Starting phenix.real_space_refine
on Wed Feb 12 15:19:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ocy_12816/02_2025/7ocy_12816_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ocy_12816/02_2025/7ocy_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_12816/02_2025/7ocy_12816.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ocy_12816/02_2025/7ocy_12816.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ocy_12816/02_2025/7ocy_12816_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ocy_12816/02_2025/7ocy_12816_neut.cif"
  }
  resolution = 4.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.048
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 10, 'ARG:plan': 15, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 25, 'ASP:plan': 14}
          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: {'GLN:plan1': 9, 'ASP:plan': 16, 'TYR:plan': 5, 'ASN:plan1': 16, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 27, 'ARG:plan': 10}
          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, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 222
  Time building chain proxies: 5.65, per 1000 atoms: 0.71
  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: 2.39
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.48
  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: 2.70

  Time building geometry restraints manager: 2.78 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:             2.760
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     24.690
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   30.910
-------------------------------------------------------------------------------
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= 0.203
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (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
 TRP   0.026   0.001   TRP A  31 
 HIS   0.001   0.000   HIS A 179 
 PHE   0.015   0.001   PHE B  86 
 TYR   0.017   0.002   TYR B  12 
 ARG   0.002   0.000   ARG B 104 

*********************** 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  : 0.961 
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: 0.1617
  time to fit residues: 36.3595
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  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 92 optimal weight:   20.0000
   chunk 51 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 95 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 58 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 110 optimal weight:   10.0000
   overall best weight:    3.3184

-------------------------------------------------------------------------------
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 = 0.3229 r_free = 0.3229 target = 0.070665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.057171 restraints weight = 39636.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.058773 restraints weight = 24513.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059931 restraints weight = 17237.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8074  Z= 0.391
  Angle     :  0.717   8.929  11019  Z= 0.404
  Chirality :  0.044   0.168   1386
  Planarity :  0.004   0.042   1450
  Dihedral  :  4.568  22.454   1274
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  9.98 %
    Favored  : 89.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.23), residues: 1231
  helix:  0.56 (0.18), residues: 765
  sheet: -0.78 (0.45), residues: 118
  loop : -0.86 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  31 
 HIS   0.003   0.001   HIS A 227 
 PHE   0.024   0.002   PHE B  86 
 TYR   0.034   0.003   TYR B  88 
 ARG   0.004   0.001   ARG A 304 

*********************** 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
  138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9088 (tpt) cc_final: 0.8868 (tpp)
REVERT: A   49 ASP cc_start: 0.8685 (p0) cc_final: 0.8440 (p0)
REVERT: A  118 ASP cc_start: 0.9286 (m-30) cc_final: 0.8990 (m-30)
REVERT: A  154 LEU cc_start: 0.9634 (mm) cc_final: 0.9421 (mt)
REVERT: A  196 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8525 (tm-30)
REVERT: A  223 GLU cc_start: 0.8880 (mp0) cc_final: 0.8580 (mp0)
REVERT: A  304 ARG cc_start: 0.9039 (ttm110) cc_final: 0.8605 (ttm110)
REVERT: B   35 LEU cc_start: 0.8929 (tp) cc_final: 0.8582 (tp)
REVERT: B   58 MET cc_start: 0.9456 (mmp) cc_final: 0.9215 (mmm)
REVERT: B   67 PHE cc_start: 0.9310 (t80) cc_final: 0.9107 (t80)
REVERT: B   71 ILE cc_start: 0.9703 (mm) cc_final: 0.9459 (mm)
REVERT: B  122 HIS cc_start: 0.8373 (m90) cc_final: 0.7926 (m90)
REVERT: B  130 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8557 (tpp80)
REVERT: B  136 ASP cc_start: 0.9153 (m-30) cc_final: 0.8898 (m-30)
REVERT: B  210 MET cc_start: 0.9645 (mtp) cc_final: 0.9210 (mtp)
REVERT: B  225 LEU cc_start: 0.9073 (mt) cc_final: 0.8797 (mt)
REVERT: B  293 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8871 (ttt)
REVERT: B  324 ARG cc_start: 0.9483 (mtt90) cc_final: 0.8749 (mtt90)
REVERT: B  327 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8603 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1706
  time to fit residues: 33.7709
Evaluate side-chains
  120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 110 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   chunk 35 optimal weight:   30.0000
   chunk 102 optimal weight:    9.9990
   chunk 113 optimal weight:    0.9980
   chunk 112 optimal weight:    7.9990
   chunk 77 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.073338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.059318 restraints weight = 38255.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.061079 restraints weight = 23034.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.062300 restraints weight = 15793.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8074  Z= 0.203
  Angle     :  0.597   9.102  11019  Z= 0.324
  Chirality :  0.042   0.212   1386
  Planarity :  0.003   0.032   1450
  Dihedral  :  4.210  21.525   1274
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.24), residues: 1231
  helix:  1.02 (0.18), residues: 768
  sheet: -0.59 (0.49), residues: 100
  loop : -0.80 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  31 
 HIS   0.002   0.001   HIS B  13 
 PHE   0.023   0.002   PHE B  86 
 TYR   0.030   0.003   TYR B  88 
 ARG   0.003   0.000   ARG A 114 

