Starting phenix.real_space_refine
on Sat Aug 23 01:09:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv7_50791/08_2025/9fv7_50791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv7_50791/08_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_50791/08_2025/9fv7_50791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv7_50791/08_2025/9fv7_50791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv7_50791/08_2025/9fv7_50791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv7_50791/08_2025/9fv7_50791.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.11, per 1000 atoms: 0.24
  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: 0.78
  Conformation dependent library (CDL) restraints added in 309.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.32
  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: 1.00

  Time building geometry restraints manager: 1.02 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: 0.01
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:             5.460
  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:          0.360
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.680
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.650
-------------------------------------------------------------------------------
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 : 10.34
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.000   ARG A 236 
 TYR   0.018   0.002   TYR B  83 
 PHE   0.021   0.002   PHE B 429 
 TRP   0.020   0.002   TRP A 165 
 HIS   0.025   0.003   HIS A 576 

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

*********************** 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  : 0.456 
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: 0.0863
  time to fit residues: 18.9647
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  : 0.440 
-------------------------------------------------------------------------------
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 108 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 427 HIS
A 405 HIS
A 487 GLN
A 527 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.083274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.065760 restraints weight = 38041.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.067831 restraints weight = 20609.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.069231 restraints weight = 13769.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.070199 restraints weight = 10419.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.070778 restraints weight = 8569.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1632

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= 0.134
  Angle     :  0.621  10.875  12092  Z= 0.324
  Chirality :  0.041   0.169   1440
  Planarity :  0.004   0.046   1532
  Dihedral  :  5.281  46.042   1242
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 28.10 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.24), residues: 1134
  helix:  0.15 (0.18), residues: 746
  sheet: -0.13 (0.78), residues: 48
  loop : -1.01 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 238 
 TYR   0.014   0.001   TYR B 439 
 PHE   0.016   0.001   PHE B 429 
 TRP   0.020   0.002   TRP B  66 
 HIS   0.006   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8950)
  covalent geometry    : angle       0.62057 (12092)
  hydrogen bonds       : bond        0.04789 (  555)
  hydrogen bonds       : angle       5.06874 ( 1626)

*********************** 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
  180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 CYS cc_start: 0.9061 (m) cc_final: 0.8817 (m)
REVERT: B   98 MET cc_start: 0.8463 (tpt) cc_final: 0.7854 (tpt)
REVERT: B  133 GLU cc_start: 0.8596 (pt0) cc_final: 0.8358 (tm-30)
REVERT: B  276 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7323 (tpp)
REVERT: A   23 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7723 (m-80)
REVERT: A  164 SER cc_start: 0.7985 (m) cc_final: 0.7665 (p)
REVERT: A  276 MET cc_start: 0.7994 (ttt) cc_final: 0.7630 (ttt)
REVERT: A  295 MET cc_start: 0.8134 (tpp) cc_final: 0.7377 (tpp)
REVERT: A  460 MET cc_start: 0.8588 (tpt) cc_final: 0.8006 (mtt)
REVERT: A  487 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8786 (tp-100)
REVERT: A  504 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9043 (tt)
REVERT: A  578 MET cc_start: 0.9394 (mtt) cc_final: 0.8819 (tmm)
  outliers start: 39
  outliers final: 22
  residues processed: 166
  average time/residue: 0.0776
  time to fit residues: 19.3716
Evaluate side-chains
  152 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  276 MET
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  395 ILE
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   42 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  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  428 LEU
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:   40.0000
   chunk 38 optimal weight:    0.9980
   chunk 96 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 579 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 = 0.081871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.064059 restraints weight = 39697.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.066130 restraints weight = 22131.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.067528 restraints weight = 14982.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.068457 restraints weight = 11478.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.069141 restraints weight = 9544.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8950  Z= 0.133
  Angle     :  0.586   7.333  12092  Z= 0.305
  Chirality :  0.041   0.170   1440
  Planarity :  0.003   0.049   1532
  Dihedral  :  5.009  54.229   1242
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 27.48 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.25), residues: 1134
  helix:  0.76 (0.19), residues: 750
  sheet:  0.03 (0.78), residues: 48
  loop : -0.88 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  61 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.016   0.001   PHE B 429 
 TRP   0.022   0.001   TRP B  66 
 HIS   0.004   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8950)
  covalent geometry    : angle       0.58619 (12092)
  hydrogen bonds       : bond        0.04448 (  555)
  hydrogen bonds       : angle       4.73137 ( 1626)

