Starting phenix.real_space_refine
on Wed Mar 12 15:44:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ocy_12816/03_2025/7ocy_12816_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ocy_12816/03_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_12816/03_2025/7ocy_12816.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ocy_12816/03_2025/7ocy_12816.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ocy_12816/03_2025/7ocy_12816_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ocy_12816/03_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-5624/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: 5.67, 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: 2.80
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.03
  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: 3.00

  Time building geometry restraints manager: 2.99 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  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:          0.290
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.330
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.010
  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:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.680
-------------------------------------------------------------------------------
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  : 0.948 
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: 0.1803
  time to fit residues: 40.8251
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  : 0.930 
-------------------------------------------------------------------------------
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 = 0.057173 restraints weight = 39636.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.058802 restraints weight = 24521.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059906 restraints weight = 17122.071|
|-----------------------------------------------------------------------------|
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   8.928  11019  Z= 0.404
  Chirality :  0.044   0.168   1386
  Planarity :  0.004   0.042   1450
  Dihedral  :  4.568  22.453   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  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9088 (tpt) cc_final: 0.8869 (tpp)
REVERT: A   49 ASP cc_start: 0.8687 (p0) cc_final: 0.8445 (p0)
REVERT: A  118 ASP cc_start: 0.9286 (m-30) cc_final: 0.8990 (m-30)
REVERT: A  154 LEU cc_start: 0.9633 (mm) cc_final: 0.9420 (mt)
REVERT: A  196 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8524 (tm-30)
REVERT: A  223 GLU cc_start: 0.8878 (mp0) cc_final: 0.8578 (mp0)
REVERT: A  304 ARG cc_start: 0.9041 (ttm110) cc_final: 0.8607 (ttm110)
REVERT: B   35 LEU cc_start: 0.8927 (tp) cc_final: 0.8579 (tp)
REVERT: B   58 MET cc_start: 0.9456 (mmp) cc_final: 0.9215 (mmm)
REVERT: B   67 PHE cc_start: 0.9309 (t80) cc_final: 0.9106 (t80)
REVERT: B   71 ILE cc_start: 0.9703 (mm) cc_final: 0.9459 (mm)
REVERT: B  122 HIS cc_start: 0.8372 (m90) cc_final: 0.7924 (m90)
REVERT: B  130 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8555 (tpp80)
REVERT: B  136 ASP cc_start: 0.9151 (m-30) cc_final: 0.8897 (m-30)
REVERT: B  210 MET cc_start: 0.9644 (mtp) cc_final: 0.9207 (mtp)
REVERT: B  225 LEU cc_start: 0.9075 (mt) cc_final: 0.8799 (mt)
REVERT: B  293 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8874 (ttt)
REVERT: B  324 ARG cc_start: 0.9482 (mtt90) cc_final: 0.8748 (mtt90)
REVERT: B  327 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8603 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1652
  time to fit residues: 33.3750
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  : 0.811 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 84 optimal weight:    0.8980
   chunk 35 optimal weight:   30.0000
   chunk 102 optimal weight:    8.9990
   chunk 113 optimal weight:   30.0000
   chunk 112 optimal weight:   10.0000