*********************** 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
  154 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8748 (p0) cc_final: 0.8167 (p0)
REVERT: A   96 GLN cc_start: 0.9311 (mp10) cc_final: 0.9080 (mm-40)
REVERT: A  118 ASP cc_start: 0.9397 (m-30) cc_final: 0.9110 (m-30)
REVERT: A  138 PHE cc_start: 0.8873 (t80) cc_final: 0.8617 (t80)
REVERT: A  196 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8451 (tm-30)
REVERT: A  223 GLU cc_start: 0.8883 (mp0) cc_final: 0.8545 (mp0)
REVERT: A  277 TYR cc_start: 0.8864 (m-80) cc_final: 0.8462 (m-80)
REVERT: A  304 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8683 (ttm110)
REVERT: B   35 LEU cc_start: 0.8895 (tp) cc_final: 0.8499 (tp)
REVERT: B   58 MET cc_start: 0.9470 (mmp) cc_final: 0.9182 (mmm)
REVERT: B   67 PHE cc_start: 0.9340 (t80) cc_final: 0.9115 (t80)
REVERT: B   71 ILE cc_start: 0.9724 (mm) cc_final: 0.9481 (mm)
REVERT: B  122 HIS cc_start: 0.8335 (m90) cc_final: 0.7861 (m90)
REVERT: B  136 ASP cc_start: 0.9189 (m-30) cc_final: 0.8934 (m-30)
REVERT: B  210 MET cc_start: 0.9641 (mtp) cc_final: 0.9197 (mtp)
REVERT: B  225 LEU cc_start: 0.8999 (mt) cc_final: 0.8752 (mt)
REVERT: B  324 ARG cc_start: 0.9480 (mtt90) cc_final: 0.8999 (mtt90)
REVERT: B  327 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8574 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1573
  time to fit residues: 35.2401
Evaluate side-chains
  129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 94 optimal weight:    0.0000
   chunk 101 optimal weight:   10.0000
   chunk 80 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0060
   chunk 30 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    0.4600

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.074467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.060118 restraints weight = 37760.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.061882 restraints weight = 23253.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.063093 restraints weight = 16092.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8074  Z= 0.154
  Angle     :  0.559   7.610  11019  Z= 0.303
  Chirality :  0.040   0.136   1386
  Planarity :  0.003   0.035   1450
  Dihedral  :  3.978  18.172   1274
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.24), residues: 1231
  helix:  1.22 (0.19), residues: 766
  sheet: -0.38 (0.48), residues: 99
  loop : -0.73 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.017   0.001   PHE B  86 
 TYR   0.017   0.001   TYR A 277 
 ARG   0.007   0.001   ARG B 130 

