Starting phenix.real_space_refine
on Mon May 12 09:55:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv7_50791/05_2025/9fv7_50791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv7_50791/05_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_50791/05_2025/9fv7_50791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv7_50791/05_2025/9fv7_50791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv7_50791/05_2025/9fv7_50791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv7_50791/05_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-5687/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: 6.53, per 1000 atoms: 0.74
  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: 2.34
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.94
  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: 2.64

  Time building geometry restraints manager: 2.74 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: 0.05
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:             4.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     24.740
  Find NCS groups from input model:        0.300
  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:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.610
-------------------------------------------------------------------------------
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  : 0.998 
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: 0.1768
  time to fit residues: 38.3143
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  : 0.939 
-------------------------------------------------------------------------------
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 = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.067184 restraints weight = 37757.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.069289 restraints weight = 20785.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.070695 restraints weight = 13993.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
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  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 CYS cc_start: 0.9074 (m) cc_final: 0.8815 (m)
REVERT: B   98 MET cc_start: 0.8481 (tpt) cc_final: 0.7858 (tpt)
REVERT: B  133 GLU cc_start: 0.8664 (pt0) cc_final: 0.8394 (tm-30)
REVERT: B  134 GLN cc_start: 0.9281 (tp40) cc_final: 0.9062 (tp40)
REVERT: B  312 MET cc_start: 0.7948 (mmm) cc_final: 0.7594 (mmm)
REVERT: A   23 PHE cc_start: 0.8528 (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: 0.8651 (mp0) cc_final: 0.8311 (mp0)
REVERT: A  164 SER cc_start: 0.7963 (m) cc_final: 0.7625 (p)
REVERT: A  276 MET cc_start: 0.8001 (ttt) cc_final: 0.7659 (ttt)
REVERT: A  295 MET cc_start: 0.8193 (tpp) cc_final: 0.7351 (tpp)
REVERT: A  312 MET cc_start: 0.8247 (mmt) cc_final: 0.7929 (mmt)
REVERT: A  460 MET cc_start: 0.8666 (tpt) cc_final: 0.8062 (mtt)
REVERT: A  503 ILE cc_start: 0.8893 (mm) cc_final: 0.8657 (pt)
REVERT: A  504 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9021 (tt)
REVERT: A  578 MET cc_start: 0.9454 (mtt) cc_final: 0.8885 (tmm)
  outliers start: 28
  outliers final: 16
  residues processed: 159
  average time/residue: 0.1672
  time to fit residues: 39.8291
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  : 0.921 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3659 r_free = 0.3659 target = 0.080190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.062131 restraints weight = 38786.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.064197 restraints weight = 21105.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.065534 restraints weight = 14221.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8950  Z= 0.178
  Angle     :  0.627   7.510  12092  Z= 0.329
  Chirality :  0.042   0.177   1440
  Planarity :  0.004   0.051   1532
  Dihedral  :  4.801  35.626   1241
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 25.62 %
    Favored  : 66.94 %
  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:  0.38 (0.25), residues: 1134
  helix:  0.79 (0.19), residues: 750
  sheet:  0.07 (0.77), residues: 48
  loop : -0.78 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 537 
 PHE   0.023   0.002   PHE B 429 
 TYR   0.019   0.001   TYR B 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04730 (  555)
  hydrogen bonds       : angle       4.78364 ( 1626)
  covalent geometry    : bond        0.00365 ( 8950)
  covalent geometry    : angle       0.62678 (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
  200 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 128
