Starting phenix.real_space_refine
on Sun Jul 27 01:22:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p6j_20264/07_2025/6p6j_20264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p6j_20264/07_2025/6p6j_20264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p6j_20264/07_2025/6p6j_20264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p6j_20264/07_2025/6p6j_20264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p6j_20264/07_2025/6p6j_20264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p6j_20264/07_2025/6p6j_20264.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      46      5.16       5
     C    5683      2.51       5
     N    1554      2.21       5
     O    1557      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8841
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4413
          Classifications: {'peptide': 571}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 25, 'TRANS': 545}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 4396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4396
          Classifications: {'peptide': 569}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 19, 'TRANS': 549}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' FE': 1, 'O34': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.01, per 1000 atoms: 0.68
  Number of scatterers: 8841
  At special positions: 0
  Unit cell: (77.76, 94.176, 132.192, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      46     16.00
     O    1557      8.00
     N    1554      7.00
     C    5683      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.76
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2130

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 5 sheets defined
      69.4% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 58
      removed outlier: 3.654A  pdb=" N   LEU A  29 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ALA A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 109
      removed outlier: 4.177A  pdb=" N   GLN A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 122
      removed outlier: 3.683A  pdb=" N   SER A 120 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY A 121 " --> pdb=" O   GLN A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 139
      removed outlier: 5.033A  pdb=" N   VAL A 131 " --> pdb=" O   MET A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 163
      Proline residue:  A 152  - end of helix
      removed outlier: 4.430A  pdb=" N   ILE A 156 " --> pdb=" O   PRO A 152 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   VAL A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 188
      removed outlier: 3.927A  pdb=" N   THR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   SER A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 220
      Proline residue:  A 214  - end of helix
    Processing helix  chain 'A' and resid 222 through 258
      removed outlier: 3.980A  pdb=" N   ALA A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   SER A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   PHE A 253 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 277
      removed outlier: 4.229A  pdb=" N   THR A 263 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TRP A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   TYR A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 300
      removed outlier: 4.431A  pdb=" N   ALA A 296 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLU A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ALA A 298 " --> pdb=" O   GLY A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 303
      No H-bonds generated for 'chain 'A' and resid 301 through 303'
    Processing helix  chain 'A' and resid 304 through 324
      removed outlier: 4.170A  pdb=" N   GLN A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 391
    Processing helix  chain 'A' and resid 412 through 419
    Processing helix  chain 'A' and resid 446 through 454
    Processing helix  chain 'A' and resid 459 through 465
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.598A  pdb=" N   ASN A 471 " --> pdb=" O   GLU A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 498
      removed outlier: 3.683A  pdb=" N   GLN A 487 " --> pdb=" O   GLY A 483 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 527
    Processing helix  chain 'A' and resid 561 through 569
      removed outlier: 3.756A  pdb=" N   GLY A 569 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 584
      removed outlier: 4.034A  pdb=" N   ARG A 574 " --> pdb=" O   GLY A 570 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   HIS A 584 " --> pdb=" O   GLN A 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 23
      removed outlier: 3.815A  pdb=" N   TRP B  16 " --> pdb=" O   TRP B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 59
      removed outlier: 4.196A  pdb=" N   TYR B  52 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      Proline residue:  B  53  - end of helix
    Processing helix  chain 'B' and resid 62 through 94
      removed outlier: 4.356A  pdb=" N   ALA B  72 " --> pdb=" O   ASN B  68 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   THR B  80 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   GLU B  91 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLY B  94 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 114
      removed outlier: 3.563A  pdb=" N   GLN B  98 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 122
      removed outlier: 3.658A  pdb=" N   LEU B 119 " --> pdb=" O   PRO B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 136
      removed outlier: 4.280A  pdb=" N   MET B 127 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 140
    Processing helix  chain 'B' and resid 141 through 147
    Processing helix  chain 'B' and resid 147 through 167
      Proline residue:  B 156  - end of helix
      removed outlier: 4.418A  pdb=" N   TRP B 165 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 178
      removed outlier: 3.505A  pdb=" N   ILE B 177 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 187
    Processing helix  chain 'B' and resid 188 through 216
      removed outlier: 3.927A  pdb=" N   MET B 192 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 223
    Processing helix  chain 'B' and resid 225 through 251
      removed outlier: 3.748A  pdb=" N   GLN B 250 " --> pdb=" O   ARG B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 260
      removed outlier: 3.653A  pdb=" N   THR B 255 " --> pdb=" O   GLY B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 279
      removed outlier: 4.013A  pdb=" N   VAL B 268 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 295
    Processing helix  chain 'B' and resid 297 through 325
      removed outlier: 3.560A  pdb=" N   MET B 301 " --> pdb=" O   PHE B 297 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   SER B 309 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   VAL B 310 " --> pdb=" O   SER B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 358
      removed outlier: 4.041A  pdb=" N   GLY B 358 " --> pdb=" O   GLU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 391
    Processing helix  chain 'B' and resid 410 through 412
      No H-bonds generated for 'chain 'B' and resid 410 through 412'
    Processing helix  chain 'B' and resid 413 through 419
    Processing helix  chain 'B' and resid 434 through 441
    Processing helix  chain 'B' and resid 447 through 458
      removed outlier: 3.565A  pdb=" N   VAL B 451 " --> pdb=" O   THR B 447 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU B 452 " --> pdb=" O   ARG B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 467
    Processing helix  chain 'B' and resid 483 through 498
      removed outlier: 3.514A  pdb=" N   LYS B 498 " --> pdb=" O   ARG B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 528
      removed outlier: 3.685A  pdb=" N   ASN B 526 " --> pdb=" O   LYS B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 545
    Processing helix  chain 'B' and resid 562 through 567
    Processing helix  chain 'B' and resid 571 through 578
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 367
      removed outlier: 7.401A  pdb=" N   ALA A 359 " --> pdb=" O   HIS A 350 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   HIS A 350 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   GLN A 361 " --> pdb=" O   SER A 348 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   SER A 348 " --> pdb=" O   GLN A 361 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   VAL A 363 " --> pdb=" O   GLN A 346 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   VAL A 406 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 422
    Processing sheet with id=AA3, first strand: chain 'B' and resid 361 through 364
      removed outlier: 5.335A  pdb=" N   ASN B 362 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   TYR B 351 " --> pdb=" O   ASN B 362 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 364
      removed outlier: 5.335A  pdb=" N   ASN B 362 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   TYR B 351 " --> pdb=" O   ASN B 362 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   VAL B 349 " --> pdb=" O   GLN B 399 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   GLN B 399 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL B 407 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 424
      removed outlier: 6.253A  pdb=" N   SER B 422 " --> pdb=" O   ILE B 504 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   MET B 373 " --> pdb=" O   ASN B 548 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   LEU B 550 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ALA B 375 " --> pdb=" O   LEU B 550 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   MET B 552 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL B 377 " --> pdb=" O   MET B 552 " (cutoff:3.500A)

    571 hydrogen bonds defined for protein.