*********************** 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
  189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 138
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6931 (m-80)
REVERT: B   47 LEU cc_start: 0.9128 (tp) cc_final: 0.8827 (tp)
REVERT: B   80 ILE cc_start: 0.9281 (mm) cc_final: 0.9057 (tp)
REVERT: B   88 CYS cc_start: 0.9091 (m) cc_final: 0.8815 (m)
REVERT: B   98 MET cc_start: 0.8397 (tpt) cc_final: 0.7799 (tpt)
REVERT: B  133 GLU cc_start: 0.8664 (pt0) cc_final: 0.8392 (tm-30)
REVERT: B  385 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9108 (tt)
REVERT: B  450 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9274 (tt)
REVERT: B  534 VAL cc_start: 0.9479 (t) cc_final: 0.9087 (p)
REVERT: A   13 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6875 (m-10)
REVERT: A   23 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7570 (m-80)
REVERT: A   80 ILE cc_start: 0.9224 (mm) cc_final: 0.9017 (tp)
REVERT: A  149 GLU cc_start: 0.8603 (mp0) cc_final: 0.8294 (mp0)
REVERT: A  295 MET cc_start: 0.8318 (tpp) cc_final: 0.7593 (tpp)
REVERT: A  460 MET cc_start: 0.8647 (tpt) cc_final: 0.8069 (mtt)
REVERT: A  504 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9026 (tt)
REVERT: A  578 MET cc_start: 0.9414 (mtt) cc_final: 0.8826 (tmm)
  outliers start: 51
  outliers final: 31
  residues processed: 173
  average time/residue: 0.0732
  time to fit residues: 19.1967
Evaluate side-chains
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  174 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  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  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  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  422 VAL
Chi-restraints excluded: chain A residue  428 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0770
   chunk 71 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.9540

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

Flipped N/Q/H residues before XYZ refinement:
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.081932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.063812 restraints weight = 39134.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.065911 restraints weight = 21286.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.067324 restraints weight = 14391.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.068202 restraints weight = 11010.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068899 restraints weight = 9216.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8950  Z= 0.130
  Angle     :  0.584   9.614  12092  Z= 0.300
  Chirality :  0.041   0.153   1440
  Planarity :  0.003   0.050   1532
  Dihedral  :  4.724  38.611   1242
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 27.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.25), residues: 1134
  helix:  1.09 (0.19), residues: 746
  sheet:  0.30 (0.82), residues: 44
  loop : -0.76 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  61 
 TYR   0.013   0.001   TYR A 439 
 PHE   0.014   0.001   PHE B 429 
 TRP   0.023   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8950)
  covalent geometry    : angle       0.58409 (12092)
  hydrogen bonds       : bond        0.04137 (  555)
  hydrogen bonds       : angle       4.54479 ( 1626)

*********************** 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
  200 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 135
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8040 (m-80)
REVERT: B   47 LEU cc_start: 0.9115 (tp) cc_final: 0.8807 (tp)
REVERT: B   80 ILE cc_start: 0.9291 (mm) cc_final: 0.9062 (tp)
REVERT: B   98 MET cc_start: 0.8368 (tpt) cc_final: 0.7790 (tpt)
REVERT: B  133 GLU cc_start: 0.8622 (pt0) cc_final: 0.8331 (tm-30)
REVERT: B  385 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9098 (tt)
REVERT: B  534 VAL cc_start: 0.9495 (t) cc_final: 0.9136 (p)
REVERT: B  543 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8988 (mm-30)
REVERT: A   13 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6860 (m-10)
REVERT: A   23 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7416 (m-80)
REVERT: A   80 ILE cc_start: 0.9267 (mm) cc_final: 0.9059 (tp)
REVERT: A  149 GLU cc_start: 0.8573 (mp0) cc_final: 0.8366 (mp0)
REVERT: A  276 MET cc_start: 0.7414 (ttt) cc_final: 0.7195 (ttm)
REVERT: A  295 MET cc_start: 0.8289 (tpp) cc_final: 0.8048 (tpp)
REVERT: A  460 MET cc_start: 0.8623 (tpt) cc_final: 0.8049 (mtt)
REVERT: A  487 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8853 (tp40)
REVERT: A  504 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8989 (tp)
REVERT: A  578 MET cc_start: 0.9395 (mtt) cc_final: 0.9151 (tmm)
  outliers start: 65
  outliers final: 42
  residues processed: 184
  average time/residue: 0.0625
  time to fit residues: 17.4018
Evaluate side-chains
  172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 124
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 PHE
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  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   42 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  487 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 99 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.079075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.060723 restraints weight = 39112.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.062775 restraints weight = 21009.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.064154 restraints weight = 14155.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.065084 restraints weight = 10870.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.065650 restraints weight = 9072.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8950  Z= 0.206
  Angle     :  0.659   9.275  12092  Z= 0.339
  Chirality :  0.042   0.176   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  4.623  25.190   1241
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 27.89 %
    Favored  : 65.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.25), residues: 1134
  helix:  1.09 (0.19), residues: 748
  sheet:  0.60 (0.83), residues: 42
  loop : -0.67 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  61 
 TYR   0.019   0.001   TYR B 439 
 PHE   0.018   0.002   PHE B  23 
 TRP   0.027   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8950)
  covalent geometry    : angle       0.65945 (12092)
  hydrogen bonds       : bond        0.04512 (  555)
  hydrogen bonds       : angle       4.65751 ( 1626)