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7119 (m-80)
REVERT: B   47 LEU cc_start: 0.9106 (tp) cc_final: 0.8879 (tp)
REVERT: B   80 ILE cc_start: 0.9333 (mm) cc_final: 0.9080 (tp)
REVERT: B   98 MET cc_start: 0.8482 (tpt) cc_final: 0.7881 (tpt)
REVERT: B  133 GLU cc_start: 0.8660 (pt0) cc_final: 0.8441 (tm-30)
REVERT: B  134 GLN cc_start: 0.9313 (tp40) cc_final: 0.9084 (tp40)
REVERT: B  534 VAL cc_start: 0.9501 (t) cc_final: 0.9114 (p)
REVERT: A   13 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.6928 (m-10)
REVERT: A   23 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7511 (m-80)
REVERT: A   75 MET cc_start: 0.8884 (mmm) cc_final: 0.8680 (mmm)
REVERT: A  149 GLU cc_start: 0.8574 (mp0) cc_final: 0.8297 (mp0)
REVERT: A  295 MET cc_start: 0.8361 (tpp) cc_final: 0.8096 (tpp)
REVERT: A  312 MET cc_start: 0.8462 (mmt) cc_final: 0.8100 (mmt)
REVERT: A  392 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8648 (m-10)
REVERT: A  487 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8840 (tp-100)
REVERT: A  504 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9022 (tt)
REVERT: A  578 MET cc_start: 0.9407 (mtt) cc_final: 0.8824 (tmm)
  outliers start: 72
  outliers final: 45
  residues processed: 181
  average time/residue: 0.1618
  time to fit residues: 43.6700
Evaluate side-chains
  174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 123
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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   45 LEU
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  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  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  428 LEU
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   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  109 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  169 ILE
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  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:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 92 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0770
   chunk 2 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.082050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.064631 restraints weight = 38553.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.066649 restraints weight = 20913.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.068014 restraints weight = 14083.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8950  Z= 0.126
  Angle     :  0.593   9.769  12092  Z= 0.303
  Chirality :  0.041   0.158   1440
  Planarity :  0.003   0.051   1532
  Dihedral  :  4.615  29.232   1241
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 28.20 %
    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:  0.65 (0.25), residues: 1134
  helix:  1.04 (0.19), residues: 744
  sheet:  0.37 (0.82), residues: 44
  loop : -0.78 (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 A 576 
 PHE   0.012   0.001   PHE B 429 
 TYR   0.023   0.001   TYR A 439 
 ARG   0.006   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04175 (  555)
  hydrogen bonds       : angle       4.56086 ( 1626)
  covalent geometry    : bond        0.00260 ( 8950)
  covalent geometry    : angle       0.59336 (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
  187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 134
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8079 (m-80)
REVERT: B   47 LEU cc_start: 0.9086 (tp) cc_final: 0.8829 (tp)
REVERT: B   80 ILE cc_start: 0.9299 (mm) cc_final: 0.9081 (tp)
REVERT: B   98 MET cc_start: 0.8390 (tpt) cc_final: 0.7807 (tpt)
REVERT: B  133 GLU cc_start: 0.8658 (pt0) cc_final: 0.8395 (tm-30)
REVERT: B  534 VAL cc_start: 0.9466 (t) cc_final: 0.9108 (p)
REVERT: B  543 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8981 (mm-30)
REVERT: A   13 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.6776 (m-10)
REVERT: A   23 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7443 (m-80)
REVERT: A  149 GLU cc_start: 0.8586 (mp0) cc_final: 0.8349 (mp0)
REVERT: A  276 MET cc_start: 0.7359 (ttt) cc_final: 0.7130 (ttm)
REVERT: A  295 MET cc_start: 0.8330 (tpp) cc_final: 0.8087 (tpp)
REVERT: A  312 MET cc_start: 0.8406 (mmt) cc_final: 0.8141 (mmt)
REVERT: A  504 LEU cc_start: 0.9358 (tp) cc_final: 0.8982 (tp)
REVERT: A  574 GLN cc_start: 0.9546 (OUTLIER) cc_final: 0.9216 (pm20)
REVERT: A  578 MET cc_start: 0.9405 (mtt) cc_final: 0.8805 (tmm)
  outliers start: 53
  outliers final: 32
  residues processed: 174
  average time/residue: 0.1578