   chunk 77 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    2.2986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.071738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.057959 restraints weight = 39194.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.059672 restraints weight = 23791.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.060792 restraints weight = 16334.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8074  Z= 0.287
  Angle     :  0.631   9.382  11019  Z= 0.351
  Chirality :  0.042   0.167   1386
  Planarity :  0.003   0.033   1450
  Dihedral  :  4.326  22.526   1274
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.25 (0.24), residues: 1231
  helix:  0.84 (0.18), residues: 768
  sheet: -0.72 (0.49), residues: 101
  loop : -0.87 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  31 
 HIS   0.003   0.001   HIS B  13 
 PHE   0.024   0.002   PHE B  86 
 TYR   0.030   0.003   TYR B  12 
 ARG   0.004   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
  145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8722 (p0) cc_final: 0.8495 (p0)
REVERT: A  118 ASP cc_start: 0.9379 (m-30) cc_final: 0.9054 (m-30)
REVERT: A  138 PHE cc_start: 0.8912 (t80) cc_final: 0.8655 (t80)
REVERT: A  196 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8481 (tm-30)
REVERT: A  223 GLU cc_start: 0.8889 (mp0) cc_final: 0.8556 (mp0)
REVERT: A  277 TYR cc_start: 0.9022 (m-80) cc_final: 0.8681 (m-80)
REVERT: A  304 ARG cc_start: 0.9061 (ttm110) cc_final: 0.8585 (ttm110)
REVERT: B   58 MET cc_start: 0.9467 (mmp) cc_final: 0.9240 (mmm)
REVERT: B   67 PHE cc_start: 0.9339 (t80) cc_final: 0.9121 (t80)
REVERT: B   71 ILE cc_start: 0.9734 (mm) cc_final: 0.9492 (mm)
REVERT: B  122 HIS cc_start: 0.8352 (m90) cc_final: 0.7913 (m90)
REVERT: B  136 ASP cc_start: 0.9161 (m-30) cc_final: 0.8880 (m-30)
REVERT: B  210 MET cc_start: 0.9643 (mtp) cc_final: 0.9219 (mtp)
REVERT: B  225 LEU cc_start: 0.9017 (mt) cc_final: 0.8784 (mt)
REVERT: B  306 MET cc_start: 0.8627 (mtm) cc_final: 0.8346 (mtt)
REVERT: B  324 ARG cc_start: 0.9488 (mtt90) cc_final: 0.8984 (mtt90)
REVERT: B  327 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8594 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2015
  time to fit residues: 41.9666
Evaluate side-chains
  125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 101 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 89 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
B 300 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.072968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.058632 restraints weight = 37666.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.060325 restraints weight = 22853.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.061627 restraints weight = 15836.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8074  Z= 0.168
  Angle     :  0.566   7.935  11019  Z= 0.307
  Chirality :  0.041   0.143   1386
  Planarity :  0.003   0.037   1450
  Dihedral  :  4.058  19.296   1274
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  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:  0.66 (0.24), residues: 1231
  helix:  1.18 (0.19), residues: 768
  sheet: -0.58 (0.45), residues: 112
  loop : -0.74 (0.35), residues: 351

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   0.020   0.001   PHE B  86 
 TYR   0.017   0.002   TYR B 302 
 ARG   0.011   0.001   ARG B 284 

*********************** 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
  156 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8716 (p0) cc_final: 0.8486 (p0)
REVERT: A  118 ASP cc_start: 0.9415 (m-30) cc_final: 0.9017 (m-30)
REVERT: A  131 GLN cc_start: 0.8828 (tt0) cc_final: 0.8416 (tt0)
REVERT: A  196 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8422 (tm-30)
REVERT: A  282 MET cc_start: 0.8793 (tmm) cc_final: 0.8522 (tmm)
REVERT: A  304 ARG cc_start: 0.9086 (ttm110) cc_final: 0.8660 (ttm110)
REVERT: B   58 MET cc_start: 0.9448 (mmp) cc_final: 0.9167 (mmm)
REVERT: B   71 ILE cc_start: 0.9736 (mm) cc_final: 0.9496 (mm)
REVERT: B  122 HIS cc_start: 0.8294 (m90) cc_final: 0.7801 (m90)
REVERT: B  136 ASP cc_start: 0.9153 (m-30) cc_final: 0.8938 (m-30)
