Starting phenix.real_space_refine
on Tue Mar  3 18:36:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ocy_12816/03_2026/7ocy_12816_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ocy_12816/03_2026/7ocy_12816.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ocy_12816/03_2026/7ocy_12816.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ocy_12816/03_2026/7ocy_12816.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ocy_12816/03_2026/7ocy_12816_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ocy_12816/03_2026/7ocy_12816_neut.cif"
  }
  resolution = 4.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5051      2.51       5
     N    1423      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7994
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 3613
          Classifications: {'peptide': 557}
          Incomplete info: {'truncation_to_alanine': 206}
          Link IDs: {'PTRANS': 13, 'TRANS': 543}
          Chain breaks: 1
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 715
          Unresolved non-hydrogen angles: 909
          Unresolved non-hydrogen dihedrals: 569
          Unresolved non-hydrogen chiralities: 76
          Planarities with less than four sites: {'ASP:plan': 14, 'TYR:plan': 5, 'GLU:plan': 25, 'GLN:plan1': 10, 'PHE:plan': 8, 'HIS:plan': 5, 'ARG:plan': 15, 'ASN:plan1': 6}
          Unresolved non-hydrogen planarities: 383
    Chain: "B"
      Number of atoms: 3852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 3852
          Classifications: {'peptide': 578}
          Incomplete info: {'truncation_to_alanine': 214}
          Link IDs: {'PTRANS': 10, 'TRANS': 567}
          Chain breaks: 2
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 742
          Unresolved non-hydrogen angles: 955
          Unresolved non-hydrogen dihedrals: 581
          Unresolved non-hydrogen chiralities: 83
          Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 27, 'ARG:plan': 10, 'ASN:plan1': 16, 'HIS:plan': 7, 'PHE:plan': 9, 'TYR:plan': 5, 'GLN:plan1': 9}
          Unresolved non-hydrogen planarities: 414
    Chain: "C"
      Number of atoms: 529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 529
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 104}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 344
          Unresolved non-hydrogen angles: 443
          Unresolved non-hydrogen dihedrals: 291
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 3, 'ASP:plan': 7, 'ARG:plan': 9, 'PHE:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 2, 'TYR:plan': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 222
  Time building chain proxies: 1.95, per 1000 atoms: 0.24
  Number of scatterers: 7994
  At special positions: 0
  Unit cell: (76.96, 83.2, 165.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1488      8.00
     N    1423      7.00
     C    5051      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 272.8 milliseconds
  

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2316

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      66.5% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 9
    Processing helix  chain 'A' and resid 11 through 46
      removed outlier: 4.019A  pdb=" N   ILE A  17 " --> pdb=" O   GLY A  13 " (cutoff:3.500A)
      Proline residue:  A  33  - end of helix
    Processing helix  chain 'A' and resid 47 through 97
    Processing helix  chain 'A' and resid 99 through 105
    Processing helix  chain 'A' and resid 107 through 132
      removed outlier: 4.268A  pdb=" N   ASP A 118 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 151
      removed outlier: 4.034A  pdb=" N   PHE A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 200
      removed outlier: 3.732A  pdb=" N   ILE A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A 159 " --> pdb=" O   TRP A 155 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLY A 177 " --> pdb=" O   PHE A 173 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ILE A 182 " --> pdb=" O   LYS A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 207
    Processing helix  chain 'A' and resid 208 through 258
      removed outlier: 4.304A  pdb=" N   ASN A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   HIS A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
      removed outlier: 4.033A  pdb=" N   SER A 258 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 311
      removed outlier: 4.357A  pdb=" N   ALA A 272 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   SER A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   SER A 296 " --> pdb=" O   MET A 292 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   ARG A 297 " --> pdb=" O   MET A 293 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA A 298 " --> pdb=" O   MET A 294 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLU A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   VAL A 308 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 376
      removed outlier: 3.987A  pdb=" N   ILE A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 405
      removed outlier: 3.530A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 426
    Processing helix  chain 'A' and resid 432 through 444
    Processing helix  chain 'A' and resid 445 through 451
    Processing helix  chain 'A' and resid 468 through 483
      removed outlier: 4.646A  pdb=" N   GLY A 483 " --> pdb=" O   ARG A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 524 through 529
      removed outlier: 3.705A  pdb=" N   VAL A 528 " --> pdb=" O   LYS A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 555
      removed outlier: 4.040A  pdb=" N   ALA A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ASN A 555 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 563
      removed outlier: 4.411A  pdb=" N   GLN A 559 " --> pdb=" O   ASN A 555 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLU A 560 " --> pdb=" O   PRO A 556 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE A 561 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 16
      removed outlier: 3.772A  pdb=" N   TYR B  14 " --> pdb=" O   PHE B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 60