  time to fit residues: 40.8813
Evaluate side-chains
  161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   36 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  174 LEU
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  347 VAL
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   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  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  407 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  456 MET
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:    0.7980
   chunk 35 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.080863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062775 restraints weight = 38491.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.064847 restraints weight = 20715.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.066250 restraints weight = 13948.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8950  Z= 0.139
  Angle     :  0.602   9.727  12092  Z= 0.307
  Chirality :  0.041   0.146   1440
  Planarity :  0.003   0.053   1532
  Dihedral  :  4.405  20.648   1239
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 28.51 %
    Favored  : 65.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.25), residues: 1134
  helix:  1.16 (0.19), residues: 744
  sheet:  0.43 (0.84), residues: 44
  loop : -0.68 (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   0.012   0.001   PHE B 429 
 TYR   0.022   0.001   TYR A 439 
 ARG   0.008   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04140 (  555)
  hydrogen bonds       : angle       4.47719 ( 1626)
  covalent geometry    : bond        0.00291 ( 8950)
  covalent geometry    : angle       0.60157 (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
  176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 121
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8156 (m-80)
REVERT: B   47 LEU cc_start: 0.9074 (tp) cc_final: 0.8842 (tp)
REVERT: B   67 MET cc_start: 0.9145 (mmm) cc_final: 0.8741 (tpp)
REVERT: B   80 ILE cc_start: 0.9305 (mm) cc_final: 0.9096 (tp)
REVERT: B   98 MET cc_start: 0.8364 (tpt) cc_final: 0.7794 (tpt)
REVERT: B  133 GLU cc_start: 0.8658 (pt0) cc_final: 0.8391 (tm-30)
REVERT: B  245 VAL cc_start: 0.9192 (t) cc_final: 0.8924 (p)
REVERT: B  276 MET cc_start: 0.8047 (tpp) cc_final: 0.7679 (tpp)
REVERT: B  385 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9139 (tt)
REVERT: B  534 VAL cc_start: 0.9511 (t) cc_final: 0.9167 (p)
REVERT: B  543 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9067 (mm-30)
REVERT: A   13 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6944 (m-10)
REVERT: A   23 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7492 (m-80)
REVERT: A   75 MET cc_start: 0.8809 (mmm) cc_final: 0.8597 (mmm)
REVERT: A  159 MET cc_start: 0.8992 (tpp) cc_final: 0.8768 (tpp)
REVERT: A  276 MET cc_start: 0.7458 (ttt) cc_final: 0.7132 (ttm)
REVERT: A  291 MET cc_start: 0.9400 (mmm) cc_final: 0.9036 (mpp)
REVERT: A  295 MET cc_start: 0.8381 (tpp) cc_final: 0.8082 (tpp)
REVERT: A  312 MET cc_start: 0.8473 (mmt) cc_final: 0.8270 (mmt)
REVERT: A  395 ILE cc_start: 0.7565 (mt) cc_final: 0.7147 (mt)
REVERT: A  487 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8886 (tp40)
REVERT: A  504 LEU cc_start: 0.9365 (tp) cc_final: 0.8999 (tp)
REVERT: A  578 MET cc_start: 0.9378 (mtt) cc_final: 0.9161 (tmm)
  outliers start: 55
  outliers final: 43
  residues processed: 160
  average time/residue: 0.1711
  time to fit residues: 40.6355
Evaluate side-chains
  165 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 117
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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   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  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  390 THR
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   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  225 VAL
Chi-restraints excluded: chain A residue  239 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  422 VAL
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:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:   30.0000
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 101 optimal weight:    0.0970
   chunk 106 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6578

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.081775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.063797 restraints weight = 38344.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.065882 restraints weight = 20701.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.067297 restraints weight = 13928.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2865