    1689 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.73

  Time building geometry restraints manager: 3.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2912
        1.34 -     1.46: 1967
        1.46 -     1.58: 4056
        1.58 -     1.70: 0
        1.70 -     1.82: 88
  Bond restraints: 9023
  Sorted by residual:
  bond pdb=" C17 O34 A 701 "
       pdb=" S3  O34 A 701 "
    ideal  model  delta    sigma   weight residual
    1.805  1.742  0.063 2.00e-02 2.50e+03 9.94e+00
  bond pdb=" C   MET A 213 "
       pdb=" N   PRO A 214 "
    ideal  model  delta    sigma   weight residual
    1.336  1.373 -0.037 1.20e-02 6.94e+03 9.63e+00
  bond pdb=" C   THR A 142 "
       pdb=" N   PRO A 143 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.034 1.28e-02 6.10e+03 6.92e+00
  bond pdb=" C19 O34 A 701 "
       pdb=" C21 O34 A 701 "
    ideal  model  delta    sigma   weight residual
    1.583  1.535  0.048 2.00e-02 2.50e+03 5.88e+00
  bond pdb=" CB  THR B 163 "
       pdb=" CG2 THR B 163 "
    ideal  model  delta    sigma   weight residual
    1.521  1.442  0.079 3.30e-02 9.18e+02 5.71e+00
  ... (remaining 9018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11695
        2.38 -     4.77: 496
        4.77 -     7.15: 74
        7.15 -     9.53: 14
        9.53 -    11.91: 2
  Bond angle restraints: 12281
  Sorted by residual:
  angle pdb=" N   ALA A 340 "
        pdb=" CA  ALA A 340 "
        pdb=" CB  ALA A 340 "
      ideal   model   delta    sigma   weight residual
     114.17  106.64    7.53 1.14e+00 7.69e-01 4.36e+01
  angle pdb=" C   VAL A 456 "
        pdb=" N   ALA A 457 "
        pdb=" CA  ALA A 457 "
      ideal   model   delta    sigma   weight residual
     121.19  129.32   -8.13 1.59e+00 3.96e-01 2.61e+01
  angle pdb=" C   LEU B 430 "
        pdb=" N   PHE B 431 "
        pdb=" CA  PHE B 431 "
      ideal   model   delta    sigma   weight residual
     121.54  130.76   -9.22 1.91e+00 2.74e-01 2.33e+01
  angle pdb=" C   TRP A 585 "
        pdb=" N   VAL A 586 "
        pdb=" CA  VAL A 586 "
      ideal   model   delta    sigma   weight residual
     120.33  124.11   -3.78 8.00e-01 1.56e+00 2.23e+01
  angle pdb=" N   ASN A 427 "
        pdb=" CA  ASN A 427 "
        pdb=" C   ASN A 427 "
      ideal   model   delta    sigma   weight residual
     110.91  116.12   -5.21 1.17e+00 7.31e-01 1.99e+01
  ... (remaining 12276 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.10: 5168
       29.10 -    58.19: 226
       58.19 -    87.29: 16
       87.29 -   116.38: 3
      116.38 -   145.48: 1
  Dihedral angle restraints: 5414
    sinusoidal: 2121
      harmonic: 3293
  Sorted by residual:
  dihedral pdb=" CA  ASP A 432 "
           pdb=" C   ASP A 432 "
           pdb=" N   THR A 433 "
           pdb=" CA  THR A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -124.85  -55.15     0      5.00e+00 4.00e-02 1.22e+02
  dihedral pdb=" CA  VAL A 456 "
           pdb=" C   VAL A 456 "
           pdb=" N   ALA A 457 "
           pdb=" CA  ALA A 457 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.58  -39.42     0      5.00e+00 4.00e-02 6.22e+01
  dihedral pdb=" CA  GLU A 339 "
           pdb=" C   GLU A 339 "
           pdb=" N   ALA A 340 "
           pdb=" CA  ALA A 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.13   34.87     0      5.00e+00 4.00e-02 4.86e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1310
       0.097 -    0.195: 116
       0.195 -    0.292: 9
       0.292 -    0.389: 2
       0.389 -    0.486: 1
  Chirality restraints: 1438
  Sorted by residual:
  chirality pdb=" C12 O34 A 701 "
            pdb=" C11 O34 A 701 "
            pdb=" C13 O34 A 701 "
            pdb=" N2  O34 A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.76    0.49 2.00e-01 2.50e+01 5.92e+00
  chirality pdb=" CA  LEU B 430 "
            pdb=" N   LEU B 430 "
            pdb=" C   LEU B 430 "
            pdb=" CB  LEU B 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" CB  ILE B 514 "
            pdb=" CA  ILE B 514 "
            pdb=" CG1 ILE B 514 "
            pdb=" CG2 ILE B 514 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1435 not shown)

  Planarity restraints: 1560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 126 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.93e+00
        pdb=" C   VAL A 126 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   VAL A 126 "    0.018 2.00e-02 2.50e+03
        pdb=" N   MET A 127 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  O34 A 701 "   -0.008 2.00e-02 2.50e+03   1.83e-02 6.67e+00
        pdb=" C2  O34 A 701 "   -0.010 2.00e-02 2.50e+03
        pdb=" C3  O34 A 701 "   -0.014 2.00e-02 2.50e+03
        pdb=" C4  O34 A 701 "    0.006 2.00e-02 2.50e+03
        pdb=" C5  O34 A 701 "    0.031 2.00e-02 2.50e+03
        pdb=" C6  O34 A 701 "   -0.011 2.00e-02 2.50e+03
        pdb=" C7  O34 A 701 "   -0.021 2.00e-02 2.50e+03
        pdb=" O1  O34 A 701 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 500 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO B 501 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 501 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 501 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1557 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 38
        2.50 -     3.10: 5996
        3.10 -     3.70: 14008
        3.70 -     4.30: 18289
        4.30 -     4.90: 30385
  Nonbonded interactions: 68716
  Sorted by model distance:
  nonbonded pdb=" O2  O34 A 701 "
            pdb="FE    FE A 702 "
     model   vdw
     1.901 2.260
  nonbonded pdb=" O1  O34 A 701 "
            pdb="FE    FE A 702 "
     model   vdw
     1.919 2.260
  nonbonded pdb=" O3  O34 A 701 "
            pdb="FE    FE A 702 "
     model   vdw
     2.078 2.260
  nonbonded pdb=" N1  O34 A 701 "
            pdb="FE    FE A 702 "
     model   vdw
     2.084 2.340
  nonbonded pdb=" N3  O34 A 701 "
            pdb="FE    FE A 702 "
     model   vdw
     2.131 2.340
  ... (remaining 68711 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.540
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