*********************** 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
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 122
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8278 (m-80) cc_final: 0.8065 (t80)
REVERT: B   67 MET cc_start: 0.9115 (mmm) cc_final: 0.8790 (tpp)
REVERT: B   80 ILE cc_start: 0.9343 (mm) cc_final: 0.9141 (tp)
REVERT: B   98 MET cc_start: 0.8363 (tpt) cc_final: 0.7793 (tpt)
REVERT: B  133 GLU cc_start: 0.8617 (pt0) cc_final: 0.8346 (tm-30)
REVERT: B  276 MET cc_start: 0.8210 (tpp) cc_final: 0.7887 (mmm)
REVERT: B  385 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9185 (tt)
REVERT: B  534 VAL cc_start: 0.9539 (t) cc_final: 0.9206 (p)
REVERT: B  543 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9056 (mm-30)
REVERT: A   13 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6988 (m-10)
REVERT: A   23 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7494 (m-80)
REVERT: A   98 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8096 (tpt)
REVERT: A  276 MET cc_start: 0.7575 (ttt) cc_final: 0.6881 (ttm)
REVERT: A  291 MET cc_start: 0.9412 (mmm) cc_final: 0.9048 (mpp)
REVERT: A  295 MET cc_start: 0.8351 (tpp) cc_final: 0.8031 (tpp)
REVERT: A  504 LEU cc_start: 0.9407 (tp) cc_final: 0.9049 (tp)
REVERT: A  578 MET cc_start: 0.9328 (mtt) cc_final: 0.9022 (tmm)
  outliers start: 63
  outliers final: 48
  residues processed: 171
  average time/residue: 0.0547
  time to fit residues: 14.6340
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 117
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  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 109 optimal weight:    0.4980
   chunk 95 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 108 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.081039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062823 restraints weight = 38918.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.064924 restraints weight = 21068.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.066342 restraints weight = 14205.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.067205 restraints weight = 10897.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.067898 restraints weight = 9163.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8950  Z= 0.131
  Angle     :  0.610  10.125  12092  Z= 0.309
  Chirality :  0.041   0.142   1440
  Planarity :  0.003   0.054   1532
  Dihedral  :  4.444  21.364   1239
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 29.86 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.25), residues: 1134
  helix:  1.20 (0.19), residues: 742
  sheet:  0.50 (0.84), residues: 44
  loop : -0.70 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  61 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.011   0.001   PHE A 116 
 TRP   0.025   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8950)
  covalent geometry    : angle       0.61027 (12092)
  hydrogen bonds       : bond        0.04125 (  555)
  hydrogen bonds       : angle       4.51074 ( 1626)