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= 0.122
  Angle     :  0.590  10.230  12092  Z= 0.300
  Chirality :  0.041   0.144   1440
  Planarity :  0.003   0.052   1532
  Dihedral  :  4.353  19.941   1239
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 28.51 %
    Favored  : 65.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1134
  helix:  1.26 (0.19), residues: 744
  sheet:  0.53 (0.86), residues: 44
  loop : -0.65 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.009   0.001   PHE A 116 
 TYR   0.020   0.001   TYR A 439 
 ARG   0.006   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  555)
  hydrogen bonds       : angle       4.39474 ( 1626)
  covalent geometry    : bond        0.00254 ( 8950)
  covalent geometry    : angle       0.59038 (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
  182 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 128
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7115 (m-80)
REVERT: B   43 PHE cc_start: 0.8213 (m-80) cc_final: 0.7981 (t80)
REVERT: B   47 LEU cc_start: 0.9085 (tp) cc_final: 0.8844 (tp)
REVERT: B   80 ILE cc_start: 0.9281 (mm) cc_final: 0.9078 (tp)
REVERT: B   98 MET cc_start: 0.8316 (tpt) cc_final: 0.7777 (tpt)
REVERT: B  111 MET cc_start: 0.9058 (tmm) cc_final: 0.8159 (tmm)
REVERT: B  133 GLU cc_start: 0.8667 (pt0) cc_final: 0.8378 (tm-30)
REVERT: B  276 MET cc_start: 0.8042 (tpp) cc_final: 0.7780 (mmm)
REVERT: B  385 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9152 (tt)
REVERT: B  534 VAL cc_start: 0.9507 (t) cc_final: 0.9173 (p)
REVERT: B  543 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9092 (mm-30)
REVERT: A   13 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6918 (m-10)
REVERT: A   23 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7498 (m-80)
REVERT: A  276 MET cc_start: 0.7369 (ttt) cc_final: 0.7104 (ttm)
REVERT: A  291 MET cc_start: 0.9420 (mmm) cc_final: 0.9069 (mpp)
REVERT: A  295 MET cc_start: 0.8363 (tpp) cc_final: 0.8066 (tpp)
REVERT: A  460 MET cc_start: 0.8631 (tpt) cc_final: 0.7954 (mtp)
REVERT: A  504 LEU cc_start: 0.9345 (tp) cc_final: 0.8990 (tp)
REVERT: A  578 MET cc_start: 0.9368 (mtt) cc_final: 0.9041 (tmm)
  outliers start: 54
  outliers final: 42
  residues processed: 165
  average time/residue: 0.1594
  time to fit residues: 39.5612
Evaluate side-chains
  166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 120
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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   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  174 LEU
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  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  390 THR
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   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   77 LEU
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0980
   chunk 104 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   chunk 70 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3705 r_free = 0.3705 target = 0.082410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.064473 restraints weight = 38721.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.066562 restraints weight = 20989.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.067964 restraints weight = 14106.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8950  Z= 0.116
  Angle     :  0.593  10.335  12092  Z= 0.298
  Chirality :  0.040   0.142   1440
  Planarity :  0.003   0.053   1532
  Dihedral  :  4.262  19.909   1239
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 29.24 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1134
  helix:  1.36 (0.19), residues: 742
  sheet:  0.62 (0.86), residues: 44
  loop : -0.65 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 537 
 PHE   0.009   0.001   PHE A 116 
 TYR   0.019   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  555)
  hydrogen bonds       : angle       4.31646 ( 1626)
  covalent geometry    : bond        0.00242 ( 8950)
  covalent geometry    : angle       0.59340 (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
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 127
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7222 (m-80)
REVERT: B   43 PHE cc_start: 0.8189 (m-80) cc_final: 0.7975 (t80)
REVERT: B   80 ILE cc_start: 0.9276 (mm) cc_final: 0.9068 (tp)