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      :  0.012   0.620   9025  Z= 0.925
  Angle     :  1.122  11.913  12281  Z= 0.644
  Chirality :  0.060   0.486   1438
  Planarity :  0.008   0.063   1560
  Dihedral  : 15.941 145.477   3284
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 13.06 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.33 (0.19), residues: 1136
  helix: -2.64 (0.13), residues: 737
  sheet: -1.54 (0.63), residues: 62
  loop : -3.22 (0.29), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  17 
 HIS   0.005   0.002   HIS B 529 
 PHE   0.028   0.002   PHE B 431 
 TYR   0.019   0.002   TYR A 229 
 ARG   0.005   0.001   ARG B 410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15209 (  569)
  hydrogen bonds       : angle       6.94836 ( 1689)
  covalent geometry    : bond        0.00778 ( 9023)
  covalent geometry    : angle       1.12188 (12281)
  Misc. bond           : bond        0.57635 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 276
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7209 (t)
REVERT: A  145 TYR cc_start: 0.7240 (t80) cc_final: 0.6817 (t80)
REVERT: A  213 MET cc_start: 0.7649 (tpp) cc_final: 0.7078 (tpp)
REVERT: A  234 GLU cc_start: 0.8245 (tt0) cc_final: 0.8026 (tm-30)
REVERT: A  236 TRP cc_start: 0.8935 (t60) cc_final: 0.8483 (t60)
REVERT: A  308 LEU cc_start: 0.8720 (tt) cc_final: 0.8337 (tt)
REVERT: A  417 MET cc_start: 0.8467 (mmp) cc_final: 0.7852 (mmt)
REVERT: A  436 ASN cc_start: 0.7802 (m110) cc_final: 0.7483 (m-40)
REVERT: A  501 ILE cc_start: 0.8009 (mt) cc_final: 0.7784 (tt)
REVERT: B   22 SER cc_start: 0.9333 (m) cc_final: 0.8977 (p)
REVERT: B   34 MET cc_start: 0.6145 (tmm) cc_final: 0.5735 (mmp)
REVERT: B   43 MET cc_start: 0.8521 (tpp) cc_final: 0.8293 (mmm)
REVERT: B   68 ASN cc_start: 0.8504 (m110) cc_final: 0.8111 (t0)
REVERT: B  118 LYS cc_start: 0.8746 (mttp) cc_final: 0.8294 (mmmt)
REVERT: B  184 PHE cc_start: 0.8029 (m-10) cc_final: 0.7610 (t80)
REVERT: B  513 ASP cc_start: 0.7714 (t0) cc_final: 0.7428 (t0)
REVERT: B  522 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8456 (tppt)
REVERT: B  552 MET cc_start: 0.8165 (tpp) cc_final: 0.7878 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 279
  average time/residue: 0.2226
  time to fit residues: 83.5893
Evaluate side-chains
  178 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 174
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0670
   chunk 53 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
A 335 GLN
A 436 ASN
A 544 GLN
A 564 GLN
A 568 GLN
B  18 GLN
B  98 GLN
B 248 HIS
B 323 GLN
B 416 GLN
B 530 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.116720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.090783 restraints weight = 17265.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 4.44
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9025  Z= 0.146
  Angle     :  0.711   8.090  12281  Z= 0.362
  Chirality :  0.044   0.218   1438
  Planarity :  0.005   0.066   1560
  Dihedral  :  7.898 167.238   1294
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.41 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.23), residues: 1136
  helix: -0.44 (0.18), residues: 726
  sheet:  0.07 (0.64), residues: 70
  loop : -2.62 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  85 
 HIS   0.004   0.001   HIS A 460 
 PHE   0.028   0.002   PHE B 431 
 TYR   0.018   0.001   TYR A 351 
 ARG   0.007   0.001   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  569)
  hydrogen bonds       : angle       4.80435 ( 1689)
  covalent geometry    : bond        0.00323 ( 9023)
  covalent geometry    : angle       0.71083 (12281)
  Misc. bond           : bond        0.00227 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 214
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8436 (tpp) cc_final: 0.8209 (tpp)
REVERT: A  145 TYR cc_start: 0.7150 (t80) cc_final: 0.6727 (t80)
REVERT: A  191 MET cc_start: 0.8023 (mmm) cc_final: 0.7672 (mmm)
REVERT: A  213 MET cc_start: 0.7722 (tpp) cc_final: 0.7253 (tpp)
REVERT: A  235 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: A  351 TYR cc_start: 0.9042 (m-80) cc_final: 0.8835 (m-10)
REVERT: A  411 MET cc_start: 0.7667 (tpt) cc_final: 0.7466 (tpt)
REVERT: A  417 MET cc_start: 0.8163 (mmp) cc_final: 0.7931 (mmp)
REVERT: A  436 ASN cc_start: 0.7977 (m-40) cc_final: 0.7561 (m-40)
REVERT: A  489 ILE cc_start: 0.8774 (mm) cc_final: 0.8448 (tp)
REVERT: A  541 MET cc_start: 0.7409 (tpt) cc_final: 0.7081 (tpt)
REVERT: B   34 MET cc_start: 0.5895 (tmm) cc_final: 0.5670 (mmp)
REVERT: B   43 MET cc_start: 0.8331 (tpp) cc_final: 0.7948 (mmm)
REVERT: B   68 ASN cc_start: 0.8838 (m110) cc_final: 0.8423 (t0)
REVERT: B  118 LYS cc_start: 0.8413 (mttp) cc_final: 0.8037 (mmmt)
REVERT: B  126 GLU cc_start: 0.7371 (mp0) cc_final: 0.7084 (mp0)
REVERT: B  127 MET cc_start: 0.8774 (pmm) cc_final: 0.8498 (pmm)
REVERT: B  192 MET cc_start: 0.8445 (tmm) cc_final: 0.8183 (tmm)
REVERT: B  343 ASP cc_start: 0.7944 (m-30) cc_final: 0.6988 (p0)
REVERT: B  429 TRP cc_start: 0.6260 (OUTLIER) cc_final: 0.5808 (t60)
REVERT: B  503 VAL cc_start: 0.8998 (t) cc_final: 0.8693 (m)
REVERT: B  504 ILE cc_start: 0.8646 (mt) cc_final: 0.8178 (pt)
REVERT: B  513 ASP cc_start: 0.8206 (t0) cc_final: 0.7863 (t0)
REVERT: B  522 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8302 (tptp)
  outliers start: 35
  outliers final: 17
  residues processed: 235
  average time/residue: 0.2024
  time to fit residues: 66.6311
Evaluate side-chains
  194 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  429 TRP
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  438 ASN
Chi-restraints excluded: chain B residue  471 TRP
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  526 ASN
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0270
   chunk 67 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 335 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.116905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.090391 restraints weight = 17351.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 4.42