      removed outlier: 3.857A  pdb=" N   PHE B  26 " --> pdb=" O   PHE B  22 " (cutoff:3.500A)
      Proline residue:  B  40  - end of helix
      removed outlier: 3.674A  pdb=" N   GLN B  59 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 112
    Processing helix  chain 'B' and resid 115 through 122
      removed outlier: 3.581A  pdb=" N   PHE B 119 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 133
    Processing helix  chain 'B' and resid 133 through 167
      removed outlier: 4.753A  pdb=" N   LEU B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LEU B 147 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLN B 148 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 175
    Processing helix  chain 'B' and resid 177 through 224
      removed outlier: 6.567A  pdb=" N   ARG B 218 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL B 219 " --> pdb=" O   SER B 215 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE B 220 " --> pdb=" O   GLY B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 253
    Processing helix  chain 'B' and resid 253 through 280
    Processing helix  chain 'B' and resid 283 through 330
      Proline residue:  B 304  - end of helix
      removed outlier: 4.155A  pdb=" N   SER B 313 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   MET B 314 " --> pdb=" O   SER B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 397
      removed outlier: 4.430A  pdb=" N   MET B 393 " --> pdb=" O   LYS B 389 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASN B 394 " --> pdb=" O   THR B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 425
    Processing helix  chain 'B' and resid 439 through 446
    Processing helix  chain 'B' and resid 454 through 463
      removed outlier: 3.941A  pdb=" N   GLN B 458 " --> pdb=" O   GLU B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 472
    Processing helix  chain 'B' and resid 474 through 478
    Processing helix  chain 'B' and resid 488 through 504
      removed outlier: 3.726A  pdb=" N   LYS B 492 " --> pdb=" O   SER B 488 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLN B 493 " --> pdb=" O   THR B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 536
      removed outlier: 4.194A  pdb=" N   GLY B 535 " --> pdb=" O   GLU B 531 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ARG B 536 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 549
      removed outlier: 3.568A  pdb=" N   LEU B 549 " --> pdb=" O   LYS B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 574
    Processing helix  chain 'B' and resid 576 through 583
    Processing helix  chain 'C' and resid 61 through 64
    Processing helix  chain 'C' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 353
      removed outlier: 5.941A  pdb=" N   LYS A 347 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   SER A 335 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ILE A 349 " --> pdb=" O   HIS A 333 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   VAL A 334 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   GLU A 384 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 406 through 408
      removed outlier: 6.764A  pdb=" N   MET A 358 " --> pdb=" O   ARG A 533 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   LEU A 535 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   GLY A 360 " --> pdb=" O   LEU A 535 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   LEU A 537 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   VAL A 362 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE A 534 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   GLU A 545 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL A 536 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419
    Processing sheet with id=AA4, first strand: chain 'B' and resid 366 through 369
      removed outlier: 4.749A  pdb=" N   VAL B 355 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   VAL B 355 " --> pdb=" O   GLU B 404 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   GLU B 404 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 426 through 429
      removed outlier: 5.931A  pdb=" N   LEU B 508 " --> pdb=" O   PHE B 539 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ILE B 541 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LEU B 510 " --> pdb=" O   ILE B 541 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   MET B 378 " --> pdb=" O   ARG B 553 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   ILE B 555 " --> pdb=" O   MET B 378 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ALA B 380 " --> pdb=" O   ILE B 555 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   LEU B 557 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL B 382 " --> pdb=" O   LEU B 557 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU B 564 " --> pdb=" O   VAL B 556 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 7 through 10
    Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16
      removed outlier: 6.997A  pdb=" N   VAL C  15 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE C  98 " --> pdb=" O   ARG C  33 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   ARG C  33 " --> pdb=" O   PHE C  98 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   ARG C  38 " --> pdb=" O   MET C  47 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   MET C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    666 hydrogen bonds defined for protein.
    1947 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2776
        1.34 -     1.46: 1649
        1.46 -     1.58: 3585
        1.58 -     1.69: 0
        1.69 -     1.81: 64
  Bond restraints: 8074
  Sorted by residual:
  bond pdb=" N   THR B   2 "
       pdb=" CA  THR B   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.12e+00
  bond pdb=" N   GLN C   6 "
       pdb=" CA  GLN C   6 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   ASP A   2 "
       pdb=" CA  ASP A   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.91e+00
  bond pdb=" C   GLU A 484 "
       pdb=" O   GLU A 484 "
    ideal  model  delta    sigma   weight residual
    1.233  1.241 -0.008 4.80e-03 4.34e+04 2.80e+00
  bond pdb=" CA  THR B 363 "
       pdb=" C   THR B 363 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.008 7.40e-03 1.83e+04 1.03e+00