*********************** 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
  161 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.9418 (m-30) cc_final: 0.9108 (m-30)
REVERT: A  131 GLN cc_start: 0.8808 (tt0) cc_final: 0.8387 (tt0)
REVERT: A  196 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8430 (tm-30)
REVERT: A  282 MET cc_start: 0.8763 (tmm) cc_final: 0.8509 (tmm)
REVERT: A  304 ARG cc_start: 0.9100 (ttm110) cc_final: 0.8692 (ttm110)
REVERT: B   35 LEU cc_start: 0.8965 (tp) cc_final: 0.8579 (tp)
REVERT: B   58 MET cc_start: 0.9467 (mmp) cc_final: 0.9189 (mmm)
REVERT: B   67 PHE cc_start: 0.9344 (t80) cc_final: 0.9071 (t80)
REVERT: B   71 ILE cc_start: 0.9729 (mm) cc_final: 0.9438 (mm)
REVERT: B  122 HIS cc_start: 0.8254 (m90) cc_final: 0.7747 (m90)
REVERT: B  130 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8241 (tpp80)
REVERT: B  136 ASP cc_start: 0.9111 (m-30) cc_final: 0.8883 (m-30)
REVERT: B  210 MET cc_start: 0.9640 (mtp) cc_final: 0.9271 (mtp)
REVERT: B  293 MET cc_start: 0.8978 (ttt) cc_final: 0.8269 (tmm)
REVERT: B  306 MET cc_start: 0.8432 (mtm) cc_final: 0.8118 (mtt)
REVERT: B  324 ARG cc_start: 0.9450 (mtt90) cc_final: 0.8792 (mtt90)
REVERT: B  327 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8577 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1644
  time to fit residues: 37.8601
Evaluate side-chains
  139 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 114 optimal weight:   10.0000
   chunk 87 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 117 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 110 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.073624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.059582 restraints weight = 37206.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.061275 restraints weight = 22798.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062522 restraints weight = 15688.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8074  Z= 0.188
  Angle     :  0.593   8.300  11019  Z= 0.317
  Chirality :  0.041   0.177   1386
  Planarity :  0.003   0.034   1450
  Dihedral  :  3.864  19.596   1274
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.24), residues: 1231
  helix:  1.20 (0.19), residues: 771
  sheet: -0.39 (0.47), residues: 105
  loop : -0.70 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.022   0.001   PHE B  86 
 TYR   0.037   0.002   TYR B  78 
 ARG   0.005   0.001   ARG B 284 

*********************** 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
  150 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9095 (tpt) cc_final: 0.8784 (tpp)
REVERT: A   96 GLN cc_start: 0.9293 (mm-40) cc_final: 0.9062 (mm-40)
REVERT: A  118 ASP cc_start: 0.9397 (m-30) cc_final: 0.8994 (m-30)
REVERT: A  196 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8352 (tm-30)
REVERT: A  223 GLU cc_start: 0.8852 (mp0) cc_final: 0.8476 (mp0)
REVERT: A  282 MET cc_start: 0.8781 (tmm) cc_final: 0.8445 (tmm)
REVERT: A  294 MET cc_start: 0.8939 (tmm) cc_final: 0.8700 (tmm)
REVERT: A  304 ARG cc_start: 0.9113 (ttm110) cc_final: 0.8688 (ttm110)
REVERT: B   35 LEU cc_start: 0.8939 (tp) cc_final: 0.8714 (tp)
REVERT: B   58 MET cc_start: 0.9444 (mmp) cc_final: 0.9217 (mmm)
REVERT: B   67 PHE cc_start: 0.9341 (t80) cc_final: 0.9060 (t80)
REVERT: B   71 ILE cc_start: 0.9756 (mm) cc_final: 0.9486 (mm)
REVERT: B  122 HIS cc_start: 0.8237 (m90) cc_final: 0.7739 (m90)
REVERT: B  136 ASP cc_start: 0.9149 (m-30) cc_final: 0.8942 (m-30)
REVERT: B  139 GLN cc_start: 0.9361 (tp40) cc_final: 0.9112 (tp40)
REVERT: B  210 MET cc_start: 0.9641 (mtp) cc_final: 0.9255 (mtp)
REVERT: B  257 MET cc_start: 0.9157 (mmm) cc_final: 0.8773 (tmm)
REVERT: B  293 MET cc_start: 0.8872 (ttt) cc_final: 0.8152 (tmm)
REVERT: B  324 ARG cc_start: 0.9464 (mtt90) cc_final: 0.8707 (mtt90)
REVERT: B  327 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8576 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1647
  time to fit residues: 36.0008
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  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 50 optimal weight:    6.9990
   chunk 83 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 70 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 90 optimal weight:   40.0000
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.073632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.059469 restraints weight = 37098.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.061166 restraints weight = 22731.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.062420 restraints weight = 15575.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2621