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9025  Z= 0.128
  Angle     :  0.659   7.322  12281  Z= 0.334
  Chirality :  0.043   0.244   1438
  Planarity :  0.004   0.046   1560
  Dihedral  :  7.714 177.579   1293
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 23.27 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.25), residues: 1136
  helix:  0.39 (0.19), residues: 747
  sheet:  1.09 (0.69), residues: 65
  loop : -2.61 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  85 
 HIS   0.004   0.001   HIS B 563 
 PHE   0.018   0.001   PHE B  42 
 TYR   0.017   0.002   TYR B 394 
 ARG   0.005   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03574 (  569)
  hydrogen bonds       : angle       4.40382 ( 1689)
  covalent geometry    : bond        0.00283 ( 9023)
  covalent geometry    : angle       0.65904 (12281)
  Misc. bond           : bond        0.00126 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 199
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 TYR cc_start: 0.7216 (t80) cc_final: 0.6846 (t80)
REVERT: A  191 MET cc_start: 0.8136 (mmm) cc_final: 0.7732 (mmm)
REVERT: A  213 MET cc_start: 0.7722 (tpp) cc_final: 0.7278 (tpp)
REVERT: A  235 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7867 (tm-30)
REVERT: A  236 TRP cc_start: 0.8642 (t60) cc_final: 0.8146 (t60)
REVERT: A  428 PHE cc_start: 0.8165 (t80) cc_final: 0.7557 (t80)
REVERT: A  436 ASN cc_start: 0.7965 (m-40) cc_final: 0.7601 (m-40)
REVERT: A  489 ILE cc_start: 0.8750 (mm) cc_final: 0.8447 (tp)
REVERT: A  519 LEU cc_start: 0.8824 (mt) cc_final: 0.8604 (tt)
REVERT: A  541 MET cc_start: 0.7316 (tpt) cc_final: 0.6955 (tpt)
REVERT: A  559 MET cc_start: 0.8050 (mmm) cc_final: 0.7574 (mmm)
REVERT: B   34 MET cc_start: 0.6047 (tmm) cc_final: 0.5742 (mmp)
REVERT: B   43 MET cc_start: 0.8393 (tpp) cc_final: 0.7992 (mmm)
REVERT: B   50 CYS cc_start: 0.8643 (m) cc_final: 0.7977 (t)
REVERT: B   68 ASN cc_start: 0.8740 (m110) cc_final: 0.8308 (t0)
REVERT: B  118 LYS cc_start: 0.8293 (mttp) cc_final: 0.7943 (mmmt)
REVERT: B  126 GLU cc_start: 0.7417 (mp0) cc_final: 0.7135 (mp0)
REVERT: B  127 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8579 (pmm)
REVERT: B  192 MET cc_start: 0.8546 (tmm) cc_final: 0.8259 (tmm)
REVERT: B  303 MET cc_start: 0.8065 (tpp) cc_final: 0.7778 (mmp)
REVERT: B  343 ASP cc_start: 0.7813 (m-30) cc_final: 0.6980 (p0)
REVERT: B  389 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8508 (ttmm)
REVERT: B  418 ASN cc_start: 0.8935 (m-40) cc_final: 0.8666 (m-40)
REVERT: B  429 TRP cc_start: 0.6085 (OUTLIER) cc_final: 0.5426 (t60)
REVERT: B  503 VAL cc_start: 0.8974 (t) cc_final: 0.8650 (m)
REVERT: B  504 ILE cc_start: 0.8688 (mt) cc_final: 0.8259 (pt)
REVERT: B  513 ASP cc_start: 0.8240 (t0) cc_final: 0.7895 (t0)
REVERT: B  522 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8387 (tptp)
  outliers start: 43
  outliers final: 30
  residues processed: 225
  average time/residue: 0.1942
  time to fit residues: 61.8391
Evaluate side-chains
  205 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  480 PHE
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  168 TRP
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  429 TRP
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  438 ASN
Chi-restraints excluded: chain B residue  471 TRP
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  526 ASN
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 106 optimal weight:    0.0870
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
B 521 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.116186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.090287 restraints weight = 17252.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 4.32
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9025  Z= 0.128
  Angle     :  0.635   9.047  12281  Z= 0.319
  Chirality :  0.042   0.179   1438
  Planarity :  0.004   0.036   1560
  Dihedral  :  7.526 178.560   1293
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 24.59 %
    Favored  : 69.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.26), residues: 1136
  helix:  0.92 (0.19), residues: 751
  sheet:  1.39 (0.71), residues: 65
  loop : -2.47 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  85 
 HIS   0.003   0.001   HIS B 563 
 PHE   0.018   0.001   PHE A 462 
 TYR   0.014   0.001   TYR B 394 
 ARG   0.005   0.000   ARG B 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03424 (  569)
  hydrogen bonds       : angle       4.20917 ( 1689)
  covalent geometry    : bond        0.00286 ( 9023)
  covalent geometry    : angle       0.63528 (12281)
  Misc. bond           : bond        0.00098 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 189
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7954 (mp)
REVERT: A  118 MET cc_start: 0.6901 (mmt) cc_final: 0.6690 (mmt)
REVERT: A  145 TYR cc_start: 0.7301 (t80) cc_final: 0.6971 (t80)
REVERT: A  191 MET cc_start: 0.8404 (mmm) cc_final: 0.7960 (mmm)
REVERT: A  213 MET cc_start: 0.7723 (tpp) cc_final: 0.7397 (tpp)
REVERT: A  235 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: A  236 TRP cc_start: 0.8698 (t60) cc_final: 0.8163 (t60)
REVERT: A  304 MET cc_start: 0.8751 (mtm) cc_final: 0.8525 (mtm)
REVERT: A  338 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.5934 (tm-30)
REVERT: A  351 TYR cc_start: 0.8840 (m-10) cc_final: 0.8586 (m-80)
REVERT: A  393 TYR cc_start: 0.7982 (m-80) cc_final: 0.7198 (m-10)
REVERT: A  411 MET cc_start: 0.7883 (tpt) cc_final: 0.7451 (tpt)
REVERT: A  417 MET cc_start: 0.8550 (mmp) cc_final: 0.7597 (mmp)
REVERT: A  428 PHE cc_start: 0.8132 (t80) cc_final: 0.7471 (t80)
REVERT: A  436 ASN cc_start: 0.7947 (m-40) cc_final: 0.7667 (m-40)
REVERT: A  559 MET cc_start: 0.8128 (mmm) cc_final: 0.7590 (mmm)
REVERT: B   34 MET cc_start: 0.6277 (tmm) cc_final: 0.5871 (mmp)
REVERT: B   43 MET cc_start: 0.8569 (tpp) cc_final: 0.8181 (mmm)
REVERT: B   50 CYS cc_start: 0.8648 (m) cc_final: 0.8101 (t)
REVERT: B   68 ASN cc_start: 0.8751 (m110) cc_final: 0.8358 (t0)
REVERT: B  118 LYS cc_start: 0.8288 (mttp) cc_final: 0.7954 (mmmt)
REVERT: B  126 GLU cc_start: 0.7293 (mp0) cc_final: 0.6847 (mp0)