  ... (remaining 8069 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 10483
        1.24 -     2.49: 451
        2.49 -     3.73: 59
        3.73 -     4.97: 21
        4.97 -     6.21: 5
  Bond angle restraints: 11019
  Sorted by residual:
  angle pdb=" N   ILE A 561 "
        pdb=" CA  ILE A 561 "
        pdb=" C   ILE A 561 "
      ideal   model   delta    sigma   weight residual
     111.90  107.47    4.43 8.10e-01 1.52e+00 2.98e+01
  angle pdb=" N   VAL C  48 "
        pdb=" CA  VAL C  48 "
        pdb=" C   VAL C  48 "
      ideal   model   delta    sigma   weight residual
     111.62  108.56    3.06 7.90e-01 1.60e+00 1.50e+01
  angle pdb=" N   ILE A 376 "
        pdb=" CA  ILE A 376 "
        pdb=" C   ILE A 376 "
      ideal   model   delta    sigma   weight residual
     112.35  107.76    4.59 1.20e+00 6.94e-01 1.46e+01
  angle pdb=" C   ILE A 136 "
        pdb=" CA  ILE A 136 "
        pdb=" CB  ILE A 136 "
      ideal   model   delta    sigma   weight residual
     114.00  109.50    4.50 1.31e+00 5.83e-01 1.18e+01
  angle pdb=" N   ARG B 558 "
        pdb=" CA  ARG B 558 "
        pdb=" C   ARG B 558 "
      ideal   model   delta    sigma   weight residual
     110.80  104.59    6.21 2.13e+00 2.20e-01 8.51e+00
  ... (remaining 11014 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4463
       17.53 -    35.05: 260
       35.05 -    52.58: 43
       52.58 -    70.11: 6
       70.11 -    87.64: 6
  Dihedral angle restraints: 4778
    sinusoidal: 1208
      harmonic: 3570
  Sorted by residual:
  dihedral pdb=" CA  ASN C  32 "
           pdb=" C   ASN C  32 "
           pdb=" N   ARG C  33 "
           pdb=" CA  ARG C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LEU B 557 "
           pdb=" C   LEU B 557 "
           pdb=" N   ARG B 558 "
           pdb=" CA  ARG B 558 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLY A 270 "
           pdb=" C   GLY A 270 "
           pdb=" N   VAL A 271 "
           pdb=" CA  VAL A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.10  -18.90     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 892
       0.031 -    0.062: 338
       0.062 -    0.093: 107
       0.093 -    0.124: 45
       0.124 -    0.156: 4
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  ILE B 541 "
            pdb=" N   ILE B 541 "
            pdb=" C   ILE B 541 "
            pdb=" CB  ILE B 541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  ILE A 519 "
            pdb=" N   ILE A 519 "
            pdb=" C   ILE A 519 "
            pdb=" CB  ILE A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  VAL B 356 "
            pdb=" N   VAL B 356 "
            pdb=" C   VAL B 356 "
            pdb=" CB  VAL B 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 303 "   -0.028 5.00e-02 4.00e+02   4.18e-02 2.79e+00
        pdb=" N   PRO B 304 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 304 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 304 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  31 "    0.012 2.00e-02 2.50e+03   9.44e-03 2.23e+00
        pdb=" CG  TRP A  31 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  31 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  31 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  31 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  31 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  31 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  31 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  31 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  31 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 210 "   -0.007 2.00e-02 2.50e+03   1.41e-02 2.00e+00
        pdb=" C   MET B 210 "    0.024 2.00e-02 2.50e+03
        pdb=" O   MET B 210 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP B 211 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 77
        2.56 -     3.15: 7525
        3.15 -     3.73: 12918
        3.73 -     4.32: 15305
        4.32 -     4.90: 25084
  Nonbonded interactions: 60909
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 222 "
            pdb=" OG1 THR A 225 "
     model   vdw
     1.980 3.040
  nonbonded pdb=" O   VAL A 250 "
            pdb=" OG  SER A 253 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" OE2 GLU A  89 "
            pdb=" NE  ARG A  93 "
     model   vdw
     2.077 3.120
  nonbonded pdb=" O   LYS A 219 "
            pdb=" OE1 GLU A 223 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" NZ  LYS A  94 "
            pdb=" O   MET A 309 "
     model   vdw
     2.255 3.120
  ... (remaining 60904 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.280
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8074  Z= 0.175
  Angle     :  0.616   6.212  11019  Z= 0.391
  Chirality :  0.039   0.156   1386
  Planarity :  0.003   0.042   1450
  Dihedral  : 12.493  87.635   2462
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.24), residues: 1231
  helix:  0.68 (0.18), residues: 756
  sheet: -0.97 (0.45), residues: 119
  loop : -1.15 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.017   0.002   TYR B  12 
 PHE   0.015   0.001   PHE B  86 
 TRP   0.026   0.001   TRP A  31 
 HIS   0.001   0.000   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8074)
  covalent geometry    : angle       0.61608 (11019)
  hydrogen bonds       : bond        0.14599 (  666)
  hydrogen bonds       : angle       6.24317 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9616 (mm) cc_final: 0.9406 (mp)
REVERT: A  118 ASP cc_start: 0.9208 (m-30) cc_final: 0.8883 (m-30)
REVERT: A  196 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8312 (tm-30)
REVERT: A  277 TYR cc_start: 0.8650 (m-80) cc_final: 0.8375 (m-80)
REVERT: A  287 ILE cc_start: 0.9531 (tt) cc_final: 0.9298 (tt)
REVERT: A  307 GLU cc_start: 0.9332 (pt0) cc_final: 0.8659 (pp20)
REVERT: B   67 PHE cc_start: 0.9357 (t80) cc_final: 0.9142 (t80)
REVERT: B   71 ILE cc_start: 0.9676 (mm) cc_final: 0.9471 (mm)
REVERT: B  136 ASP cc_start: 0.9160 (m-30) cc_final: 0.8897 (m-30)
REVERT: B  210 MET cc_start: 0.9661 (mtp) cc_final: 0.9297 (mtp)
REVERT: B  225 LEU cc_start: 0.9082 (mt) cc_final: 0.8786 (mt)