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= 0.166
  Angle     :  0.561   9.120  11019  Z= 0.301
  Chirality :  0.041   0.167   1386
  Planarity :  0.003   0.032   1450
  Dihedral  :  3.763  18.060   1274
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1231
  helix:  1.29 (0.19), residues: 771
  sheet: -0.19 (0.48), residues: 104
  loop : -0.66 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 172 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.021   0.001   PHE B  86 
 TYR   0.035   0.002   TYR B 297 
 ARG   0.006   0.000   ARG B 130 

*********************** 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
  155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8993 (mm-40)
REVERT: A  118 ASP cc_start: 0.9417 (m-30) cc_final: 0.8923 (m-30)
REVERT: A  131 GLN cc_start: 0.8784 (tt0) cc_final: 0.8368 (tt0)
REVERT: A  196 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8393 (tm-30)
REVERT: A  275 MET cc_start: 0.9331 (ppp) cc_final: 0.9066 (ppp)
REVERT: A  282 MET cc_start: 0.8805 (tmm) cc_final: 0.8397 (tmm)
REVERT: A  294 MET cc_start: 0.8958 (tmm) cc_final: 0.8727 (tmm)
REVERT: A  304 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8664 (ttm110)
REVERT: B   35 LEU cc_start: 0.8941 (tp) cc_final: 0.8721 (tp)
REVERT: B   58 MET cc_start: 0.9417 (mmp) cc_final: 0.9172 (mmm)
REVERT: B   67 PHE cc_start: 0.9334 (t80) cc_final: 0.9026 (t80)
REVERT: B   71 ILE cc_start: 0.9769 (mm) cc_final: 0.9500 (mm)
REVERT: B  122 HIS cc_start: 0.8278 (m90) cc_final: 0.7747 (m90)
REVERT: B  136 ASP cc_start: 0.9188 (m-30) cc_final: 0.8948 (m-30)
REVERT: B  139 GLN cc_start: 0.9367 (tp40) cc_final: 0.9119 (tp40)
REVERT: B  210 MET cc_start: 0.9597 (mtp) cc_final: 0.9265 (mtp)
REVERT: B  297 TYR cc_start: 0.8960 (m-80) cc_final: 0.8678 (m-80)
REVERT: B  306 MET cc_start: 0.8528 (mtm) cc_final: 0.8178 (mtt)
REVERT: B  324 ARG cc_start: 0.9441 (mtt90) cc_final: 0.8842 (mtp85)
REVERT: B  327 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8583 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1723
  time to fit residues: 38.2201
Evaluate side-chains
  134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 110 optimal weight:    9.9990
   chunk 88 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.074260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.060179 restraints weight = 37232.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.061937 restraints weight = 23031.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.063089 restraints weight = 15923.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2793

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= 0.168
  Angle     :  0.559   8.013  11019  Z= 0.302
  Chirality :  0.041   0.309   1386
  Planarity :  0.003   0.032   1450
  Dihedral  :  3.716  18.524   1274
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1231
  helix:  1.28 (0.19), residues: 770
  sheet: -0.02 (0.48), residues: 104
  loop : -0.63 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.019   0.001   PHE A 138 
 TYR   0.024   0.002   TYR A 277 
 ARG   0.006   0.001   ARG A  88 

