Starting phenix.real_space_refine
on Thu Feb 13 09:27:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jt0_9883/02_2025/6jt0_9883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jt0_9883/02_2025/6jt0_9883.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jt0_9883/02_2025/6jt0_9883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jt0_9883/02_2025/6jt0_9883.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jt0_9883/02_2025/6jt0_9883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jt0_9883/02_2025/6jt0_9883.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      59      5.16       5
     C    5529      2.51       5
     N    1462      2.21       5
     O    1551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8602
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4087
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 542, 4084
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 217
          Unresolved non-hydrogen angles: 267
          Unresolved non-hydrogen dihedrals: 175
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 166
      Conformer: "B"
        Number of residues, atoms: 542, 4084
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 217
          Unresolved non-hydrogen angles: 267
          Unresolved non-hydrogen dihedrals: 175
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 166
          bond proxies already assigned to first conformer: 4165
    Chain: "B"
      Number of atoms: 4472
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 576, 4468
          Classifications: {'peptide': 576}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 114
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 84
      Conformer: "B"
        Number of residues, atoms: 576, 4468
          Classifications: {'peptide': 576}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 114
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 84
          bond proxies already assigned to first conformer: 4553
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLU A 147 " occ=0.91
      ... (3 atoms not shown)
      pdb=" CB  GLU A 147 " occ=0.91
  Time building chain proxies: 9.21, per 1000 atoms: 1.07
  Number of scatterers: 8602
  At special positions: 0
  Unit cell: (148.39, 96.14, 74.195, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      59     16.00
     O    1551      8.00
     N    1462      7.00
     C    5529      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: 2.31
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      48.2% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 83
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 128 through 149
      removed outlier: 3.588A  pdb=" N   ASP A 148 " --> pdb=" O   CYS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 156
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 4.595A  pdb=" N   SER A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   THR A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   SER A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 227
    Processing helix  chain 'A' and resid 237 through 242
      removed outlier: 4.090A  pdb=" N   HIS A 241 " --> pdb=" O   PRO A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 302 through 309
    Processing helix  chain 'A' and resid 319 through 323
      removed outlier: 3.845A  pdb=" N   TYR A 323 " --> pdb=" O   ASN A 319 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 319 through 323'
    Processing helix  chain 'A' and resid 334 through 341
      removed outlier: 4.043A  pdb=" N   MET A 341 " --> pdb=" O   GLY A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 394
      removed outlier: 3.925A  pdb=" N   THR A 394 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 419
      removed outlier: 4.471A  pdb=" N   GLY A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   GLU A 417 " --> pdb=" O   VAL A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 458
      removed outlier: 3.941A  pdb=" N   GLY A 430 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 468
      removed outlier: 3.621A  pdb=" N   GLN A 468 " --> pdb=" O   GLN A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 496
      removed outlier: 3.771A  pdb=" N   ILE A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 521
    Processing helix  chain 'A' and resid 544 through 561
    Processing helix  chain 'A' and resid 598 through 609
      removed outlier: 3.970A  pdb=" N   THR A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 627
      removed outlier: 3.912A  pdb=" N   LEU A 625 " --> pdb=" O   THR A 621 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 30
      removed outlier: 3.675A  pdb=" N   ASN B   6 " --> pdb=" O   TYR B   2 " (cutoff:3.500A)
      Proline residue:  B  19  - end of helix
      removed outlier: 3.931A  pdb=" N   TRP B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.927A  pdb=" N   THR B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 81
    Processing helix  chain 'B' and resid 83 through 90
    Processing helix  chain 'B' and resid 93 through 100
    Processing helix  chain 'B' and resid 102 through 112
      removed outlier: 3.521A  pdb=" N   ASP B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE B 111 " --> pdb=" O   HIS B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 157
    Processing helix  chain 'B' and resid 210 through 217
    Processing helix  chain 'B' and resid 233 through 240
    Processing helix  chain 'B' and resid 241 through 244
    Processing helix  chain 'B' and resid 264 through 271
    Processing helix  chain 'B' and resid 329 through 337
      removed outlier: 3.757A  pdb=" N   LEU B 333 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 354
      removed outlier: 4.173A  pdb=" N   ASP B 351 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 395
      removed outlier: 4.209A  pdb=" N   TYR B 363 " --> pdb=" O   PHE B 359 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU B 378 " --> pdb=" O   ASP B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 407
    Processing helix  chain 'B' and resid 429 through 437
      removed outlier: 3.603A  pdb=" N   HIS B 437 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 461
      removed outlier: 3.709A  pdb=" N   LYS B 445 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 508