REVERT: B  127 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8508 (pmm)
REVERT: B  194 ARG cc_start: 0.8438 (tmm-80) cc_final: 0.8173 (ttp80)
REVERT: B  299 GLU cc_start: 0.8635 (tt0) cc_final: 0.8229 (mt-10)
REVERT: B  303 MET cc_start: 0.8161 (tpp) cc_final: 0.7933 (mmp)
REVERT: B  343 ASP cc_start: 0.7819 (m-30) cc_final: 0.7048 (p0)
REVERT: B  352 ARG cc_start: 0.8343 (mtp85) cc_final: 0.8021 (mmm-85)
REVERT: B  389 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8482 (ttmm)
REVERT: B  418 ASN cc_start: 0.8855 (m-40) cc_final: 0.8537 (m-40)
REVERT: B  503 VAL cc_start: 0.9033 (t) cc_final: 0.8674 (m)
REVERT: B  504 ILE cc_start: 0.8734 (mt) cc_final: 0.8325 (pt)
REVERT: B  513 ASP cc_start: 0.8242 (t0) cc_final: 0.7888 (t0)
REVERT: B  522 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8368 (tptp)
  outliers start: 56
  outliers final: 35
  residues processed: 222
  average time/residue: 0.1792
  time to fit residues: 56.8552
Evaluate side-chains
  210 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 172
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  480 PHE
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  471 TRP
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  526 ASN
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0040
   chunk 108 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
B 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.116244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.090195 restraints weight = 17319.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 4.29
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9025  Z= 0.134
  Angle     :  0.641   8.950  12281  Z= 0.316
  Chirality :  0.043   0.241   1438
  Planarity :  0.004   0.038   1560
  Dihedral  :  7.470 179.713   1293
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 25.03 %
    Favored  : 68.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1136
  helix:  1.25 (0.19), residues: 751
  sheet:  1.70 (0.72), residues: 65
  loop : -2.37 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 429 
 HIS   0.003   0.001   HIS B 563 
 PHE   0.021   0.001   PHE B 297 
 TYR   0.013   0.001   TYR B 394 
 ARG   0.007   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  569)
  hydrogen bonds       : angle       4.16664 ( 1689)
  covalent geometry    : bond        0.00305 ( 9023)
  covalent geometry    : angle       0.64082 (12281)
  Misc. bond           : bond        0.00105 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 185
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 TYR cc_start: 0.7288 (t80) cc_final: 0.6938 (t80)
REVERT: A  191 MET cc_start: 0.8396 (mmm) cc_final: 0.7919 (mmm)
REVERT: A  213 MET cc_start: 0.7805 (tpp) cc_final: 0.7449 (tpp)
REVERT: A  235 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: A  236 TRP cc_start: 0.8658 (t60) cc_final: 0.8107 (t60)
REVERT: A  351 TYR cc_start: 0.8865 (m-80) cc_final: 0.8589 (m-80)
REVERT: A  417 MET cc_start: 0.8420 (mmp) cc_final: 0.7392 (mmp)
REVERT: A  436 ASN cc_start: 0.7948 (m-40) cc_final: 0.7723 (m-40)
REVERT: A  559 MET cc_start: 0.8059 (mmm) cc_final: 0.7846 (mmm)
REVERT: B   34 MET cc_start: 0.6291 (tmm) cc_final: 0.5954 (mmp)
REVERT: B   43 MET cc_start: 0.8528 (tpp) cc_final: 0.8138 (mmm)
REVERT: B   50 CYS cc_start: 0.8605 (m) cc_final: 0.8113 (t)
REVERT: B  118 LYS cc_start: 0.8241 (mttp) cc_final: 0.7899 (mmmt)
REVERT: B  126 GLU cc_start: 0.7252 (mp0) cc_final: 0.6828 (mp0)
REVERT: B  127 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8512 (pmm)
REVERT: B  184 PHE cc_start: 0.8337 (m-10) cc_final: 0.7331 (t80)
REVERT: B  192 MET cc_start: 0.8493 (tmm) cc_final: 0.8254 (tmm)
REVERT: B  299 GLU cc_start: 0.8561 (tt0) cc_final: 0.8139 (mt-10)
REVERT: B  303 MET cc_start: 0.8085 (tpp) cc_final: 0.7869 (mmp)
REVERT: B  343 ASP cc_start: 0.7696 (m-30) cc_final: 0.6943 (p0)
REVERT: B  352 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7934 (mmm-85)
REVERT: B  389 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8440 (ttmm)
REVERT: B  418 ASN cc_start: 0.8854 (m-40) cc_final: 0.8579 (m-40)
REVERT: B  504 ILE cc_start: 0.8726 (mt) cc_final: 0.8322 (pt)
REVERT: B  513 ASP cc_start: 0.8205 (t0) cc_final: 0.7777 (t0)
REVERT: B  522 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8332 (tptp)
  outliers start: 59
  outliers final: 40
  residues processed: 230
  average time/residue: 0.1901
  time to fit residues: 62.8240
Evaluate side-chains
  213 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 172
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  480 PHE
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  477 GLU
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  526 ASN
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 581 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.115084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.088728 restraints weight = 17411.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 4.35
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9025  Z= 0.148
  Angle     :  0.668  10.408  12281  Z= 0.330
  Chirality :  0.044   0.265   1438
  Planarity :  0.004   0.037   1560
  Dihedral  :  7.431 178.035   1293
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 26.13 %
    Favored  : 67.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1136
  helix:  1.39 (0.19), residues: 749
  sheet:  1.61 (0.72), residues: 66
  loop : -2.22 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 577 
 HIS   0.002   0.001   HIS A 135 
 PHE   0.020   0.001   PHE B 431 
 TYR   0.012   0.001   TYR B 394 
 ARG   0.005   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03450 (  569)
  hydrogen bonds       : angle       4.10935 ( 1689)
  covalent geometry    : bond        0.00339 ( 9023)
  covalent geometry    : angle       0.66815 (12281)
  Misc. bond           : bond        0.00158 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 178
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8766 (tpp) cc_final: 0.8426 (mmp)
REVERT: A   80 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8015 (mp)