*********************** 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
  173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 124
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8248 (m-80) cc_final: 0.8023 (t80)
REVERT: B   98 MET cc_start: 0.8287 (tpt) cc_final: 0.7730 (tpt)
REVERT: B  111 MET cc_start: 0.9037 (tmm) cc_final: 0.8724 (tmm)
REVERT: B  133 GLU cc_start: 0.8621 (pt0) cc_final: 0.8316 (tm-30)
REVERT: B  276 MET cc_start: 0.8162 (tpp) cc_final: 0.7900 (tpp)
REVERT: B  385 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9177 (tt)
REVERT: B  534 VAL cc_start: 0.9530 (t) cc_final: 0.9201 (p)
REVERT: B  543 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9066 (mm-30)
REVERT: A   13 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6929 (m-10)
REVERT: A   23 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7479 (m-80)
REVERT: A   48 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9218 (tt)
REVERT: A  244 MET cc_start: 0.8566 (mtp) cc_final: 0.8331 (mtp)
REVERT: A  276 MET cc_start: 0.6936 (ttt) cc_final: 0.6638 (ttm)
REVERT: A  291 MET cc_start: 0.9415 (mmm) cc_final: 0.9052 (mpp)
REVERT: A  295 MET cc_start: 0.8318 (tpp) cc_final: 0.8012 (tpp)
REVERT: A  504 LEU cc_start: 0.9377 (tp) cc_final: 0.9046 (tp)
  outliers start: 49
  outliers final: 35
  residues processed: 159
  average time/residue: 0.0593
  time to fit residues: 14.4407
Evaluate side-chains
  158 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 119
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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   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  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  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  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 104 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 109 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.078053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.059750 restraints weight = 39094.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.061770 restraints weight = 20886.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.063138 restraints weight = 14057.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.064044 restraints weight = 10807.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.064641 restraints weight = 9011.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8950  Z= 0.216
  Angle     :  0.677   9.518  12092  Z= 0.348
  Chirality :  0.042   0.143   1440
  Planarity :  0.004   0.056   1532
  Dihedral  :  4.575  23.409   1239
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 29.65 %
    Favored  : 64.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.25), residues: 1134
  helix:  1.08 (0.19), residues: 750
  sheet:  0.81 (0.85), residues: 42
  loop : -0.66 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  61 
 TYR   0.023   0.001   TYR B 439 
 PHE   0.015   0.002   PHE A  23 
 TRP   0.023   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 8950)
  covalent geometry    : angle       0.67661 (12092)
  hydrogen bonds       : bond        0.04581 (  555)
  hydrogen bonds       : angle       4.68755 ( 1626)

*********************** 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
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 115
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 PHE cc_start: 0.8267 (m-80) cc_final: 0.8063 (t80)
REVERT: B   67 MET cc_start: 0.9073 (tpp) cc_final: 0.8672 (mmm)
REVERT: B   98 MET cc_start: 0.8317 (tpt) cc_final: 0.7789 (tpt)
REVERT: B  111 MET cc_start: 0.9123 (tmm) cc_final: 0.8774 (tmm)
REVERT: B  133 GLU cc_start: 0.8620 (pt0) cc_final: 0.8342 (tm-30)
REVERT: B  312 MET cc_start: 0.8732 (mmm) cc_final: 0.8353 (mmm)
REVERT: B  385 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9189 (tt)
REVERT: B  460 MET cc_start: 0.8762 (tpt) cc_final: 0.8386 (tpt)
REVERT: B  534 VAL cc_start: 0.9550 (t) cc_final: 0.9235 (p)
REVERT: A   13 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7131 (m-10)
REVERT: A   23 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7627 (m-80)
REVERT: A   53 ASP cc_start: 0.8547 (t0) cc_final: 0.8163 (t0)
REVERT: A   88 CYS cc_start: 0.9020 (m) cc_final: 0.8494 (p)
REVERT: A   98 MET cc_start: 0.8374 (tpt) cc_final: 0.8053 (tpt)
REVERT: A  291 MET cc_start: 0.9449 (mmm) cc_final: 0.9031 (mpp)
REVERT: A  295 MET cc_start: 0.8433 (tpp) cc_final: 0.8151 (tpp)
REVERT: A  460 MET cc_start: 0.8673 (tpt) cc_final: 0.8356 (tpt)
REVERT: A  487 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8855 (tp-100)
REVERT: A  504 LEU cc_start: 0.9326 (tp) cc_final: 0.9008 (tp)
  outliers start: 56
  outliers final: 42
  residues processed: 159
  average time/residue: 0.0674
  time to fit residues: 16.5776
Evaluate side-chains
  158 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 112
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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   48 LEU
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain 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   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  285 THR
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  428 LEU
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 99 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
A 427 HIS
A 487 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.080260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.062089 restraints weight = 38431.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.064173 restraints weight = 20585.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.065571 restraints weight = 13831.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.066515 restraints weight = 10589.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.067151 restraints weight = 8814.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8950  Z= 0.135
  Angle     :  0.636   9.647  12092  Z= 0.320
  Chirality :  0.042   0.217   1440
  Planarity :  0.003   0.055   1532
  Dihedral  :  4.502  23.515   1239
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 29.55 %
    Favored  : 65.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1134
  helix:  1.22 (0.19), residues: 742
  sheet:  1.02 (0.85), residues: 42
  loop : -0.75 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 486 
 TYR   0.031   0.001   TYR A 439 
 PHE   0.009   0.001   PHE B 429 
 TRP   0.023   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.63647 (12092)
  hydrogen bonds       : bond        0.04193 (  555)
  hydrogen bonds       : angle       4.51394 ( 1626)