REVERT: B   98 MET cc_start: 0.8309 (tpt) cc_final: 0.7724 (tpt)
REVERT: B  111 MET cc_start: 0.9060 (tmm) cc_final: 0.8680 (tmm)
REVERT: B  133 GLU cc_start: 0.8674 (pt0) cc_final: 0.8369 (tm-30)
REVERT: B  200 MET cc_start: 0.8401 (mmp) cc_final: 0.8106 (mmm)
REVERT: B  276 MET cc_start: 0.8069 (tpp) cc_final: 0.7766 (mmm)
REVERT: B  385 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9146 (tt)
REVERT: B  466 MET cc_start: 0.7650 (pmm) cc_final: 0.7446 (pmm)
REVERT: B  534 VAL cc_start: 0.9490 (t) cc_final: 0.9153 (p)
REVERT: B  548 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (mp)
REVERT: A   13 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6799 (m-10)
REVERT: A   23 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7471 (m-80)
REVERT: A   98 MET cc_start: 0.8406 (tpt) cc_final: 0.7700 (tpt)
REVERT: A  265 PHE cc_start: 0.8994 (t80) cc_final: 0.8708 (t80)
REVERT: A  291 MET cc_start: 0.9401 (mmm) cc_final: 0.9054 (mpp)
REVERT: A  295 MET cc_start: 0.8369 (tpp) cc_final: 0.8056 (tpp)
REVERT: A  312 MET cc_start: 0.8458 (mmt) cc_final: 0.8227 (mmt)
REVERT: A  460 MET cc_start: 0.8642 (tpt) cc_final: 0.7969 (mtp)
REVERT: A  487 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8858 (tp40)
REVERT: A  504 LEU cc_start: 0.9302 (tp) cc_final: 0.8986 (tp)
  outliers start: 51
  outliers final: 40
  residues processed: 164
  average time/residue: 0.1562
  time to fit residues: 38.5999
Evaluate side-chains
  167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 121
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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   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  174 LEU
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  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 B residue  548 ILE
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   61 ARG
Chi-restraints excluded: chain A residue   77 LEU
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  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  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:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 102 optimal weight:    0.2980
   chunk 99 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
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 209 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 = 0.3622 r_free = 0.3622 target = 0.078515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.060484 restraints weight = 39378.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.062508 restraints weight = 21112.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.063854 restraints weight = 14131.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   8950  Z= 0.213
  Angle     :  0.684   9.482  12092  Z= 0.349
  Chirality :  0.042   0.142   1440
  Planarity :  0.004   0.053   1532
  Dihedral  :  4.498  24.129   1239
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 29.34 %
    Favored  : 65.19 %
  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:  0.89 (0.25), residues: 1134
  helix:  1.21 (0.19), residues: 746
  sheet:  0.91 (0.86), residues: 42
  loop : -0.71 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  66 
 HIS   0.005   0.001   HIS B 214 
 PHE   0.020   0.002   PHE B  23 
 TYR   0.024   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04472 (  555)
  hydrogen bonds       : angle       4.58627 ( 1626)
  covalent geometry    : bond        0.00444 ( 8950)
  covalent geometry    : angle       0.68381 (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
  168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 115
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8273 (m-80) cc_final: 0.8047 (t80)
REVERT: B   67 MET cc_start: 0.9327 (mmm) cc_final: 0.9074 (tpp)
REVERT: B   98 MET cc_start: 0.8365 (tpt) cc_final: 0.7821 (tpt)
REVERT: B  111 MET cc_start: 0.9116 (tmm) cc_final: 0.8714 (tmm)
REVERT: B  133 GLU cc_start: 0.8698 (pt0) cc_final: 0.8402 (tm-30)
REVERT: B  276 MET cc_start: 0.8405 (tpp) cc_final: 0.8162 (tpp)
REVERT: B  385 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9223 (tt)
REVERT: B  534 VAL cc_start: 0.9556 (t) cc_final: 0.9229 (p)
REVERT: A   13 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7074 (m-10)
REVERT: A   23 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7683 (m-80)
REVERT: A   88 CYS cc_start: 0.9013 (m) cc_final: 0.8509 (p)
REVERT: A   98 MET cc_start: 0.8482 (tpt) cc_final: 0.8060 (tpt)
REVERT: A  210 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8317 (tpp)