REVERT: A  145 TYR cc_start: 0.7353 (t80) cc_final: 0.7013 (t80)
REVERT: A  191 MET cc_start: 0.8459 (mmm) cc_final: 0.7913 (mmm)
REVERT: A  213 MET cc_start: 0.7861 (tpp) cc_final: 0.7515 (tpp)
REVERT: A  231 ARG cc_start: 0.8623 (tpp80) cc_final: 0.8209 (tpp80)
REVERT: A  235 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: A  236 TRP cc_start: 0.8748 (t60) cc_final: 0.8217 (t60)
REVERT: A  351 TYR cc_start: 0.8856 (m-80) cc_final: 0.8337 (m-80)
REVERT: A  411 MET cc_start: 0.7904 (tpt) cc_final: 0.7615 (tpt)
REVERT: A  417 MET cc_start: 0.8355 (mmp) cc_final: 0.7310 (mmp)
REVERT: A  559 MET cc_start: 0.8178 (mmm) cc_final: 0.7849 (mmm)
REVERT: B   34 MET cc_start: 0.6469 (tmm) cc_final: 0.6069 (mmp)
REVERT: B   43 MET cc_start: 0.8670 (tpp) cc_final: 0.8307 (mmm)
REVERT: B   50 CYS cc_start: 0.8643 (m) cc_final: 0.8212 (t)
REVERT: B  118 LYS cc_start: 0.8295 (mttp) cc_final: 0.7950 (mmmt)
REVERT: B  126 GLU cc_start: 0.7198 (mp0) cc_final: 0.6765 (mp0)
REVERT: B  127 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8466 (pmm)
REVERT: B  184 PHE cc_start: 0.8406 (m-10) cc_final: 0.7397 (t80)
REVERT: B  192 MET cc_start: 0.8528 (tmm) cc_final: 0.8249 (tmm)
REVERT: B  335 GLN cc_start: 0.7396 (pm20) cc_final: 0.7162 (pp30)
REVERT: B  343 ASP cc_start: 0.7684 (m-30) cc_final: 0.7005 (p0)
REVERT: B  389 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8568 (ttmm)
REVERT: B  390 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8542 (mp)
REVERT: B  418 ASN cc_start: 0.8927 (m-40) cc_final: 0.8640 (m-40)
REVERT: B  504 ILE cc_start: 0.8783 (mt) cc_final: 0.8476 (pt)
REVERT: B  513 ASP cc_start: 0.8131 (t0) cc_final: 0.7830 (t0)
REVERT: B  522 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8376 (tptp)
  outliers start: 57
  outliers final: 44
  residues processed: 216
  average time/residue: 0.1825
  time to fit residues: 56.3875
Evaluate side-chains
  212 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 165
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  480 PHE
Chi-restraints excluded: chain B residue   22 SER
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  473 THR
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  526 ASN
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 52 optimal weight:    0.5980
   chunk 94 optimal weight:    0.0570
   chunk 97 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 88 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0060
   chunk 37 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.2514

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.119152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.092834 restraints weight = 17321.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 4.32
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9025  Z= 0.113
  Angle     :  0.646  10.838  12281  Z= 0.313
  Chirality :  0.043   0.273   1438
  Planarity :  0.004   0.036   1560
  Dihedral  :  7.249 175.688   1293
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 29.20 %
    Favored  : 66.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1136
  helix:  1.47 (0.19), residues: 747
  sheet:  1.62 (0.71), residues: 66
  loop : -2.21 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 577 
 HIS   0.002   0.000   HIS A 578 
 PHE   0.013   0.001   PHE B 431 
 TYR   0.014   0.001   TYR A  90 
 ARG   0.006   0.000   ARG B 410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03121 (  569)
  hydrogen bonds       : angle       3.99164 ( 1689)
  covalent geometry    : bond        0.00251 ( 9023)
  covalent geometry    : angle       0.64631 (12281)
  Misc. bond           : bond        0.00116 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8721 (tpp) cc_final: 0.8407 (mmm)
REVERT: A  118 MET cc_start: 0.7164 (mmm) cc_final: 0.6842 (mmm)
REVERT: A  145 TYR cc_start: 0.7355 (t80) cc_final: 0.6971 (t80)
REVERT: A  191 MET cc_start: 0.8424 (mmm) cc_final: 0.7749 (mmm)
REVERT: A  213 MET cc_start: 0.7837 (tpp) cc_final: 0.7534 (tpp)
REVERT: A  231 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8155 (tpp80)
REVERT: A  235 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: A  338 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5423 (tm-30)
REVERT: A  351 TYR cc_start: 0.8719 (m-80) cc_final: 0.8405 (m-80)
REVERT: A  411 MET cc_start: 0.7869 (tpt) cc_final: 0.7603 (tpt)
REVERT: A  417 MET cc_start: 0.8163 (mmp) cc_final: 0.7079 (mmp)
REVERT: B   34 MET cc_start: 0.6441 (tmm) cc_final: 0.5967 (mmp)
REVERT: B   43 MET cc_start: 0.8572 (tpp) cc_final: 0.8188 (mmm)
REVERT: B   50 CYS cc_start: 0.8502 (m) cc_final: 0.8126 (t)
REVERT: B  118 LYS cc_start: 0.8191 (mttp) cc_final: 0.7894 (mmmt)
REVERT: B  126 GLU cc_start: 0.7145 (mp0) cc_final: 0.6774 (mp0)
REVERT: B  127 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8506 (pmm)
REVERT: B  189 ARG cc_start: 0.7956 (tmm-80) cc_final: 0.7604 (ttm-80)
REVERT: B  335 GLN cc_start: 0.7446 (pm20) cc_final: 0.7122 (pp30)
REVERT: B  343 ASP cc_start: 0.7529 (m-30) cc_final: 0.7182 (p0)
REVERT: B  389 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8340 (ttmm)
REVERT: B  418 ASN cc_start: 0.8838 (m-40) cc_final: 0.8532 (m-40)
REVERT: B  436 LEU cc_start: 0.7148 (mm) cc_final: 0.6694 (tt)
REVERT: B  504 ILE cc_start: 0.8773 (mt) cc_final: 0.8502 (pt)
REVERT: B  513 ASP cc_start: 0.8157 (t0) cc_final: 0.7881 (t0)
REVERT: B  522 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8293 (tptp)
  outliers start: 36
  outliers final: 24
  residues processed: 207
  average time/residue: 0.1811
  time to fit residues: 54.0101
Evaluate side-chains
  196 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  477 GLU
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 84 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0570
   chunk 106 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0770
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.2656

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.118726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.092232 restraints weight = 17221.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 4.37