*********************** 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
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 120
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 MET cc_start: 0.9075 (tpp) cc_final: 0.8732 (mmm)
REVERT: B   98 MET cc_start: 0.8225 (tpt) cc_final: 0.7702 (tpt)
REVERT: B  111 MET cc_start: 0.9097 (tmm) cc_final: 0.8747 (tmm)
REVERT: B  133 GLU cc_start: 0.8630 (pt0) cc_final: 0.8321 (tm-30)
REVERT: B  200 MET cc_start: 0.8457 (mmp) cc_final: 0.8148 (mmm)
REVERT: B  276 MET cc_start: 0.8212 (tpp) cc_final: 0.7946 (tpp)
REVERT: B  385 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9175 (tt)
REVERT: B  460 MET cc_start: 0.8674 (tpt) cc_final: 0.8366 (tpt)
REVERT: B  534 VAL cc_start: 0.9542 (t) cc_final: 0.9218 (p)
REVERT: A   13 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6951 (m-10)
REVERT: A   23 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7548 (m-80)
REVERT: A   98 MET cc_start: 0.8341 (tpt) cc_final: 0.7874 (tpt)
REVERT: A  291 MET cc_start: 0.9456 (mmm) cc_final: 0.9034 (mpp)
REVERT: A  295 MET cc_start: 0.8391 (tpp) cc_final: 0.8047 (tpp)
REVERT: A  487 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.9038 (tp40)
REVERT: A  504 LEU cc_start: 0.9301 (tp) cc_final: 0.8967 (tp)
  outliers start: 49
  outliers final: 39
  residues processed: 159
  average time/residue: 0.0645
  time to fit residues: 15.7574
Evaluate side-chains
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 117
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  197 GLN
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  389 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  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  487 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0470
   chunk 1 optimal weight:    0.6980
   chunk 105 optimal weight:   10.0000
   chunk 9 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0670
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.4416

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.081781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.063880 restraints weight = 38227.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.065996 restraints weight = 20539.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.067415 restraints weight = 13780.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.068402 restraints weight = 10526.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068962 restraints weight = 8704.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3287

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= 0.122
  Angle     :  0.636   9.486  12092  Z= 0.315
  Chirality :  0.041   0.145   1440
  Planarity :  0.003   0.054   1532
  Dihedral  :  4.370  21.820   1238
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 31.20 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.25), residues: 1134
  helix:  1.25 (0.19), residues: 742
  sheet:  1.20 (0.87), residues: 42
  loop : -0.66 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  61 
 TYR   0.025   0.001   TYR A 439 
 PHE   0.015   0.001   PHE A 116 
 TRP   0.019   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8950)
  covalent geometry    : angle       0.63569 (12092)
  hydrogen bonds       : bond        0.03984 (  555)
  hydrogen bonds       : angle       4.40774 ( 1626)

*********************** 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: 37
    poor density    : 127
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 MET cc_start: 0.9156 (tpp) cc_final: 0.8758 (mmm)
REVERT: B   98 MET cc_start: 0.8203 (tpt) cc_final: 0.7676 (tpt)
REVERT: B  111 MET cc_start: 0.9046 (tmm) cc_final: 0.8790 (tmm)
REVERT: B  133 GLU cc_start: 0.8639 (pt0) cc_final: 0.8318 (tm-30)
REVERT: B  200 MET cc_start: 0.8535 (mmp) cc_final: 0.8120 (mmm)
REVERT: B  276 MET cc_start: 0.8174 (tpp) cc_final: 0.7819 (tpp)
REVERT: B  385 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9162 (tt)
REVERT: B  534 VAL cc_start: 0.9517 (t) cc_final: 0.9195 (p)
REVERT: A   13 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6837 (m-10)
REVERT: A   23 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7501 (m-80)
REVERT: A  276 MET cc_start: 0.6913 (ttt) cc_final: 0.6664 (ttm)
REVERT: A  291 MET cc_start: 0.9451 (mmm) cc_final: 0.9029 (mpp)
REVERT: A  295 MET cc_start: 0.8325 (tpp) cc_final: 0.7978 (tpp)
REVERT: A  578 MET cc_start: 0.9189 (ptp) cc_final: 0.8733 (ppp)
  outliers start: 37
  outliers final: 30
  residues processed: 155
  average time/residue: 0.0691
  time to fit residues: 16.5024
Evaluate side-chains
  153 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
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  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   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  428 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 61 optimal weight:    0.2980
   chunk 92 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.081277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.063451 restraints weight = 38517.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.065548 restraints weight = 20698.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.066942 restraints weight = 13840.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.067871 restraints weight = 10582.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.068479 restraints weight = 8824.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3386