REVERT: B  210 MET cc_start: 0.9636 (mtp) cc_final: 0.9281 (mtp)
REVERT: B  293 MET cc_start: 0.9275 (ttt) cc_final: 0.8243 (tmm)
REVERT: B  306 MET cc_start: 0.8485 (mtm) cc_final: 0.8175 (mtt)
REVERT: B  324 ARG cc_start: 0.9468 (mtt90) cc_final: 0.9014 (mtt90)
REVERT: B  327 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8551 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1554
  time to fit residues: 34.9459
Evaluate side-chains
  132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 114 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 93 optimal weight:   20.0000
   chunk 117 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0070
   chunk 110 optimal weight:   30.0000
   chunk 43 optimal weight:    6.9990
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
B 226 GLN
** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.073720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.059607 restraints weight = 37116.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.061298 restraints weight = 22568.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.062487 restraints weight = 15594.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8074  Z= 0.173
  Angle     :  0.584   7.930  11019  Z= 0.310
  Chirality :  0.041   0.171   1386
  Planarity :  0.003   0.036   1450
  Dihedral  :  3.890  19.146   1274
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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:  0.77 (0.24), residues: 1231
  helix:  1.25 (0.19), residues: 772
  sheet: -0.38 (0.48), residues: 104
  loop : -0.75 (0.35), residues: 355

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   0.021   0.001   PHE B  86 
 TYR   0.023   0.002   TYR B  12 
 ARG   0.005   0.001   ARG B 130 

*********************** 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
  156 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8752 (p0) cc_final: 0.8516 (p0)
REVERT: A  118 ASP cc_start: 0.9406 (m-30) cc_final: 0.9010 (m-30)
REVERT: A  131 GLN cc_start: 0.8636 (tt0) cc_final: 0.8417 (tt0)
REVERT: A  196 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8406 (tm-30)
REVERT: A  223 GLU cc_start: 0.8842 (mp0) cc_final: 0.8471 (mp0)
REVERT: A  277 TYR cc_start: 0.9071 (m-10) cc_final: 0.8607 (m-80)
REVERT: A  282 MET cc_start: 0.8791 (tmm) cc_final: 0.8437 (tmm)
REVERT: A  294 MET cc_start: 0.8980 (tmm) cc_final: 0.8752 (tmm)
REVERT: A  304 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8686 (ttm110)
REVERT: B   58 MET cc_start: 0.9442 (mmp) cc_final: 0.9188 (mmm)
REVERT: B   71 ILE cc_start: 0.9748 (mm) cc_final: 0.9507 (mm)
REVERT: B  122 HIS cc_start: 0.8256 (m90) cc_final: 0.7781 (m90)
REVERT: B  136 ASP cc_start: 0.9187 (m-30) cc_final: 0.8969 (m-30)
REVERT: B  139 GLN cc_start: 0.9340 (tp40) cc_final: 0.9113 (tp40)
REVERT: B  163 MET cc_start: 0.8985 (mtm) cc_final: 0.8160 (mmm)
REVERT: B  210 MET cc_start: 0.9646 (mtp) cc_final: 0.9269 (mtp)
REVERT: B  297 TYR cc_start: 0.8730 (m-10) cc_final: 0.8522 (m-10)
REVERT: B  306 MET cc_start: 0.8493 (mtm) cc_final: 0.8149 (mtt)
REVERT: B  324 ARG cc_start: 0.9455 (mtt90) cc_final: 0.9025 (mtt90)
REVERT: B  327 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8569 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1661
  time to fit residues: 37.3471
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  : 0.934 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 83 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0970
   chunk 36 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 90 optimal weight:   30.0000
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
** 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 = 0.3299 r_free = 0.3299 target = 0.074123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.059965 restraints weight = 37474.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.061677 restraints weight = 23011.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.062982 restraints weight = 15895.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2698

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= 0.164