REVERT: B  327 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8572 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0629
  time to fit residues: 14.6309
Evaluate side-chains
  121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:   30.0000
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:   40.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 117 optimal weight:    0.9980
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.3290 r_free = 0.3290 target = 0.073578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.059753 restraints weight = 38067.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.061429 restraints weight = 23745.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.062496 restraints weight = 16587.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.063436 restraints weight = 12851.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.064013 restraints weight = 10274.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8074  Z= 0.164
  Angle     :  0.613   7.215  11019  Z= 0.337
  Chirality :  0.041   0.151   1386
  Planarity :  0.003   0.033   1450
  Dihedral  :  4.322  20.882   1274
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  7.99 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.24), residues: 1231
  helix:  1.00 (0.18), residues: 763
  sheet: -0.71 (0.46), residues: 103
  loop : -0.90 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 304 
 TYR   0.035   0.002   TYR B  88 
 PHE   0.022   0.002   PHE A  98 
 TRP   0.020   0.002   TRP A  31 
 HIS   0.002   0.001   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8074)
  covalent geometry    : angle       0.61294 (11019)
  hydrogen bonds       : bond        0.05264 (  666)
  hydrogen bonds       : angle       4.82897 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8584 (p0) cc_final: 0.8338 (p0)
REVERT: A  118 ASP cc_start: 0.9253 (m-30) cc_final: 0.8931 (m-30)
REVERT: A  151 LEU cc_start: 0.9269 (mt) cc_final: 0.8979 (mp)
REVERT: A  196 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8389 (tm-30)
REVERT: A  223 GLU cc_start: 0.8820 (mp0) cc_final: 0.8531 (mp0)
REVERT: A  277 TYR cc_start: 0.8779 (m-80) cc_final: 0.8536 (m-80)
REVERT: A  282 MET cc_start: 0.8821 (tmm) cc_final: 0.8588 (tmm)
REVERT: A  283 MET cc_start: 0.8476 (ttm) cc_final: 0.8203 (ttm)
REVERT: A  287 ILE cc_start: 0.9542 (tt) cc_final: 0.9306 (tt)
REVERT: A  307 GLU cc_start: 0.9333 (pt0) cc_final: 0.8715 (pp20)
REVERT: B   35 LEU cc_start: 0.8794 (tp) cc_final: 0.8419 (tp)
REVERT: B   67 PHE cc_start: 0.9323 (t80) cc_final: 0.9072 (t80)
REVERT: B   71 ILE cc_start: 0.9675 (mm) cc_final: 0.9461 (mm)
REVERT: B  122 HIS cc_start: 0.8332 (m90) cc_final: 0.7911 (m90)
REVERT: B  136 ASP cc_start: 0.9112 (m-30) cc_final: 0.8912 (m-30)
REVERT: B  210 MET cc_start: 0.9625 (mtp) cc_final: 0.9245 (mtp)
REVERT: B  225 LEU cc_start: 0.9001 (mt) cc_final: 0.8700 (mt)
REVERT: B  293 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8179 (ppp)
REVERT: B  294 PHE cc_start: 0.9199 (m-80) cc_final: 0.8884 (m-80)
REVERT: B  302 TYR cc_start: 0.9310 (m-10) cc_final: 0.9009 (m-10)
REVERT: B  327 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8568 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0609
  time to fit residues: 14.1700
Evaluate side-chains
  128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 113 optimal weight:   20.0000
   chunk 98 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 108 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
B 326 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.074550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.060428 restraints weight = 38019.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.062205 restraints weight = 23108.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.063489 restraints weight = 15997.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.064413 restraints weight = 11976.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.064895 restraints weight = 9463.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8074  Z= 0.155
  Angle     :  0.587   8.219  11019  Z= 0.321
  Chirality :  0.042   0.164   1386
  Planarity :  0.003   0.029   1450
  Dihedral  :  4.101  21.180   1274
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.24), residues: 1231
  helix:  1.14 (0.18), residues: 763
  sheet: -0.67 (0.47), residues: 105
  loop : -0.61 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 304 
 TYR   0.029   0.003   TYR B  12 
 PHE   0.019   0.002   PHE B  86 
 TRP   0.012   0.001   TRP A  31 
 HIS   0.003   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8074)
  covalent geometry    : angle       0.58706 (11019)
  hydrogen bonds       : bond        0.04902 (  666)
  hydrogen bonds       : angle       4.61323 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8670 (p0) cc_final: 0.8138 (p0)
REVERT: A  118 ASP cc_start: 0.9231 (m-30) cc_final: 0.8974 (m-30)
REVERT: A  148 MET cc_start: 0.8381 (tmm) cc_final: 0.8162 (tmm)
REVERT: A  195 LYS cc_start: 0.9559 (tptm) cc_final: 0.9323 (tppt)
REVERT: A  196 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8438 (tm-30)
REVERT: A  223 GLU cc_start: 0.8806 (mp0) cc_final: 0.8476 (mp0)
REVERT: A  277 TYR cc_start: 0.8774 (m-80) cc_final: 0.8353 (m-80)
REVERT: A  282 MET cc_start: 0.8846 (tmm) cc_final: 0.8534 (tmm)
REVERT: A  287 ILE cc_start: 0.9468 (tt) cc_final: 0.9037 (tt)
REVERT: A  294 MET cc_start: 0.8752 (tmm) cc_final: 0.8487 (tmm)
REVERT: A  307 GLU cc_start: 0.9258 (pt0) cc_final: 0.8657 (pp20)
REVERT: B   35 LEU cc_start: 0.8911 (tp) cc_final: 0.8524 (tp)
REVERT: B   67 PHE cc_start: 0.9334 (t80) cc_final: 0.9062 (t80)
REVERT: B   71 ILE cc_start: 0.9719 (mm) cc_final: 0.9474 (mm)
REVERT: B  122 HIS cc_start: 0.8251 (m90) cc_final: 0.7778 (m90)
REVERT: B  136 ASP cc_start: 0.9141 (m-30) cc_final: 0.8914 (m-30)
REVERT: B  163 MET cc_start: 0.9020 (mtm) cc_final: 0.8174 (mmm)
REVERT: B  295 VAL cc_start: 0.9507 (t) cc_final: 0.9163 (t)
REVERT: B  324 ARG cc_start: 0.9461 (mtt90) cc_final: 0.8964 (mtt90)
REVERT: B  327 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8587 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0645
  time to fit residues: 14.8017