*********************** 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
  160 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8961 (mm-40)
REVERT: A  118 ASP cc_start: 0.9414 (m-30) cc_final: 0.8992 (m-30)
REVERT: A  131 GLN cc_start: 0.8750 (tt0) cc_final: 0.8422 (tt0)
REVERT: A  133 LEU cc_start: 0.9152 (mm) cc_final: 0.8624 (mm)
REVERT: A  196 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8155 (tm-30)
REVERT: A  275 MET cc_start: 0.9312 (ppp) cc_final: 0.9071 (ppp)
REVERT: A  282 MET cc_start: 0.8856 (tmm) cc_final: 0.8412 (tmm)
REVERT: A  304 ARG cc_start: 0.9073 (ttm110) cc_final: 0.8637 (ttm110)
REVERT: B   35 LEU cc_start: 0.8916 (tp) cc_final: 0.8695 (tp)
REVERT: B   58 MET cc_start: 0.9401 (mmp) cc_final: 0.9165 (mmm)
REVERT: B   67 PHE cc_start: 0.9293 (t80) cc_final: 0.8981 (t80)
REVERT: B   71 ILE cc_start: 0.9770 (mm) cc_final: 0.9508 (mm)
REVERT: B  122 HIS cc_start: 0.8255 (m90) cc_final: 0.7699 (m90)
REVERT: B  136 ASP cc_start: 0.9186 (m-30) cc_final: 0.8948 (m-30)
REVERT: B  139 GLN cc_start: 0.9370 (tp40) cc_final: 0.9138 (tp40)
REVERT: B  210 MET cc_start: 0.9588 (mtp) cc_final: 0.9249 (mtp)
REVERT: B  225 LEU cc_start: 0.9090 (mt) cc_final: 0.8885 (mt)
REVERT: B  257 MET cc_start: 0.9089 (mmm) cc_final: 0.8696 (tmm)
REVERT: B  306 MET cc_start: 0.8545 (mtm) cc_final: 0.8205 (mtt)
REVERT: B  324 ARG cc_start: 0.9373 (mtt90) cc_final: 0.8968 (mtp85)
REVERT: B  327 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8579 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1500
  time to fit residues: 35.0892
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  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 56 optimal weight:    0.8980
   chunk 93 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 113 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 300 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.073741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.059903 restraints weight = 36995.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.061622 restraints weight = 22732.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.062862 restraints weight = 15720.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2932

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= 0.180
  Angle     :  0.573   7.353  11019  Z= 0.312
  Chirality :  0.041   0.223   1386
  Planarity :  0.003   0.036   1450
  Dihedral  :  3.709  18.089   1274
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.24), residues: 1231
  helix:  1.30 (0.19), residues: 770
  sheet:  0.13 (0.48), residues: 104
  loop : -0.64 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.020   0.001   PHE B  86 
 TYR   0.025   0.002   TYR B 302 
 ARG   0.004   0.000   ARG A  88 

*********************** 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
  159 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8807 (mm-40)
REVERT: A  118 ASP cc_start: 0.9388 (m-30) cc_final: 0.8947 (m-30)
REVERT: A  131 GLN cc_start: 0.8811 (tt0) cc_final: 0.8512 (tt0)
REVERT: A  170 MET cc_start: 0.8338 (ppp) cc_final: 0.8039 (ppp)
REVERT: A  196 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8145 (tm-30)
REVERT: A  282 MET cc_start: 0.8838 (tmm) cc_final: 0.8371 (tmm)
REVERT: A  304 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8673 (ttm110)
REVERT: B   35 LEU cc_start: 0.8879 (tp) cc_final: 0.8557 (tp)
REVERT: B   58 MET cc_start: 0.9397 (mmp) cc_final: 0.9176 (mmm)
REVERT: B   67 PHE cc_start: 0.9268 (t80) cc_final: 0.8965 (t80)
REVERT: B   71 ILE cc_start: 0.9749 (mm) cc_final: 0.9484 (mm)
REVERT: B  110 LYS cc_start: 0.9151 (tppt) cc_final: 0.8942 (tppt)
REVERT: B  122 HIS cc_start: 0.8221 (m90) cc_final: 0.7727 (m90)
REVERT: B  136 ASP cc_start: 0.9146 (m-30) cc_final: 0.8893 (m-30)
REVERT: B  139 GLN cc_start: 0.9350 (tp40) cc_final: 0.9134 (tp40)
REVERT: B  210 MET cc_start: 0.9574 (mtp) cc_final: 0.9183 (mtm)
REVERT: B  225 LEU cc_start: 0.9024 (mt) cc_final: 0.8814 (mt)
REVERT: B  324 ARG cc_start: 0.9360 (mtt90) cc_final: 0.9026 (mtt90)
REVERT: B  327 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8577 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1513
  time to fit residues: 35.5816
Evaluate side-chains
  134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 120 optimal weight:    0.0770
   chunk 3 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 92 optimal weight:   20.0000
   chunk 55 optimal weight:    0.0170
   chunk 41 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 103 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 300 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 = 0.3298 r_free = 0.3298 target = 0.073769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.059587 restraints weight = 38089.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.061381 restraints weight = 23344.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.062626 restraints weight = 16117.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8074  Z= 0.181
  Angle     :  0.594  11.853  11019  Z= 0.315
  Chirality :  0.042   0.198   1386
  Planarity :  0.003   0.034   1450
  Dihedral  :  3.646  18.073   1274
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.24), residues: 1231
  helix:  1.25 (0.19), residues: 774
  sheet:  0.24 (0.48), residues: 104
  loop : -0.61 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.020   0.001   PHE B  86 
 TYR   0.017   0.002   TYR B 302 
 ARG   0.003   0.000   ARG A  88 

