
REVERT: A  312 MET cc_start: 0.8557 (mmt) cc_final: 0.8226 (mmt)
REVERT: A  460 MET cc_start: 0.8694 (tpt) cc_final: 0.8368 (tpt)
REVERT: A  504 LEU cc_start: 0.9331 (tp) cc_final: 0.8975 (tp)
  outliers start: 59
  outliers final: 46
  residues processed: 166
  average time/residue: 0.1539
  time to fit residues: 38.8853
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 119
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  374 LEU
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  210 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  499 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0470
   chunk 79 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.7282

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
** A 487 GLN ** 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 = 0.3678 r_free = 0.3678 target = 0.081187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.063643 restraints weight = 38221.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.065706 restraints weight = 20357.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.067091 restraints weight = 13554.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8950  Z= 0.128
  Angle     :  0.649  10.454  12092  Z= 0.321
  Chirality :  0.041   0.147   1440
  Planarity :  0.003   0.052   1532
  Dihedral  :  4.410  23.379   1238
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 30.37 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.91 (0.26), residues: 1134
  helix:  1.21 (0.19), residues: 742
  sheet:  0.96 (0.87), residues: 44
  loop : -0.67 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 537 
 PHE   0.016   0.001   PHE A 116 
 TYR   0.016   0.001   TYR B 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  555)
  hydrogen bonds       : angle       4.40157 ( 1626)
  covalent geometry    : bond        0.00271 ( 8950)
  covalent geometry    : angle       0.64932 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 127
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8291 (m-80) cc_final: 0.8088 (t80)
REVERT: B   98 MET cc_start: 0.8283 (tpt) cc_final: 0.7701 (tpt)
REVERT: B  111 MET cc_start: 0.9145 (tmm) cc_final: 0.8769 (tmm)
REVERT: B  133 GLU cc_start: 0.8697 (pt0) cc_final: 0.8366 (tm-30)
REVERT: B  200 MET cc_start: 0.8519 (mmp) cc_final: 0.8035 (mmm)
REVERT: B  244 MET cc_start: 0.8711 (ttm) cc_final: 0.8379 (ttp)
REVERT: B  276 MET cc_start: 0.8240 (tpp) cc_final: 0.7875 (tpp)
REVERT: B  385 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9187 (tt)
REVERT: B  534 VAL cc_start: 0.9501 (t) cc_final: 0.9172 (p)
REVERT: A   13 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6875 (m-10)
REVERT: A   23 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7523 (m-80)
REVERT: A  143 LEU cc_start: 0.9242 (tp) cc_final: 0.8949 (tt)
REVERT: A  160 MET cc_start: 0.8804 (mmt) cc_final: 0.8565 (mtt)
REVERT: A  244 MET cc_start: 0.8650 (mtp) cc_final: 0.8396 (mtp)
REVERT: A  295 MET cc_start: 0.8418 (tpp) cc_final: 0.8079 (tpp)
REVERT: A  312 MET cc_start: 0.8506 (mmt) cc_final: 0.8156 (mmt)
REVERT: A  460 MET cc_start: 0.8625 (tpt) cc_final: 0.8316 (tpt)
REVERT: A  504 LEU cc_start: 0.9274 (tp) cc_final: 0.8959 (tp)
  outliers start: 48
  outliers final: 42
  residues processed: 160
  average time/residue: 0.1686
  time to fit residues: 41.2650
Evaluate side-chains
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 119
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  534 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 95 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 GLN ** 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 = 0.3682 r_free = 0.3682 target = 0.081385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.063567 restraints weight = 38375.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.065619 restraints weight = 20676.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.067018 restraints weight = 13872.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8950  Z= 0.129
  Angle     :  0.654  11.317  12092  Z= 0.323
  Chirality :  0.041   0.150   1440
  Planarity :  0.003   0.052   1532
  Dihedral  :  4.387  22.693   1238
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 30.99 %
    Favored  : 64.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.95 (0.26), residues: 1134
  helix:  1.23 (0.19), residues: 744
  sheet:  0.98 (0.87), residues: 44
  loop : -0.63 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 537 
 PHE   0.015   0.001   PHE A 116 
 TYR   0.015   0.001   TYR B 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03998 (  555)
  hydrogen bonds       : angle       4.39979 ( 1626)
  covalent geometry    : bond        0.00275 ( 8950)
  covalent geometry    : angle       0.65425 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 121
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8256 (m-80) cc_final: 0.8048 (t80)
REVERT: B   98 MET cc_start: 0.8309 (tpt) cc_final: 0.7733 (tpt)
REVERT: B  111 MET cc_start: 0.9112 (tmm) cc_final: 0.8770 (tmm)
REVERT: B  133 GLU cc_start: 0.8695 (pt0) cc_final: 0.8378 (tm-30)
REVERT: B  276 MET cc_start: 0.8227 (tpp) cc_final: 0.7857 (tpp)
REVERT: B  385 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9176 (tt)
REVERT: B  466 MET cc_start: 0.7583 (pmm) cc_final: 0.7329 (pmm)
REVERT: B  534 VAL cc_start: 0.9502 (t) cc_final: 0.9175 (p)
REVERT: A   13 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6850 (m-10)
REVERT: A   23 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7535 (m-80)
REVERT: A  143 LEU cc_start: 0.9267 (tp) cc_final: 0.8949 (tt)
REVERT: A  244 MET cc_start: 0.8581 (mtp) cc_final: 0.8312 (mtp)
REVERT: A  295 MET cc_start: 0.8410 (tpp) cc_final: 0.8060 (tpp)
REVERT: A  312 MET cc_start: 0.8511 (mmt) cc_final: 0.8207 (mmt)
REVERT: A  460 MET cc_start: 0.8624 (tpt) cc_final: 0.8311 (tpt)
  outliers start: 47
  outliers final: 41
  residues processed: 155
  average time/residue: 0.1591
  time to fit residues: 37.5173
Evaluate side-chains
  161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 117
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  534 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 111 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.079614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.061707 restraints weight = 38551.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.063728 restraints weight = 20642.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.065072 restraints weight = 13895.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8950  Z= 0.166
  Angle     :  0.672  10.009  12092  Z= 0.336
  Chirality :  0.042   0.151   1440
  Planarity :  0.003   0.053   1532
  Dihedral  :  4.418  21.713   1238
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 30.37 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.91 (0.26), residues: 1134
  helix:  1.21 (0.19), residues: 744
  sheet:  0.86 (0.86), residues: 44
  loop : -0.66 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 537 
 PHE   0.017   0.001   PHE A 116 
 TYR   0.018   0.001   TYR B 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  555)
  hydrogen bonds       : angle       4.46437 ( 1626)
  covalent geometry    : bond        0.00356 ( 8950)
  covalent geometry    : angle       0.67161 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3656.36 seconds
wall clock time: 65 minutes 22.43 seconds (3922.43 seconds total)