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9025  Z= 0.114
  Angle     :  0.640  10.929  12281  Z= 0.311
  Chirality :  0.043   0.284   1438
  Planarity :  0.003   0.035   1560
  Dihedral  :  7.193 175.906   1293
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 29.31 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1136
  helix:  1.55 (0.19), residues: 750
  sheet:  1.68 (0.72), residues: 66
  loop : -2.25 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 577 
 HIS   0.002   0.000   HIS B 248 
 PHE   0.017   0.001   PHE B 431 
 TYR   0.025   0.001   TYR A  90 
 ARG   0.005   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  569)
  hydrogen bonds       : angle       3.91268 ( 1689)
  covalent geometry    : bond        0.00251 ( 9023)
  covalent geometry    : angle       0.63958 (12281)
  Misc. bond           : bond        0.00118 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 183
  time to evaluate  : 1.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8745 (tpp) cc_final: 0.8424 (mmm)
REVERT: A  118 MET cc_start: 0.7238 (mmm) cc_final: 0.7015 (mmm)
REVERT: A  145 TYR cc_start: 0.7324 (t80) cc_final: 0.6901 (t80)
REVERT: A  176 PHE cc_start: 0.7287 (t80) cc_final: 0.7020 (t80)
REVERT: A  191 MET cc_start: 0.8440 (mmm) cc_final: 0.7663 (mmm)
REVERT: A  213 MET cc_start: 0.7931 (tpp) cc_final: 0.7612 (tpp)
REVERT: A  231 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8120 (tpp80)
REVERT: A  235 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7777 (tm-30)
REVERT: A  338 GLN cc_start: 0.5742 (OUTLIER) cc_final: 0.5416 (tm-30)
REVERT: A  351 TYR cc_start: 0.8660 (m-80) cc_final: 0.8336 (m-80)
REVERT: A  411 MET cc_start: 0.7922 (tpt) cc_final: 0.7643 (tpt)
REVERT: A  417 MET cc_start: 0.8160 (mmp) cc_final: 0.7088 (mmp)
REVERT: A  424 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8064 (m-80)
REVERT: A  559 MET cc_start: 0.8190 (mmm) cc_final: 0.7749 (mmm)
REVERT: B   34 MET cc_start: 0.6484 (tmm) cc_final: 0.6017 (mmp)
REVERT: B   43 MET cc_start: 0.8608 (tpp) cc_final: 0.8250 (mmm)
REVERT: B   50 CYS cc_start: 0.8427 (m) cc_final: 0.8128 (t)
REVERT: B   68 ASN cc_start: 0.8743 (m110) cc_final: 0.8271 (t0)
REVERT: B  118 LYS cc_start: 0.8223 (mttp) cc_final: 0.7927 (mmmt)
REVERT: B  126 GLU cc_start: 0.7022 (mp0) cc_final: 0.6654 (mp0)
REVERT: B  127 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8442 (pmm)
REVERT: B  189 ARG cc_start: 0.7984 (tmm-80) cc_final: 0.7676 (ttm-80)
REVERT: B  194 ARG cc_start: 0.8557 (tmm-80) cc_final: 0.8333 (ttp80)
REVERT: B  303 MET cc_start: 0.8404 (mmp) cc_final: 0.7994 (mmt)
REVERT: B  335 GLN cc_start: 0.7514 (pm20) cc_final: 0.7174 (pp30)
REVERT: B  343 ASP cc_start: 0.7491 (m-30) cc_final: 0.7024 (p0)
REVERT: B  389 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8426 (ttmm)
REVERT: B  418 ASN cc_start: 0.8797 (m-40) cc_final: 0.8510 (m-40)
REVERT: B  436 LEU cc_start: 0.7028 (mm) cc_final: 0.6540 (tt)
REVERT: B  504 ILE cc_start: 0.8773 (mt) cc_final: 0.8508 (pt)
REVERT: B  513 ASP cc_start: 0.8176 (t0) cc_final: 0.7944 (t0)
REVERT: B  522 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8331 (tptp)
  outliers start: 39
  outliers final: 26
  residues processed: 208
  average time/residue: 0.2092
  time to fit residues: 63.2781
Evaluate side-chains
  201 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  163 ASP
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  303 MET
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  438 ASN
Chi-restraints excluded: chain B residue  477 GLU
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0050
   chunk 24 optimal weight:    0.9980
   chunk 87 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
B  26 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.118674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.092264 restraints weight = 17325.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 4.35
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9025  Z= 0.121
  Angle     :  0.645  11.167  12281  Z= 0.313
  Chirality :  0.043   0.292   1438
  Planarity :  0.003   0.033   1560
  Dihedral  :  7.156 175.563   1293
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 29.75 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1136
  helix:  1.63 (0.19), residues: 749
  sheet:  1.56 (0.71), residues: 66
  loop : -2.23 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 577 
 HIS   0.002   0.000   HIS A 135 
 PHE   0.015   0.001   PHE B 431 
 TYR   0.021   0.001   TYR A  90 
 ARG   0.004   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03139 (  569)
  hydrogen bonds       : angle       3.87812 ( 1689)
  covalent geometry    : bond        0.00276 ( 9023)
  covalent geometry    : angle       0.64494 (12281)
  Misc. bond           : bond        0.00124 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 180
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 TYR cc_start: 0.7248 (t80) cc_final: 0.6818 (t80)
REVERT: A  176 PHE cc_start: 0.7283 (t80) cc_final: 0.7056 (t80)
REVERT: A  191 MET cc_start: 0.8453 (mmm) cc_final: 0.7638 (mmm)
REVERT: A  213 MET cc_start: 0.7887 (tpp) cc_final: 0.7555 (tpp)
REVERT: A  231 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8102 (tpp80)
REVERT: A  235 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: A  351 TYR cc_start: 0.8730 (m-80) cc_final: 0.8392 (m-80)
REVERT: A  411 MET cc_start: 0.7940 (tpt) cc_final: 0.7658 (tpt)
REVERT: A  417 MET cc_start: 0.8128 (mmp) cc_final: 0.7038 (mmp)
REVERT: A  424 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8075 (m-80)
REVERT: A  541 MET cc_start: 0.7307 (tpt) cc_final: 0.7049 (tpt)
REVERT: A  559 MET cc_start: 0.8232 (mmm) cc_final: 0.7777 (mmm)
REVERT: B   34 MET cc_start: 0.6392 (tmm) cc_final: 0.5966 (mmp)
REVERT: B   43 MET cc_start: 0.8596 (tpp) cc_final: 0.8253 (mmm)
REVERT: B   50 CYS cc_start: 0.8363 (m) cc_final: 0.8093 (t)
REVERT: B   68 ASN cc_start: 0.8699 (m110) cc_final: 0.8224 (t0)
REVERT: B  118 LYS cc_start: 0.8204 (mttp) cc_final: 0.7905 (mmmt)
REVERT: B  126 GLU cc_start: 0.7025 (mp0) cc_final: 0.6690 (mp0)
REVERT: B  127 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8480 (pmm)