Evaluate side-chains
  127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 112 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0370
   chunk 92 optimal weight:   20.0000
   chunk 119 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.2060

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

Flipped N/Q/H residues before XYZ refinement:
** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.074152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.060100 restraints weight = 38556.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.061900 restraints weight = 23677.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.063211 restraints weight = 16492.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.064113 restraints weight = 12324.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.064825 restraints weight = 9839.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8074  Z= 0.155
  Angle     :  0.582   8.041  11019  Z= 0.317
  Chirality :  0.041   0.197   1386
  Planarity :  0.003   0.034   1450
  Dihedral  :  3.978  21.219   1274
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.24), residues: 1231
  helix:  1.19 (0.19), residues: 772
  sheet: -0.46 (0.48), residues: 100
  loop : -0.63 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 130 
 TYR   0.015   0.002   TYR B  88 
 PHE   0.021   0.001   PHE B  86 
 TRP   0.014   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8074)
  covalent geometry    : angle       0.58239 (11019)
  hydrogen bonds       : bond        0.04718 (  666)
  hydrogen bonds       : angle       4.46851 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9580 (mm) cc_final: 0.9380 (mp)
REVERT: A  118 ASP cc_start: 0.9200 (m-30) cc_final: 0.8660 (m-30)
REVERT: A  133 LEU cc_start: 0.9166 (mm) cc_final: 0.8632 (mm)
REVERT: A  195 LYS cc_start: 0.9536 (tptm) cc_final: 0.9320 (tppt)
REVERT: A  196 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8426 (tm-30)
REVERT: A  223 GLU cc_start: 0.8842 (mp0) cc_final: 0.8485 (mp0)
REVERT: A  275 MET cc_start: 0.9263 (ppp) cc_final: 0.8958 (ppp)
REVERT: A  282 MET cc_start: 0.8876 (tmm) cc_final: 0.8470 (tmm)
REVERT: A  294 MET cc_start: 0.8725 (tmm) cc_final: 0.8460 (tmm)
REVERT: A  304 ARG cc_start: 0.9287 (ptp-110) cc_final: 0.8934 (ptp90)
REVERT: B   35 LEU cc_start: 0.8968 (tp) cc_final: 0.8585 (tp)
REVERT: B   67 PHE cc_start: 0.9319 (t80) cc_final: 0.9032 (t80)
REVERT: B   71 ILE cc_start: 0.9739 (mm) cc_final: 0.9480 (mm)
REVERT: B  122 HIS cc_start: 0.8234 (m90) cc_final: 0.7719 (m90)
REVERT: B  130 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8212 (tpp80)
REVERT: B  136 ASP cc_start: 0.9139 (m-30) cc_final: 0.8910 (m-30)
REVERT: B  163 MET cc_start: 0.9007 (mtm) cc_final: 0.8186 (mmm)
REVERT: B  210 MET cc_start: 0.9655 (mtp) cc_final: 0.9293 (mtp)
REVERT: B  297 TYR cc_start: 0.8759 (m-10) cc_final: 0.8528 (m-10)
REVERT: B  324 ARG cc_start: 0.9454 (mtt90) cc_final: 0.8779 (mtt90)
REVERT: B  327 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8593 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0675
  time to fit residues: 15.0787
Evaluate side-chains
  132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0370
   chunk 57 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 84 optimal weight:    0.5980
   chunk 98 optimal weight:    0.3980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.074972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.060704 restraints weight = 37777.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.062450 restraints weight = 22923.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.063637 restraints weight = 15916.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.064702 restraints weight = 12212.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.065305 restraints weight = 9530.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8074  Z= 0.127
  Angle     :  0.566   8.012  11019  Z= 0.302
  Chirality :  0.041   0.143   1386
  Planarity :  0.003   0.030   1450
  Dihedral  :  3.832  18.072   1274
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.24), residues: 1231
  helix:  1.27 (0.19), residues: 774
  sheet: -0.27 (0.47), residues: 103
  loop : -0.65 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 130 
 TYR   0.021   0.001   TYR B  12 
 PHE   0.018   0.001   PHE B  86 
 TRP   0.016   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8074)
  covalent geometry    : angle       0.56616 (11019)
  hydrogen bonds       : bond        0.04515 (  666)
  hydrogen bonds       : angle       4.31533 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8995 (tpt) cc_final: 0.8634 (tpp)
REVERT: A   75 PHE cc_start: 0.9161 (m-10) cc_final: 0.8952 (m-80)
REVERT: A  118 ASP cc_start: 0.9177 (m-30) cc_final: 0.8719 (m-30)
REVERT: A  131 GLN cc_start: 0.8621 (tt0) cc_final: 0.8326 (tt0)
REVERT: A  195 LYS cc_start: 0.9549 (tptm) cc_final: 0.9319 (tppt)
REVERT: A  196 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8401 (tm-30)
REVERT: A  223 GLU cc_start: 0.8786 (mp0) cc_final: 0.8405 (mp0)
REVERT: A  275 MET cc_start: 0.9274 (ppp) cc_final: 0.8905 (ppp)
REVERT: A  277 TYR cc_start: 0.9054 (m-80) cc_final: 0.8509 (m-80)
REVERT: A  282 MET cc_start: 0.8843 (tmm) cc_final: 0.8373 (tmm)
REVERT: A  287 ILE cc_start: 0.9411 (tt) cc_final: 0.9057 (tt)
REVERT: A  294 MET cc_start: 0.8720 (tmm) cc_final: 0.8498 (tmm)
REVERT: A  304 ARG cc_start: 0.9246 (ptp-110) cc_final: 0.9012 (ptp90)
REVERT: B   35 LEU cc_start: 0.8918 (tp) cc_final: 0.8672 (tp)
REVERT: B   58 MET cc_start: 0.9426 (mmp) cc_final: 0.9217 (mmm)
REVERT: B   67 PHE cc_start: 0.9255 (t80) cc_final: 0.8962 (t80)
REVERT: B   71 ILE cc_start: 0.9726 (mm) cc_final: 0.9466 (mm)
REVERT: B  122 HIS cc_start: 0.8252 (m90) cc_final: 0.7748 (m90)
REVERT: B  136 ASP cc_start: 0.9119 (m-30) cc_final: 0.8892 (m-30)
REVERT: B  139 GLN cc_start: 0.9393 (tp40) cc_final: 0.9135 (tp40)
REVERT: B  210 MET cc_start: 0.9608 (mtp) cc_final: 0.9229 (mtp)
REVERT: B  257 MET cc_start: 0.9140 (mmm) cc_final: 0.8733 (tmm)
REVERT: B  302 TYR cc_start: 0.8980 (m-10) cc_final: 0.8713 (m-10)
REVERT: B  324 ARG cc_start: 0.9462 (mtt90) cc_final: 0.8987 (mtt90)