  Angle     :  0.556   9.339  11019  Z= 0.299
  Chirality :  0.041   0.157   1386
  Planarity :  0.003   0.037   1450
  Dihedral  :  3.771  18.350   1274
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.36 %
    Favored  : 97.46 %
  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:  0.89 (0.24), residues: 1231
  helix:  1.33 (0.19), residues: 771
  sheet: -0.20 (0.48), residues: 104
  loop : -0.69 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 172 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.022   0.001   PHE B  86 
 TYR   0.016   0.001   TYR B  88 
 ARG   0.010   0.001   ARG A  88 

*********************** 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
  152 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8780 (p0) cc_final: 0.8514 (p0)
REVERT: A  118 ASP cc_start: 0.9415 (m-30) cc_final: 0.8973 (m-30)
REVERT: A  131 GLN cc_start: 0.8761 (tt0) cc_final: 0.8395 (tt0)
REVERT: A  195 LYS cc_start: 0.9606 (tppp) cc_final: 0.9361 (tppt)
REVERT: A  196 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8404 (tm-30)
REVERT: A  223 GLU cc_start: 0.8870 (mp0) cc_final: 0.8516 (mp0)
REVERT: A  275 MET cc_start: 0.9311 (ppp) cc_final: 0.9010 (ppp)
REVERT: A  282 MET cc_start: 0.8796 (tmm) cc_final: 0.8383 (tmm)
REVERT: A  294 MET cc_start: 0.8965 (tmm) cc_final: 0.8735 (tmm)
REVERT: A  304 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8646 (ttm110)
REVERT: B   58 MET cc_start: 0.9420 (mmp) cc_final: 0.9179 (mmm)
REVERT: B   67 PHE cc_start: 0.9312 (t80) cc_final: 0.9039 (t80)
REVERT: B   71 ILE cc_start: 0.9755 (mm) cc_final: 0.9474 (mm)
REVERT: B  122 HIS cc_start: 0.8223 (m90) cc_final: 0.7730 (m90)
REVERT: B  130 ARG cc_start: 0.8409 (tpp80) cc_final: 0.7874 (tpp80)
REVERT: B  136 ASP cc_start: 0.9204 (m-30) cc_final: 0.8952 (m-30)
REVERT: B  139 GLN cc_start: 0.9338 (tp40) cc_final: 0.9100 (tp40)
REVERT: B  163 MET cc_start: 0.9030 (mtm) cc_final: 0.8121 (mmm)
REVERT: B  210 MET cc_start: 0.9607 (mtp) cc_final: 0.9129 (mtm)
REVERT: B  297 TYR cc_start: 0.8739 (m-10) cc_final: 0.8524 (m-10)
REVERT: B  306 MET cc_start: 0.8522 (mtm) cc_final: 0.8171 (mtt)
REVERT: B  324 ARG cc_start: 0.9409 (mtt90) cc_final: 0.9049 (mtp85)
REVERT: B  327 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8585 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1759
  time to fit residues: 39.0273
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  : 0.952 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 103 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 110 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
** 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 = 0.3288 r_free = 0.3288 target = 0.073511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.059585 restraints weight = 37779.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061277 restraints weight = 23241.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.062506 restraints weight = 16194.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8074  Z= 0.185
  Angle     :  0.563   7.947  11019  Z= 0.306
  Chirality :  0.041   0.289   1386
  Planarity :  0.003   0.035   1450
  Dihedral  :  3.745  19.726   1274
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.81 %
    Favored  : 98.00 %
  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:  1.34 (0.19), residues: 769
  sheet: -0.05 (0.48), residues: 104
  loop : -0.68 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  31 
 HIS   0.003   0.001   HIS A 179 
 PHE   0.019   0.001   PHE B  86 
 TYR   0.025   0.002   TYR B  78 
 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
  155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8685 (p0) cc_final: 0.8446 (p0)
REVERT: A  118 ASP cc_start: 0.9405 (m-30) cc_final: 0.8920 (m-30)
REVERT: A  131 GLN cc_start: 0.8797 (tt0) cc_final: 0.8475 (tt0)
REVERT: A  196 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8184 (tm-30)
REVERT: A  277 TYR cc_start: 0.8861 (m-80) cc_final: 0.8555 (m-80)