*********************** 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
  158 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9365 (pp30) cc_final: 0.8861 (pp30)
REVERT: A   96 GLN cc_start: 0.9316 (mm-40) cc_final: 0.8828 (mm-40)
REVERT: A  118 ASP cc_start: 0.9365 (m-30) cc_final: 0.8990 (m-30)
REVERT: A  131 GLN cc_start: 0.8828 (tt0) cc_final: 0.8494 (tt0)
REVERT: A  138 PHE cc_start: 0.8716 (t80) cc_final: 0.8492 (t80)
REVERT: A  196 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8080 (tm-30)
REVERT: A  223 GLU cc_start: 0.8793 (mp0) cc_final: 0.8451 (mp0)
REVERT: A  282 MET cc_start: 0.8846 (tmm) cc_final: 0.8369 (tmm)
REVERT: A  286 ILE cc_start: 0.9414 (pt) cc_final: 0.9200 (pt)
REVERT: A  304 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8678 (ttm110)
REVERT: B   35 LEU cc_start: 0.8893 (tp) cc_final: 0.8558 (tp)
REVERT: B   58 MET cc_start: 0.9410 (mmp) cc_final: 0.9179 (mmm)
REVERT: B   67 PHE cc_start: 0.9296 (t80) cc_final: 0.8985 (t80)
REVERT: B   71 ILE cc_start: 0.9747 (mm) cc_final: 0.9473 (mm)
REVERT: B  110 LYS cc_start: 0.9164 (tppt) cc_final: 0.8952 (tppt)
REVERT: B  122 HIS cc_start: 0.8222 (m90) cc_final: 0.7683 (m90)
REVERT: B  136 ASP cc_start: 0.9154 (m-30) cc_final: 0.8912 (m-30)
REVERT: B  139 GLN cc_start: 0.9358 (tp40) cc_final: 0.9113 (tp40)
REVERT: B  210 MET cc_start: 0.9571 (mtp) cc_final: 0.9243 (mtp)
REVERT: B  261 MET cc_start: 0.9433 (tpp) cc_final: 0.8961 (tpt)
REVERT: B  293 MET cc_start: 0.9021 (ttt) cc_final: 0.8328 (tmm)
REVERT: B  327 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8612 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1530
  time to fit residues: 35.6552
Evaluate side-chains
  133 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 116 optimal weight:   20.0000
   chunk 58 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 53 optimal weight:   20.0000
   chunk 35 optimal weight:   30.0000
   chunk 68 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 47 optimal weight:   10.0000
   chunk 34 optimal weight:   30.0000
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 300 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 = 0.3303 r_free = 0.3303 target = 0.073894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.059902 restraints weight = 37570.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.061628 restraints weight = 23268.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.062913 restraints weight = 16196.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8074  Z= 0.172
  Angle     :  0.596  11.271  11019  Z= 0.312
  Chirality :  0.042   0.177   1386
  Planarity :  0.003   0.036   1450
  Dihedral  :  3.639  18.132   1274
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.24), residues: 1231
  helix:  1.26 (0.19), residues: 773
  sheet:  0.30 (0.49), residues: 104
  loop : -0.60 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.020   0.001   PHE B  86 
 TYR   0.026   0.002   TYR A 277 
 ARG   0.004   0.000   ARG B 324 