REVERT: B  327 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8571 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0721
  time to fit residues: 16.9549
Evaluate side-chains
  135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 115 optimal weight:    9.9990
   chunk 121 optimal weight:    0.0010
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
B 226 GLN
B 237 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.075144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.060959 restraints weight = 37296.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062737 restraints weight = 22927.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.063946 restraints weight = 15928.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.064922 restraints weight = 12206.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.065522 restraints weight = 9752.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8074  Z= 0.129
  Angle     :  0.570   9.261  11019  Z= 0.302
  Chirality :  0.040   0.159   1386
  Planarity :  0.003   0.033   1450
  Dihedral  :  3.749  17.416   1274
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.18 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.24), residues: 1231
  helix:  1.28 (0.19), residues: 773
  sheet: -0.08 (0.46), residues: 103
  loop : -0.64 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  88 
 TYR   0.011   0.002   TYR B  88 
 PHE   0.020   0.001   PHE B  86 
 TRP   0.014   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8074)
  covalent geometry    : angle       0.57036 (11019)
  hydrogen bonds       : bond        0.04469 (  666)
  hydrogen bonds       : angle       4.25985 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9566 (mm) cc_final: 0.9310 (mp)
REVERT: A  118 ASP cc_start: 0.9200 (m-30) cc_final: 0.8782 (m-30)
REVERT: A  133 LEU cc_start: 0.9181 (mm) cc_final: 0.8679 (mm)
REVERT: A  170 MET cc_start: 0.8334 (ppp) cc_final: 0.8040 (ppp)
REVERT: A  195 LYS cc_start: 0.9555 (tptm) cc_final: 0.9304 (tppt)
REVERT: A  196 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8385 (tm-30)
REVERT: A  223 GLU cc_start: 0.8806 (mp0) cc_final: 0.8442 (mp0)
REVERT: A  275 MET cc_start: 0.9279 (ppp) cc_final: 0.8873 (ppp)
REVERT: A  277 TYR cc_start: 0.8906 (m-80) cc_final: 0.8571 (m-80)
REVERT: A  282 MET cc_start: 0.8852 (tmm) cc_final: 0.8324 (tmm)
REVERT: A  286 ILE cc_start: 0.9382 (pt) cc_final: 0.9177 (pt)
REVERT: A  304 ARG cc_start: 0.9248 (ptp-110) cc_final: 0.9042 (ptp90)
REVERT: B   35 LEU cc_start: 0.8914 (tp) cc_final: 0.8686 (tp)
REVERT: B   67 PHE cc_start: 0.9265 (t80) cc_final: 0.8960 (t80)
REVERT: B   71 ILE cc_start: 0.9748 (mm) cc_final: 0.9490 (mm)
REVERT: B  110 LYS cc_start: 0.9151 (tppt) cc_final: 0.8944 (tppt)
REVERT: B  122 HIS cc_start: 0.8234 (m90) cc_final: 0.7747 (m90)
REVERT: B  136 ASP cc_start: 0.9142 (m-30) cc_final: 0.8910 (m-30)
REVERT: B  139 GLN cc_start: 0.9384 (tp40) cc_final: 0.9122 (tp40)
REVERT: B  210 MET cc_start: 0.9588 (mtp) cc_final: 0.9207 (mtm)
REVERT: B  324 ARG cc_start: 0.9448 (mtt90) cc_final: 0.9051 (mtt90)
REVERT: B  327 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8579 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0646
  time to fit residues: 15.9042
Evaluate side-chains
  138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.075349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.061208 restraints weight = 37035.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.062966 restraints weight = 22821.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.064204 restraints weight = 15858.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.065164 restraints weight = 12062.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.065978 restraints weight = 9544.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8074  Z= 0.124
  Angle     :  0.571   7.501  11019  Z= 0.302
  Chirality :  0.040   0.147   1386
  Planarity :  0.003   0.032   1450
  Dihedral  :  3.640  17.012   1274
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.54 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.24), residues: 1231
  helix:  1.32 (0.19), residues: 773
  sheet:  0.05 (0.47), residues: 105
  loop : -0.58 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  88 
 TYR   0.038   0.002   TYR B  78 
 PHE   0.020   0.001   PHE B  86 
 TRP   0.016   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8074)
  covalent geometry    : angle       0.57052 (11019)
  hydrogen bonds       : bond        0.04408 (  666)
  hydrogen bonds       : angle       4.19541 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9376 (pp30) cc_final: 0.8967 (pp30)
REVERT: A  118 ASP cc_start: 0.9197 (m-30) cc_final: 0.8716 (m-30)
REVERT: A  131 GLN cc_start: 0.8730 (tt0) cc_final: 0.8302 (tt0)
REVERT: A  133 LEU cc_start: 0.9177 (mm) cc_final: 0.8680 (mm)
REVERT: A  195 LYS cc_start: 0.9584 (tptm) cc_final: 0.9315 (tppt)
REVERT: A  196 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8373 (tm-30)
REVERT: A  223 GLU cc_start: 0.8834 (mp0) cc_final: 0.8373 (pm20)
REVERT: A  275 MET cc_start: 0.9243 (ppp) cc_final: 0.8876 (ppp)
REVERT: A  277 TYR cc_start: 0.9017 (m-80) cc_final: 0.8492 (m-80)
REVERT: A  282 MET cc_start: 0.8840 (tmm) cc_final: 0.8308 (tmm)
REVERT: A  286 ILE cc_start: 0.9376 (pt) cc_final: 0.9152 (pt)
REVERT: A  287 ILE cc_start: 0.9395 (tt) cc_final: 0.9047 (tt)
REVERT: A  294 MET cc_start: 0.8895 (tmm) cc_final: 0.8692 (tmm)
REVERT: B   35 LEU cc_start: 0.8916 (tp) cc_final: 0.8585 (tp)
REVERT: B   67 PHE cc_start: 0.9264 (t80) cc_final: 0.8973 (t80)
REVERT: B   71 ILE cc_start: 0.9774 (mm) cc_final: 0.9517 (mm)
REVERT: B  110 LYS cc_start: 0.9158 (tppt) cc_final: 0.8949 (tppt)
REVERT: B  122 HIS cc_start: 0.8268 (m90) cc_final: 0.7755 (m90)
REVERT: B  130 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8131 (tpp80)
REVERT: B  136 ASP cc_start: 0.9133 (m-30) cc_final: 0.8901 (m-30)
REVERT: B  139 GLN cc_start: 0.9406 (tp40) cc_final: 0.9138 (tp40)
REVERT: B  163 MET cc_start: 0.9104 (mtm) cc_final: 0.8180 (mpp)
REVERT: B  210 MET cc_start: 0.9587 (mtp) cc_final: 0.9287 (mtp)
REVERT: B  257 MET cc_start: 0.9056 (mmm) cc_final: 0.8802 (tmm)
REVERT: B  261 MET cc_start: 0.9486 (tpp) cc_final: 0.9047 (tpt)