REVERT: A  282 MET cc_start: 0.8833 (tmm) cc_final: 0.8380 (tmm)
REVERT: A  286 ILE cc_start: 0.9410 (pt) cc_final: 0.9207 (pt)
REVERT: A  294 MET cc_start: 0.8954 (tmm) cc_final: 0.8749 (tmm)
REVERT: A  304 ARG cc_start: 0.9075 (ttm110) cc_final: 0.8646 (ttm110)
REVERT: B   35 LEU cc_start: 0.8983 (tp) cc_final: 0.8771 (tp)
REVERT: B   58 MET cc_start: 0.9406 (mmp) cc_final: 0.9175 (mmm)
REVERT: B   67 PHE cc_start: 0.9304 (t80) cc_final: 0.9036 (t80)
REVERT: B   71 ILE cc_start: 0.9737 (mm) cc_final: 0.9464 (mm)
REVERT: B  122 HIS cc_start: 0.8238 (m90) cc_final: 0.7709 (m90)
REVERT: B  136 ASP cc_start: 0.9182 (m-30) cc_final: 0.8950 (m-30)
REVERT: B  139 GLN cc_start: 0.9383 (tp40) cc_final: 0.9149 (tp40)
REVERT: B  210 MET cc_start: 0.9600 (mtp) cc_final: 0.9294 (mtp)
REVERT: B  257 MET cc_start: 0.9165 (mmm) cc_final: 0.8776 (tmm)
REVERT: B  306 MET cc_start: 0.8571 (mtm) cc_final: 0.8223 (mtt)
REVERT: B  324 ARG cc_start: 0.9429 (mtt90) cc_final: 0.9018 (mtt90)
REVERT: B  327 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8568 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1542
  time to fit residues: 35.0165
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  : 1.076 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 113 optimal weight:   30.0000
   chunk 76 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 166 GLN
B 237 ASN
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.073380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.059454 restraints weight = 37439.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061157 restraints weight = 23253.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.062256 restraints weight = 16252.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8074  Z= 0.173
  Angle     :  0.567   7.444  11019  Z= 0.305
  Chirality :  0.041   0.216   1386
  Planarity :  0.003   0.041   1450
  Dihedral  :  3.696  19.033   1274
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.81 %
    Favored  : 98.00 %
  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:  1.31 (0.19), residues: 772
  sheet:  0.12 (0.49), residues: 104
  loop : -0.71 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.021   0.001   PHE B  86 
 TYR   0.016   0.002   TYR B  12 
 ARG   0.006   0.001   ARG B 130 

*********************** 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
  160 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8659 (p0) cc_final: 0.8405 (p0)
REVERT: A  118 ASP cc_start: 0.9391 (m-30) cc_final: 0.8959 (m-30)
REVERT: A  131 GLN cc_start: 0.8824 (tt0) cc_final: 0.8529 (tt0)
REVERT: A  138 PHE cc_start: 0.8811 (t80) cc_final: 0.8485 (t80)
REVERT: A  196 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8173 (tm-30)
REVERT: A  277 TYR cc_start: 0.8793 (m-80) cc_final: 0.8492 (m-80)
REVERT: A  282 MET cc_start: 0.8825 (tmm) cc_final: 0.8346 (tmm)
REVERT: A  286 ILE cc_start: 0.9433 (pt) cc_final: 0.9212 (pt)
REVERT: A  304 ARG cc_start: 0.9112 (ttm110) cc_final: 0.8679 (ttm110)
REVERT: B   35 LEU cc_start: 0.8864 (tp) cc_final: 0.8627 (tp)
REVERT: B   37 VAL cc_start: 0.9823 (t) cc_final: 0.9407 (p)
REVERT: B   58 MET cc_start: 0.9406 (mmp) cc_final: 0.9171 (mmm)
REVERT: B   67 PHE cc_start: 0.9287 (t80) cc_final: 0.9009 (t80)
REVERT: B   71 ILE cc_start: 0.9731 (mm) cc_final: 0.9456 (mm)
REVERT: B  110 LYS cc_start: 0.9182 (tppt) cc_final: 0.8978 (tppt)
REVERT: B  122 HIS cc_start: 0.8274 (m90) cc_final: 0.7738 (m90)
REVERT: B  130 ARG cc_start: 0.8386 (tpp80) cc_final: 0.7912 (tpp80)
REVERT: B  136 ASP cc_start: 0.9156 (m-30) cc_final: 0.8913 (m-30)
REVERT: B  139 GLN cc_start: 0.9377 (tp40) cc_final: 0.9171 (tp40)
REVERT: B  162 MET cc_start: 0.9024 (tpt) cc_final: 0.8794 (tpp)
REVERT: B  210 MET cc_start: 0.9595 (mtp) cc_final: 0.9151 (mtm)
REVERT: B  225 LEU cc_start: 0.9056 (mt) cc_final: 0.8855 (mt)
REVERT: B  261 MET cc_start: 0.9469 (tpp) cc_final: 0.9022 (tpt)
REVERT: B  306 MET cc_start: 0.8583 (mtm) cc_final: 0.8211 (mtt)
REVERT: B  324 ARG cc_start: 0.9408 (mtt90) cc_final: 0.9065 (mtp85)