********************** 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  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9358 (pp30) cc_final: 0.8852 (pp30)
REVERT: A   96 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8796 (mm-40)
REVERT: A  118 ASP cc_start: 0.9374 (m-30) cc_final: 0.8950 (m-30)
REVERT: A  131 GLN cc_start: 0.8794 (tt0) cc_final: 0.8482 (tt0)
REVERT: A  138 PHE cc_start: 0.8651 (t80) cc_final: 0.8412 (t80)
REVERT: A  170 MET cc_start: 0.8207 (ppp) cc_final: 0.7931 (ppp)
REVERT: A  196 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8055 (tm-30)
REVERT: A  223 GLU cc_start: 0.8719 (mp0) cc_final: 0.8386 (mp0)
REVERT: A  282 MET cc_start: 0.8813 (tmm) cc_final: 0.8305 (tmm)
REVERT: A  286 ILE cc_start: 0.9420 (pt) cc_final: 0.9185 (pt)
REVERT: A  304 ARG cc_start: 0.9144 (ttm110) cc_final: 0.8754 (ttm110)
REVERT: B   35 LEU cc_start: 0.8926 (tp) cc_final: 0.8575 (tp)
REVERT: B   58 MET cc_start: 0.9405 (mmp) cc_final: 0.9196 (mmm)
REVERT: B   67 PHE cc_start: 0.9247 (t80) cc_final: 0.8925 (t80)
REVERT: B   71 ILE cc_start: 0.9733 (mm) cc_final: 0.9465 (mm)
REVERT: B  110 LYS cc_start: 0.9168 (tppt) cc_final: 0.8965 (tppt)
REVERT: B  122 HIS cc_start: 0.8226 (m90) cc_final: 0.7690 (m90)
REVERT: B  130 ARG cc_start: 0.8312 (tpp80) cc_final: 0.8102 (tpp80)
REVERT: B  136 ASP cc_start: 0.9116 (m-30) cc_final: 0.8856 (m-30)
REVERT: B  139 GLN cc_start: 0.9381 (tp40) cc_final: 0.9139 (tp40)
REVERT: B  163 MET cc_start: 0.8867 (mtm) cc_final: 0.7641 (mmm)
REVERT: B  197 ASP cc_start: 0.9141 (m-30) cc_final: 0.8750 (m-30)
REVERT: B  210 MET cc_start: 0.9541 (mtp) cc_final: 0.9262 (mtp)
REVERT: B  261 MET cc_start: 0.9424 (tpp) cc_final: 0.8964 (tpt)
REVERT: B  297 TYR cc_start: 0.8879 (m-80) cc_final: 0.7530 (m-80)
REVERT: B  324 ARG cc_start: 0.9382 (mtt90) cc_final: 0.8917 (mtp85)
REVERT: B  327 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8616 (mt-10)
REVERT: B  330 ASP cc_start: 0.9059 (m-30) cc_final: 0.8735 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1724
  time to fit residues: 42.1723
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  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 91 optimal weight:    0.5980
   chunk 109 optimal weight:    0.4980
   chunk 100 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 88 optimal weight:    0.3980
   chunk 47 optimal weight:    0.0770
   chunk 64 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.075178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061318 restraints weight = 37277.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.063104 restraints weight = 23048.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.064392 restraints weight = 16019.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8074  Z= 0.158
  Angle     :  0.591  11.319  11019  Z= 0.309
  Chirality :  0.041   0.155   1386
  Planarity :  0.003   0.039   1450
  Dihedral  :  3.575  17.269   1274
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.24), residues: 1231
  helix:  1.28 (0.19), residues: 771
  sheet:  0.28 (0.47), residues: 110
  loop : -0.51 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  31 
 HIS   0.003   0.001   HIS A 179 
 PHE   0.020   0.001   PHE B  86 
 TYR   0.025   0.002   TYR A 277 
 ARG   0.005   0.001   ARG B 324 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2195.56 seconds
wall clock time: 40 minutes 7.94 seconds (2407.94 seconds total)