REVERT: B  293 MET cc_start: 0.8946 (ttt) cc_final: 0.8266 (tmm)
REVERT: B  297 TYR cc_start: 0.8734 (m-10) cc_final: 0.8227 (m-10)
REVERT: B  306 MET cc_start: 0.8553 (mtm) cc_final: 0.8190 (mtt)
REVERT: B  324 ARG cc_start: 0.9452 (mtt90) cc_final: 0.8849 (mtp85)
REVERT: B  327 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8592 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0654
  time to fit residues: 16.7787
Evaluate side-chains
  138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.075550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.061555 restraints weight = 37721.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.063310 restraints weight = 23522.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.064618 restraints weight = 16500.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.065580 restraints weight = 12361.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.066305 restraints weight = 9838.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8074  Z= 0.134
  Angle     :  0.563   7.377  11019  Z= 0.305
  Chirality :  0.041   0.174   1386
  Planarity :  0.003   0.032   1450
  Dihedral  :  3.655  17.145   1274
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.63 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.24), residues: 1231
  helix:  1.37 (0.19), residues: 770
  sheet:  0.20 (0.48), residues: 104
  loop : -0.55 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  88 
 TYR   0.032   0.002   TYR B 302 
 PHE   0.020   0.001   PHE B 164 
 TRP   0.017   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8074)
  covalent geometry    : angle       0.56272 (11019)
  hydrogen bonds       : bond        0.04425 (  666)
  hydrogen bonds       : angle       4.20956 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ASP cc_start: 0.8765 (t0) cc_final: 0.8554 (t0)
REVERT: A   54 LEU cc_start: 0.9554 (mm) cc_final: 0.9283 (mp)
REVERT: A   81 GLN cc_start: 0.9361 (pp30) cc_final: 0.8933 (pp30)
REVERT: A  131 GLN cc_start: 0.8724 (tt0) cc_final: 0.8402 (tt0)
REVERT: A  170 MET cc_start: 0.8264 (ppp) cc_final: 0.7931 (ppp)
REVERT: A  195 LYS cc_start: 0.9591 (tptm) cc_final: 0.9303 (tppt)
REVERT: A  196 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8300 (tm-30)
REVERT: A  275 MET cc_start: 0.9273 (ppp) cc_final: 0.8852 (ppp)
REVERT: A  277 TYR cc_start: 0.8874 (m-80) cc_final: 0.8593 (m-80)
REVERT: A  282 MET cc_start: 0.8838 (tmm) cc_final: 0.8293 (tmm)
REVERT: A  286 ILE cc_start: 0.9389 (pt) cc_final: 0.9148 (pt)
REVERT: A  294 MET cc_start: 0.8913 (tmm) cc_final: 0.8699 (tmm)
REVERT: A  307 GLU cc_start: 0.9212 (pt0) cc_final: 0.8547 (pp20)
REVERT: B   35 LEU cc_start: 0.8953 (tp) cc_final: 0.8612 (tp)
REVERT: B   67 PHE cc_start: 0.9247 (t80) cc_final: 0.8966 (t80)
REVERT: B   71 ILE cc_start: 0.9763 (mm) cc_final: 0.9497 (mm)
REVERT: B  110 LYS cc_start: 0.9113 (tppt) cc_final: 0.8887 (tppt)
REVERT: B  122 HIS cc_start: 0.8265 (m90) cc_final: 0.7722 (m90)
REVERT: B  136 ASP cc_start: 0.9128 (m-30) cc_final: 0.8843 (m-30)
REVERT: B  139 GLN cc_start: 0.9397 (tp40) cc_final: 0.9128 (tp40)
REVERT: B  163 MET cc_start: 0.9183 (mtm) cc_final: 0.8863 (mpp)
REVERT: B  197 ASP cc_start: 0.9121 (m-30) cc_final: 0.8731 (m-30)
REVERT: B  210 MET cc_start: 0.9558 (mtp) cc_final: 0.9326 (mtp)
REVERT: B  225 LEU cc_start: 0.8998 (mt) cc_final: 0.8796 (mt)
REVERT: B  293 MET cc_start: 0.9108 (ttt) cc_final: 0.8087 (tmm)
REVERT: B  306 MET cc_start: 0.8539 (mtm) cc_final: 0.8161 (mtt)
REVERT: B  324 ARG cc_start: 0.9465 (mtt90) cc_final: 0.8975 (mtp85)
REVERT: B  327 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8659 (mt-10)
REVERT: B  330 ASP cc_start: 0.8991 (m-30) cc_final: 0.8734 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0607
  time to fit residues: 15.7000
Evaluate side-chains
  140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:   20.0000
   chunk 72 optimal weight:    0.8980
   chunk 34 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 326 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.074888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.060678 restraints weight = 37155.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.062401 restraints weight = 23007.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.063685 restraints weight = 16004.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.064666 restraints weight = 12003.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.065389 restraints weight = 9461.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8074  Z= 0.126
  Angle     :  0.586  11.575  11019  Z= 0.307
  Chirality :  0.041   0.180   1386
  Planarity :  0.003   0.036   1450
  Dihedral  :  3.612  17.190   1274
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.45 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.24), residues: 1231
  helix:  1.34 (0.19), residues: 773
  sheet:  0.39 (0.48), residues: 104
  loop : -0.57 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  88 
 TYR   0.026   0.002   TYR B 302 
 PHE   0.019   0.001   PHE B  86 
 TRP   0.020   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8074)
  covalent geometry    : angle       0.58610 (11019)
  hydrogen bonds       : bond        0.04385 (  666)
  hydrogen bonds       : angle       4.16456 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ASP cc_start: 0.8807 (t0) cc_final: 0.8602 (t0)
REVERT: A   54 LEU cc_start: 0.9546 (mm) cc_final: 0.9271 (mp)
REVERT: A   81 GLN cc_start: 0.9345 (pp30) cc_final: 0.8886 (pp30)
REVERT: A  131 GLN cc_start: 0.8727 (tt0) cc_final: 0.8410 (tt0)
REVERT: A  170 MET cc_start: 0.8253 (ppp) cc_final: 0.7928 (ppp)
REVERT: A  195 LYS cc_start: 0.9591 (tptm) cc_final: 0.9298 (tppt)
REVERT: A  196 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8247 (tm-30)
REVERT: A  223 GLU cc_start: 0.8794 (mp0) cc_final: 0.8450 (mp0)
REVERT: A  275 MET cc_start: 0.9231 (ppp) cc_final: 0.8854 (ppp)
REVERT: A  277 TYR cc_start: 0.8892 (m-80) cc_final: 0.8525 (m-80)
REVERT: A  282 MET cc_start: 0.8790 (tmm) cc_final: 0.8253 (tmm)
REVERT: A  286 ILE cc_start: 0.9397 (pt) cc_final: 0.9147 (pt)
REVERT: A  287 ILE cc_start: 0.9404 (tt) cc_final: 0.9102 (tt)
REVERT: A  294 MET cc_start: 0.8894 (tmm) cc_final: 0.8680 (tmm)