REVERT: B  327 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8598 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1464
  time to fit residues: 34.2841
Evaluate side-chains
  141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 120 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 92 optimal weight:   20.0000
   chunk 55 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   chunk 103 optimal weight:    0.2980
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 237 ASN
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.073766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.059722 restraints weight = 37755.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.061441 restraints weight = 23280.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.062718 restraints weight = 16245.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8074  Z= 0.164
  Angle     :  0.585  11.006  11019  Z= 0.311
  Chirality :  0.041   0.188   1386
  Planarity :  0.003   0.040   1450
  Dihedral  :  3.688  18.855   1274
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.54 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.24), residues: 1231
  helix:  1.27 (0.19), residues: 772
  sheet:  0.22 (0.49), residues: 104
  loop : -0.70 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.020   0.001   PHE B  86 
 TYR   0.035   0.002   TYR B 302 
 ARG   0.006   0.001   ARG B 130 

*********************** 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
  167 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ASP cc_start: 0.8662 (p0) cc_final: 0.8136 (p0)
REVERT: A   81 GLN cc_start: 0.9373 (pp30) cc_final: 0.8871 (pp30)
REVERT: A  118 ASP cc_start: 0.9378 (m-30) cc_final: 0.8974 (m-30)
REVERT: A  131 GLN cc_start: 0.8761 (tt0) cc_final: 0.8437 (tt0)
REVERT: A  138 PHE cc_start: 0.8798 (t80) cc_final: 0.8219 (t80)
REVERT: A  170 MET cc_start: 0.8285 (ppp) cc_final: 0.7984 (ppp)
REVERT: A  196 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8105 (tm-30)
REVERT: A  223 GLU cc_start: 0.8780 (mp0) cc_final: 0.8440 (mp0)
REVERT: A  282 MET cc_start: 0.8846 (tmm) cc_final: 0.8344 (tmm)
REVERT: A  286 ILE cc_start: 0.9416 (pt) cc_final: 0.9171 (pt)
REVERT: A  304 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8751 (ttm110)
REVERT: B   35 LEU cc_start: 0.8880 (tp) cc_final: 0.8652 (tp)
REVERT: B   37 VAL cc_start: 0.9816 (t) cc_final: 0.9383 (p)
REVERT: B   58 MET cc_start: 0.9396 (mmp) cc_final: 0.9159 (mmm)
REVERT: B   67 PHE cc_start: 0.9275 (t80) cc_final: 0.8996 (t80)
REVERT: B   71 ILE cc_start: 0.9741 (mm) cc_final: 0.9469 (mm)
REVERT: B  110 LYS cc_start: 0.9170 (tppt) cc_final: 0.8961 (tppt)
REVERT: B  122 HIS cc_start: 0.8262 (m90) cc_final: 0.7716 (m90)
REVERT: B  136 ASP cc_start: 0.9166 (m-30) cc_final: 0.8930 (m-30)
REVERT: B  139 GLN cc_start: 0.9358 (tp40) cc_final: 0.9141 (tp40)
REVERT: B  162 MET cc_start: 0.9038 (tpt) cc_final: 0.8728 (tpp)
REVERT: B  210 MET cc_start: 0.9589 (mtp) cc_final: 0.9292 (mtp)
REVERT: B  257 MET cc_start: 0.9027 (mmm) cc_final: 0.8679 (tmm)
REVERT: B  306 MET cc_start: 0.8528 (mtm) cc_final: 0.8188 (mtt)
REVERT: B  324 ARG cc_start: 0.9411 (mtt90) cc_final: 0.9037 (mmm-85)
REVERT: B  327 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8611 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1529
  time to fit residues: 37.4330
Evaluate side-chains
  138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   chunk 35 optimal weight:   30.0000
   chunk 68 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 34 optimal weight:   30.0000
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 265 ASN
B 326 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.073571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.059434 restraints weight = 37793.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.061172 restraints weight = 23476.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.062418 restraints weight = 16386.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3197