REVERT: B  189 ARG cc_start: 0.7977 (tmm-80) cc_final: 0.7674 (ttm-80)
REVERT: B  335 GLN cc_start: 0.7548 (pm20) cc_final: 0.7190 (pp30)
REVERT: B  343 ASP cc_start: 0.7456 (m-30) cc_final: 0.6985 (p0)
REVERT: B  372 SER cc_start: 0.8382 (t) cc_final: 0.7987 (p)
REVERT: B  389 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8468 (ttmm)
REVERT: B  418 ASN cc_start: 0.8810 (m-40) cc_final: 0.8527 (m-40)
REVERT: B  436 LEU cc_start: 0.7032 (mm) cc_final: 0.6540 (tt)
REVERT: B  504 ILE cc_start: 0.8760 (mt) cc_final: 0.8492 (pt)
REVERT: B  513 ASP cc_start: 0.8232 (t0) cc_final: 0.7989 (t0)
REVERT: B  522 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8324 (tptp)
  outliers start: 35
  outliers final: 28
  residues processed: 201
  average time/residue: 0.1758
  time to fit residues: 51.9893
Evaluate side-chains
  205 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 175
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  477 GLU
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0030
   chunk 106 optimal weight:    0.0470
   chunk 32 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0770
   chunk 3 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.3046

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.120065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093391 restraints weight = 17166.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 4.42
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9025  Z= 0.113
  Angle     :  0.648  11.330  12281  Z= 0.313
  Chirality :  0.043   0.296   1438
  Planarity :  0.003   0.029   1560
  Dihedral  :  7.110 175.109   1293
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 30.95 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1136
  helix:  1.67 (0.19), residues: 749
  sheet:  1.58 (0.71), residues: 66
  loop : -2.28 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 577 
 HIS   0.002   0.000   HIS B 563 
 PHE   0.015   0.001   PHE B 431 
 TYR   0.021   0.001   TYR A  90 
 ARG   0.005   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03054 (  569)
  hydrogen bonds       : angle       3.81373 ( 1689)
  covalent geometry    : bond        0.00251 ( 9023)
  covalent geometry    : angle       0.64805 (12281)
  Misc. bond           : bond        0.00116 (    2)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8792 (tpp) cc_final: 0.8536 (mmp)
REVERT: A  145 TYR cc_start: 0.7218 (t80) cc_final: 0.6796 (t80)
REVERT: A  176 PHE cc_start: 0.7275 (t80) cc_final: 0.7045 (t80)
REVERT: A  191 MET cc_start: 0.8450 (mmm) cc_final: 0.7560 (mmm)
REVERT: A  213 MET cc_start: 0.7903 (tpp) cc_final: 0.7555 (tpp)
REVERT: A  231 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8111 (tpp80)
REVERT: A  235 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7938 (tm-30)
REVERT: A  338 GLN cc_start: 0.5609 (OUTLIER) cc_final: 0.5267 (tm-30)
REVERT: A  411 MET cc_start: 0.7932 (tpt) cc_final: 0.7667 (tpt)
REVERT: A  417 MET cc_start: 0.8063 (mmp) cc_final: 0.6992 (mmp)
REVERT: A  424 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8046 (m-80)
REVERT: A  541 MET cc_start: 0.7257 (tpt) cc_final: 0.6996 (tpt)
REVERT: A  559 MET cc_start: 0.8216 (mmm) cc_final: 0.7764 (mmm)
REVERT: B   34 MET cc_start: 0.6414 (tmm) cc_final: 0.5962 (mmp)
REVERT: B   43 MET cc_start: 0.8615 (tpp) cc_final: 0.8264 (mmm)
REVERT: B   50 CYS cc_start: 0.8327 (m) cc_final: 0.8111 (t)
REVERT: B  118 LYS cc_start: 0.8186 (mttp) cc_final: 0.7905 (mmmt)
REVERT: B  126 GLU cc_start: 0.7035 (mp0) cc_final: 0.6697 (mp0)
REVERT: B  127 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8466 (pmm)
REVERT: B  189 ARG cc_start: 0.7961 (tmm-80) cc_final: 0.7672 (ttm-80)
REVERT: B  335 GLN cc_start: 0.7596 (pm20) cc_final: 0.7221 (pp30)
REVERT: B  343 ASP cc_start: 0.7557 (m-30) cc_final: 0.7061 (p0)
REVERT: B  372 SER cc_start: 0.8309 (t) cc_final: 0.7971 (p)
REVERT: B  389 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8440 (ttmm)
REVERT: B  418 ASN cc_start: 0.8788 (m-40) cc_final: 0.8497 (m-40)
REVERT: B  436 LEU cc_start: 0.7055 (mm) cc_final: 0.6548 (tt)
REVERT: B  504 ILE cc_start: 0.8772 (mt) cc_final: 0.8524 (pt)
REVERT: B  522 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8316 (tptp)
  outliers start: 28
  outliers final: 22
  residues processed: 202
  average time/residue: 0.1725
  time to fit residues: 50.7189
Evaluate side-chains
  205 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  244 TYR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  424 PHE
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  203 HIS
Chi-restraints excluded: chain B residue  222 THR
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  342 TYR
Chi-restraints excluded: chain B residue  477 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0270
   chunk 53 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8642

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.117499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.091048 restraints weight = 17387.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 4.32
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9025  Z= 0.139
  Angle     :  0.670  11.319  12281  Z= 0.325
  Chirality :  0.044   0.303   1438
  Planarity :  0.003   0.028   1560
  Dihedral  :  7.130 174.128   1292
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 30.85 %
    Favored  : 65.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1136
  helix:  1.69 (0.19), residues: 747
  sheet:  1.42 (0.70), residues: 66
  loop : -2.21 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 577 
 HIS   0.003   0.001   HIS A 135 
 PHE   0.015   0.001   PHE B 431 
 TYR   0.020   0.001   TYR A  90 
 ARG   0.011   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  569)
  hydrogen bonds       : angle       3.85803 ( 1689)
  covalent geometry    : bond        0.00324 ( 9023)
  covalent geometry    : angle       0.66999 (12281)
  Misc. bond           : bond        0.00158 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3438.11 seconds
wall clock time: 61 minutes 16.88 seconds (3676.88 seconds total)