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= 0.129
  Angle     :  0.641   9.294  12092  Z= 0.317
  Chirality :  0.041   0.152   1440
  Planarity :  0.003   0.054   1532
  Dihedral  :  4.305  20.892   1238
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 30.99 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1134
  helix:  1.31 (0.19), residues: 742
  sheet:  1.13 (0.87), residues: 42
  loop : -0.63 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  61 
 TYR   0.025   0.001   TYR A 439 
 PHE   0.013   0.001   PHE A 116 
 TRP   0.019   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8950)
  covalent geometry    : angle       0.64058 (12092)
  hydrogen bonds       : bond        0.04005 (  555)
  hydrogen bonds       : angle       4.38648 ( 1626)

********************** 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
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 MET cc_start: 0.9178 (tpp) cc_final: 0.8940 (mmm)
REVERT: B   98 MET cc_start: 0.8255 (tpt) cc_final: 0.7701 (tpt)
REVERT: B  111 MET cc_start: 0.9111 (tmm) cc_final: 0.8773 (tmm)
REVERT: B  133 GLU cc_start: 0.8678 (pt0) cc_final: 0.8345 (tm-30)
REVERT: B  276 MET cc_start: 0.8220 (tpp) cc_final: 0.7912 (tpp)
REVERT: B  385 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9169 (tt)
REVERT: B  460 MET cc_start: 0.8712 (tpt) cc_final: 0.8326 (tpt)
REVERT: B  466 MET cc_start: 0.7552 (pmm) cc_final: 0.7306 (pmm)
REVERT: B  534 VAL cc_start: 0.9524 (t) cc_final: 0.9204 (p)
REVERT: A   13 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6880 (m-10)
REVERT: A   23 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7519 (m-80)
REVERT: A  276 MET cc_start: 0.7005 (ttt) cc_final: 0.6744 (ttm)
REVERT: A  291 MET cc_start: 0.9442 (mmm) cc_final: 0.9009 (mpp)
REVERT: A  295 MET cc_start: 0.8338 (tpp) cc_final: 0.7995 (tpp)
REVERT: A  487 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8904 (tp40)
REVERT: A  504 LEU cc_start: 0.9146 (tp) cc_final: 0.8908 (tp)
REVERT: A  578 MET cc_start: 0.9179 (ptp) cc_final: 0.8745 (ppp)
  outliers start: 39
  outliers final: 34
  residues processed: 149
  average time/residue: 0.0630
  time to fit residues: 14.3732
Evaluate side-chains
  154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  304 VAL
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0670
   chunk 49 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7122

-------------------------------------------------------------------------------
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 = 0.3691 r_free = 0.3691 target = 0.081702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.063794 restraints weight = 37795.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.065904 restraints weight = 20530.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.067319 restraints weight = 13798.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.068186 restraints weight = 10592.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068848 restraints weight = 8885.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8950  Z= 0.127
  Angle     :  0.650   9.188  12092  Z= 0.321
  Chirality :  0.041   0.171   1440
  Planarity :  0.003   0.054   1532
  Dihedral  :  4.289  20.255   1238
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 31.20 %
    Favored  : 64.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1134
  helix:  1.30 (0.19), residues: 740
  sheet:  0.80 (0.87), residues: 44
  loop : -0.53 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  61 
 TYR   0.024   0.001   TYR A 439 
 PHE   0.014   0.001   PHE A 116 
 TRP   0.019   0.001   TRP B  66 
 HIS   0.004   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8950)
  covalent geometry    : angle       0.65004 (12092)
  hydrogen bonds       : bond        0.04011 (  555)
  hydrogen bonds       : angle       4.38199 ( 1626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1639.98 seconds
wall clock time: 29 minutes 5.12 seconds (1745.12 seconds total)