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= 0.176
  Angle     :  0.589  11.159  11019  Z= 0.315
  Chirality :  0.042   0.203   1386
  Planarity :  0.003   0.042   1450
  Dihedral  :  3.675  18.148   1274
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.36 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.93 (0.24), residues: 1231
  helix:  1.27 (0.19), residues: 773
  sheet:  0.30 (0.49), residues: 104
  loop : -0.62 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.022   0.001   PHE A 217 
 TYR   0.026   0.002   TYR B 302 
 ARG   0.004   0.000   ARG A  88 

********************** 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
  160 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.9372 (pp30) cc_final: 0.8869 (pp30)
REVERT: A  118 ASP cc_start: 0.9401 (m-30) cc_final: 0.8999 (m-30)
REVERT: A  131 GLN cc_start: 0.8790 (tt0) cc_final: 0.8478 (tt0)
REVERT: A  133 LEU cc_start: 0.9178 (mm) cc_final: 0.8657 (mm)
REVERT: A  138 PHE cc_start: 0.8821 (t80) cc_final: 0.8379 (t80)
REVERT: A  196 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8066 (tm-30)
REVERT: A  223 GLU cc_start: 0.8777 (mp0) cc_final: 0.8449 (mp0)
REVERT: A  282 MET cc_start: 0.8821 (tmm) cc_final: 0.8317 (tmm)
REVERT: A  286 ILE cc_start: 0.9429 (pt) cc_final: 0.9186 (pt)
REVERT: A  304 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8758 (ttm110)
REVERT: B   35 LEU cc_start: 0.8872 (tp) cc_final: 0.8649 (tp)
REVERT: B   37 VAL cc_start: 0.9822 (t) cc_final: 0.9506 (p)
REVERT: B   58 MET cc_start: 0.9410 (mmp) cc_final: 0.9182 (mmm)
REVERT: B   67 PHE cc_start: 0.9256 (t80) cc_final: 0.8972 (t80)
REVERT: B   71 ILE cc_start: 0.9730 (mm) cc_final: 0.9460 (mm)
REVERT: B  110 LYS cc_start: 0.9174 (tppt) cc_final: 0.8970 (tppt)
REVERT: B  122 HIS cc_start: 0.8286 (m90) cc_final: 0.7744 (m90)
REVERT: B  136 ASP cc_start: 0.9160 (m-30) cc_final: 0.8915 (m-30)
REVERT: B  139 GLN cc_start: 0.9358 (tp40) cc_final: 0.9119 (tp40)
REVERT: B  162 MET cc_start: 0.8999 (tpt) cc_final: 0.8189 (tmm)
REVERT: B  163 MET cc_start: 0.8999 (mtm) cc_final: 0.8479 (mtm)
REVERT: B  210 MET cc_start: 0.9600 (mtp) cc_final: 0.9359 (mtp)
REVERT: B  261 MET cc_start: 0.9409 (tpp) cc_final: 0.8962 (tpt)
REVERT: B  297 TYR cc_start: 0.8783 (m-10) cc_final: 0.7904 (m-10)
REVERT: B  324 ARG cc_start: 0.9364 (mtt90) cc_final: 0.9145 (mtt90)
REVERT: B  327 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8597 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1405
  time to fit residues: 33.2665
Evaluate side-chains
  136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 91 optimal weight:   30.0000
   chunk 109 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 88 optimal weight:    0.0270
   chunk 47 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5036

-------------------------------------------------------------------------------
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 237 ASN
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.074303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.060162 restraints weight = 37399.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.061886 restraints weight = 23241.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.063200 restraints weight = 16301.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8074  Z= 0.158
  Angle     :  0.584  10.901  11019  Z= 0.308
  Chirality :  0.041   0.176   1386
  Planarity :  0.003   0.040   1450
  Dihedral  :  3.632  17.977   1274
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.00 %
    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:  0.98 (0.24), residues: 1231
  helix:  1.28 (0.19), residues: 774
  sheet:  0.34 (0.49), residues: 104
  loop : -0.55 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  31 
 HIS   0.002   0.001   HIS A 179 
 PHE   0.020   0.001   PHE B  86 
 TYR   0.023   0.002   TYR B 302 
 ARG   0.005   0.000   ARG A  88 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2586.61 seconds
wall clock time: 47 minutes 0.19 seconds (2820.19 seconds total)