REVERT: A  291 MET cc_start: 0.9434 (mmm) cc_final: 0.9043 (mpp)
REVERT: A  295 MET cc_start: 0.8490 (tpp) cc_final: 0.8143 (tpp)
REVERT: A  312 MET cc_start: 0.8608 (mmt) cc_final: 0.8309 (mmt)
REVERT: A  460 MET cc_start: 0.8690 (tpt) cc_final: 0.8343 (tpt)
REVERT: A  487 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8996 (tp40)
REVERT: A  504 LEU cc_start: 0.9280 (tp) cc_final: 0.8906 (tp)
  outliers start: 53
  outliers final: 42
  residues processed: 155
  average time/residue: 0.1549
  time to fit residues: 36.4629
Evaluate side-chains
  157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 110
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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   66 TRP
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  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  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   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  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  487 GLN
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:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0570
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A 427 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.081286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.063243 restraints weight = 38312.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.065334 restraints weight = 20542.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.066769 restraints weight = 13799.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8950  Z= 0.127
  Angle     :  0.653   9.816  12092  Z= 0.322
  Chirality :  0.042   0.239   1440
  Planarity :  0.003   0.053   1532
  Dihedral  :  4.388  22.230   1238
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 30.79 %
    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:  0.89 (0.25), residues: 1134
  helix:  1.22 (0.19), residues: 742
  sheet:  0.73 (0.85), residues: 44
  loop : -0.71 (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   0.015   0.001   PHE A 116 
 TYR   0.033   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  555)
  hydrogen bonds       : angle       4.43876 ( 1626)
  covalent geometry    : bond        0.00273 ( 8950)
  covalent geometry    : angle       0.65317 (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
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 122
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7027 (m-80)
REVERT: B   43 PHE cc_start: 0.8201 (m-80) cc_final: 0.7986 (t80)
REVERT: B   98 MET cc_start: 0.8293 (tpt) cc_final: 0.7751 (tpt)
REVERT: B  111 MET cc_start: 0.9152 (tmm) cc_final: 0.8755 (tmm)
REVERT: B  133 GLU cc_start: 0.8666 (pt0) cc_final: 0.8364 (tm-30)
REVERT: B  200 MET cc_start: 0.8491 (mmp) cc_final: 0.8176 (mmm)
REVERT: B  276 MET cc_start: 0.8216 (tpp) cc_final: 0.7928 (tpp)
REVERT: B  385 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9167 (tt)
REVERT: B  534 VAL cc_start: 0.9526 (t) cc_final: 0.9196 (p)
REVERT: A   13 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6884 (m-10)
REVERT: A   23 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7542 (m-80)
REVERT: A   98 MET cc_start: 0.8392 (tpt) cc_final: 0.7787 (tpt)
REVERT: A  295 MET cc_start: 0.8425 (tpp) cc_final: 0.8117 (tpp)
REVERT: A  312 MET cc_start: 0.8531 (mmt) cc_final: 0.8224 (mmt)
REVERT: A  460 MET cc_start: 0.8637 (tpt) cc_final: 0.8332 (tpt)
REVERT: A  504 LEU cc_start: 0.9219 (tp) cc_final: 0.8920 (tp)
  outliers start: 42
  outliers final: 32
  residues processed: 151
  average time/residue: 0.1565
  time to fit residues: 35.8236
Evaluate side-chains
  153 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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   40 SER
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  143 LEU
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  374 LEU
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
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  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
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  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  456 MET
Chi-restraints excluded: chain A residue  499 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.0000
   chunk 95 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.081483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.063489 restraints weight = 38468.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.065602 restraints weight = 20632.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.067031 restraints weight = 13857.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3359