REVERT: B   35 LEU cc_start: 0.8931 (tp) cc_final: 0.8571 (tp)
REVERT: B   67 PHE cc_start: 0.9263 (t80) cc_final: 0.8958 (t80)
REVERT: B   71 ILE cc_start: 0.9754 (mm) cc_final: 0.9481 (mm)
REVERT: B  110 LYS cc_start: 0.9115 (tppt) cc_final: 0.8881 (tppt)
REVERT: B  122 HIS cc_start: 0.8278 (m90) cc_final: 0.7738 (m90)
REVERT: B  136 ASP cc_start: 0.9126 (m-30) cc_final: 0.8880 (m-30)
REVERT: B  139 GLN cc_start: 0.9383 (tp40) cc_final: 0.9120 (tp40)
REVERT: B  163 MET cc_start: 0.9139 (mtm) cc_final: 0.8685 (mpp)
REVERT: B  197 ASP cc_start: 0.9111 (m-30) cc_final: 0.8720 (m-30)
REVERT: B  210 MET cc_start: 0.9573 (mtp) cc_final: 0.9261 (mtp)
REVERT: B  257 MET cc_start: 0.9057 (mmm) cc_final: 0.8788 (tmm)
REVERT: B  261 MET cc_start: 0.9451 (tpp) cc_final: 0.8584 (tpt)
REVERT: B  293 MET cc_start: 0.9113 (ttt) cc_final: 0.8128 (tmm)
REVERT: B  297 TYR cc_start: 0.8830 (m-10) cc_final: 0.8628 (m-80)
REVERT: B  327 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8613 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0603
  time to fit residues: 15.6143
Evaluate side-chains
  140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 112 optimal weight:   30.0000
   chunk 68 optimal weight:    0.9990
   chunk 98 optimal weight:   20.0000
   chunk 109 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 326 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.074830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.060885 restraints weight = 37173.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.062627 restraints weight = 23100.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.063807 restraints weight = 16084.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.064752 restraints weight = 12285.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.065489 restraints weight = 9819.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8074  Z= 0.133
  Angle     :  0.590  10.695  11019  Z= 0.315
  Chirality :  0.041   0.158   1386
  Planarity :  0.003   0.039   1450
  Dihedral  :  3.592  17.562   1274
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.24), residues: 1231
  helix:  1.38 (0.19), residues: 773
  sheet:  0.41 (0.49), residues: 104
  loop : -0.53 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 130 
 TYR   0.017   0.002   TYR B 302 
 PHE   0.019   0.001   PHE B  86 
 TRP   0.030   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8074)
  covalent geometry    : angle       0.58970 (11019)
  hydrogen bonds       : bond        0.04394 (  666)
  hydrogen bonds       : angle       4.18174 ( 1947)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.9540 (mm) cc_final: 0.9257 (mp)
REVERT: A   81 GLN cc_start: 0.9348 (pp30) cc_final: 0.8859 (pp30)
REVERT: A  131 GLN cc_start: 0.8743 (tt0) cc_final: 0.8463 (tt0)
REVERT: A  170 MET cc_start: 0.8230 (ppp) cc_final: 0.7905 (ppp)
REVERT: A  195 LYS cc_start: 0.9600 (tptm) cc_final: 0.9335 (tptt)
REVERT: A  196 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8234 (tm-30)
REVERT: A  223 GLU cc_start: 0.8750 (mp0) cc_final: 0.8431 (mp0)
REVERT: A  275 MET cc_start: 0.9300 (ppp) cc_final: 0.8849 (ppp)
REVERT: A  277 TYR cc_start: 0.8883 (m-80) cc_final: 0.8519 (m-80)
REVERT: A  282 MET cc_start: 0.8813 (tmm) cc_final: 0.8284 (tmm)
REVERT: A  286 ILE cc_start: 0.9400 (pt) cc_final: 0.9162 (pt)
REVERT: A  294 MET cc_start: 0.8900 (tmm) cc_final: 0.8690 (tmm)
REVERT: A  307 GLU cc_start: 0.9251 (pt0) cc_final: 0.8627 (pp20)
REVERT: B   35 LEU cc_start: 0.8966 (tp) cc_final: 0.8606 (tp)
REVERT: B   67 PHE cc_start: 0.9255 (t80) cc_final: 0.8955 (t80)
REVERT: B   71 ILE cc_start: 0.9753 (mm) cc_final: 0.9487 (mm)
REVERT: B  110 LYS cc_start: 0.9097 (tppt) cc_final: 0.8864 (tppt)
REVERT: B  122 HIS cc_start: 0.8257 (m90) cc_final: 0.7698 (m90)
REVERT: B  130 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7450 (tpp80)
REVERT: B  134 ASP cc_start: 0.7203 (m-30) cc_final: 0.6577 (m-30)
REVERT: B  136 ASP cc_start: 0.9089 (m-30) cc_final: 0.8840 (m-30)
REVERT: B  139 GLN cc_start: 0.9386 (tp40) cc_final: 0.9113 (tp40)
REVERT: B  163 MET cc_start: 0.9177 (mtm) cc_final: 0.8800 (mpp)
REVERT: B  197 ASP cc_start: 0.9121 (m-30) cc_final: 0.8721 (m-30)
REVERT: B  210 MET cc_start: 0.9573 (mtp) cc_final: 0.9341 (mtp)
REVERT: B  225 LEU cc_start: 0.8998 (mt) cc_final: 0.8778 (mt)
REVERT: B  261 MET cc_start: 0.9406 (tpp) cc_final: 0.8964 (tpt)
REVERT: B  293 MET cc_start: 0.9139 (ttt) cc_final: 0.8079 (tmm)
REVERT: B  297 TYR cc_start: 0.8910 (m-10) cc_final: 0.8618 (m-10)
REVERT: B  327 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8596 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0580
  time to fit residues: 14.7907
Evaluate side-chains
  149 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 326 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.074881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.060937 restraints weight = 36774.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.062673 restraints weight = 22973.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.063974 restraints weight = 16038.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.064890 restraints weight = 11993.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.065674 restraints weight = 9505.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8074  Z= 0.132
  Angle     :  0.591  11.023  11019  Z= 0.313
  Chirality :  0.041   0.146   1386
  Planarity :  0.003   0.037   1450
  Dihedral  :  3.564  17.057   1274
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.36 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.24), residues: 1231
  helix:  1.40 (0.19), residues: 773
  sheet:  0.34 (0.48), residues: 110
  loop : -0.47 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  88 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.019   0.001   PHE B  86 
 TRP   0.031   0.002   TRP A  31 
 HIS   0.003   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8074)
  covalent geometry    : angle       0.59107 (11019)
  hydrogen bonds       : bond        0.04370 (  666)
  hydrogen bonds       : angle       4.14541 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1175.62 seconds
wall clock time: 20 minutes 58.76 seconds (1258.76 seconds total)