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= 0.127
  Angle     :  0.647   9.610  12092  Z= 0.319
  Chirality :  0.041   0.151   1440
  Planarity :  0.003   0.053   1532
  Dihedral  :  4.320  19.672   1238
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 31.30 %
    Favored  : 64.36 %
  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:  0.96 (0.26), residues: 1134
  helix:  1.28 (0.19), residues: 742
  sheet:  0.77 (0.86), residues: 44
  loop : -0.69 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 537 
 PHE   0.022   0.001   PHE A 429 
 TYR   0.028   0.001   TYR A 439 
 ARG   0.004   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04016 (  555)
  hydrogen bonds       : angle       4.36623 ( 1626)
  covalent geometry    : bond        0.00272 ( 8950)
  covalent geometry    : angle       0.64690 (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
  165 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 123
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6997 (m-80)
REVERT: B   43 PHE cc_start: 0.8212 (m-80) cc_final: 0.8003 (t80)
REVERT: B   67 MET cc_start: 0.9191 (tpp) cc_final: 0.8982 (tpp)
REVERT: B   98 MET cc_start: 0.8298 (tpt) cc_final: 0.7739 (tpt)
REVERT: B  111 MET cc_start: 0.9129 (tmm) cc_final: 0.8723 (tmm)
REVERT: B  133 GLU cc_start: 0.8696 (pt0) cc_final: 0.8378 (tm-30)
REVERT: B  200 MET cc_start: 0.8514 (mmp) cc_final: 0.8146 (mmm)
REVERT: B  276 MET cc_start: 0.8272 (tpp) cc_final: 0.7966 (tpp)
REVERT: B  385 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9172 (tt)
REVERT: B  466 MET cc_start: 0.7641 (pmm) cc_final: 0.7376 (pmm)
REVERT: B  534 VAL cc_start: 0.9517 (t) cc_final: 0.9187 (p)
REVERT: B  548 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8381 (mp)
REVERT: A   13 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6889 (m-10)
REVERT: A   23 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7554 (m-80)
REVERT: A   98 MET cc_start: 0.8388 (tpt) cc_final: 0.7807 (tpt)
REVERT: A  244 MET cc_start: 0.8677 (mtp) cc_final: 0.8472 (mtp)
REVERT: A  295 MET cc_start: 0.8445 (tpp) cc_final: 0.8108 (tpp)
REVERT: A  312 MET cc_start: 0.8524 (mmt) cc_final: 0.8236 (mmt)
REVERT: A  460 MET cc_start: 0.8661 (tpt) cc_final: 0.8346 (tpt)
REVERT: A  487 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.9053 (tp-100)
REVERT: A  504 LEU cc_start: 0.9190 (tp) cc_final: 0.8905 (tp)
REVERT: A  578 MET cc_start: 0.9208 (ptp) cc_final: 0.8713 (ppp)
  outliers start: 42
  outliers final: 36
  residues processed: 152
  average time/residue: 0.1629
  time to fit residues: 37.1144
Evaluate side-chains
  161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 119
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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   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  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  374 LEU
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  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 B residue  548 ILE
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 111 optimal weight:    9.9990
   chunk 102 optimal weight:    0.0970
   chunk 84 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
B 485 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.081453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.063415 restraints weight = 38740.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.065528 restraints weight = 20959.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.066925 restraints weight = 14127.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8950  Z= 0.132
  Angle     :  0.655   9.385  12092  Z= 0.323
  Chirality :  0.041   0.146   1440
  Planarity :  0.003   0.054   1532
  Dihedral  :  4.342  19.516   1238
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 31.30 %
    Favored  : 64.26 %
  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:  0.97 (0.26), residues: 1134
  helix:  1.28 (0.19), residues: 742
  sheet:  0.77 (0.86), residues: 44
  loop : -0.65 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 537 
 PHE   0.048   0.001   PHE A 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        0.03960 (  555)
  hydrogen bonds       : angle       4.43458 ( 1626)
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.65468 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3001.17 seconds
wall clock time: 54 minutes 20.04 seconds (3260.04 seconds total)