      removed outlier: 4.028A  pdb=" N   GLY B 508 " --> pdb=" O   MET B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 557
      removed outlier: 3.986A  pdb=" N   ASN B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 573
    Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193
      removed outlier: 4.003A  pdb=" N   SER A 189 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300
      removed outlier: 6.744A  pdb=" N   MET A 291 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE A 290 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 482
      removed outlier: 5.484A  pdb=" N   LYS A 476 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ALA A 584 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 583 " --> pdb=" O   PHE A 597 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487
      removed outlier: 7.599A  pdb=" N   MET A 573 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   ASN A 617 " --> pdb=" O   MET A 573 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ILE A 575 " --> pdb=" O   ASN A 617 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE A 616 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 525
      removed outlier: 3.741A  pdb=" N   TYR A 523 " --> pdb=" O   ALA A 535 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 124
      removed outlier: 6.612A  pdb=" N   GLN B 178 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.672A  pdb=" N   ILE B 222 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   CYS B 232 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   HIS B 220 " --> pdb=" O   CYS B 232 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE B 223 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 471
      removed outlier: 3.737A  pdb=" N   ASN B 419 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLY B 526 " --> pdb=" O   ASN B 419 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   THR B 421 " --> pdb=" O   HIS B 524 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   HIS B 524 " --> pdb=" O   THR B 421 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   LEU B 423 " --> pdb=" O   GLY B 522 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY B 522 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL B 529 " --> pdb=" O   PHE B 543 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 471
      removed outlier: 3.737A  pdb=" N   ASN B 419 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLY B 526 " --> pdb=" O   ASN B 419 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   THR B 421 " --> pdb=" O   HIS B 524 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   HIS B 524 " --> pdb=" O   THR B 421 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   LEU B 423 " --> pdb=" O   GLY B 522 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLY B 522 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   SER B 565 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   ILE B 523 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ILE B 562 " --> pdb=" O   LEU B 604 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL B 601 " --> pdb=" O   GLY B 588 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLY B 588 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   PHE B 603 " --> pdb=" O   HIS B 586 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   HIS B 586 " --> pdb=" O   PHE B 603 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   SER B 605 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   LEU B 584 " --> pdb=" O   SER B 605 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512

    457 hydrogen bonds defined for protein.
    1298 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 3085
        1.38 -     1.55: 5579
        1.55 -     1.71: 26
        1.71 -     1.88: 90
        1.88 -     2.05: 4
  Bond restraints: 8784
  Sorted by residual:
  bond pdb=" C   ASP B 106 "
       pdb=" O   ASP B 106 "
    ideal  model  delta    sigma   weight residual
    1.237  1.266 -0.029 1.17e-02 7.31e+03 6.10e+00
  bond pdb=" C   ALA B 103 "
       pdb=" O   ALA B 103 "
    ideal  model  delta    sigma   weight residual
    1.237  1.263 -0.026 1.17e-02 7.31e+03 4.90e+00
  bond pdb=" CA  ALA B 103 "
       pdb=" C   ALA B 103 "
    ideal  model  delta    sigma   weight residual
    1.523  1.552 -0.028 1.30e-02 5.92e+03 4.74e+00
  bond pdb=" CA  GLU A 230 "
       pdb=" CB  GLU A 230 "
    ideal  model  delta    sigma   weight residual
    1.524  1.551 -0.026 1.22e-02 6.72e+03 4.62e+00
  bond pdb=" CA  THR B 110 "
       pdb=" C   THR B 110 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.028 1.30e-02 5.92e+03 4.59e+00
  ... (remaining 8779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 11684
        2.05 -     4.09: 207
        4.09 -     6.14: 33
        6.14 -     8.18: 9
        8.18 -    10.23: 2
  Bond angle restraints: 11935
  Sorted by residual:
  angle pdb=" C   THR B 110 "
        pdb=" N   ILE B 111 "
        pdb=" CA  ILE B 111 "
      ideal   model   delta    sigma   weight residual
     120.56  130.79  -10.23 1.28e+00 6.10e-01 6.38e+01
  angle pdb=" N   VAL A 231 "
        pdb=" CA  VAL A 231 "
        pdb=" C   VAL A 231 "
      ideal   model   delta    sigma   weight residual
     108.17  115.21   -7.04 1.46e+00 4.69e-01 2.33e+01
  angle pdb=" C   LEU B 338 "
        pdb=" N   TYR B 339 "
        pdb=" CA  TYR B 339 "
      ideal   model   delta    sigma   weight residual
     121.54  128.89   -7.35 1.91e+00 2.74e-01 1.48e+01
  angle pdb=" C   LEU B 108 "
        pdb=" N   ALA B 109 "
        pdb=" CA  ALA B 109 "
      ideal   model   delta    sigma   weight residual
     120.28  125.10   -4.82 1.34e+00 5.57e-01 1.29e+01
  angle pdb=" N   TYR B 395 "
        pdb=" CA  TYR B 395 "
        pdb=" C   TYR B 395 "
      ideal   model   delta    sigma   weight residual
     110.06  115.00   -4.94 1.43e+00 4.89e-01 1.19e+01
  ... (remaining 11930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4896
       17.53 -    35.05: 289
       35.05 -    52.58: 48
       52.58 -    70.10: 12
       70.10 -    87.63: 7
  Dihedral angle restraints: 5252
    sinusoidal: 1996
      harmonic: 3256
  Sorted by residual:
  dihedral pdb=" CA  LEU A 398 "
           pdb=" C   LEU A 398 "
           pdb=" N   TYR A 399 "
           pdb=" CA  TYR A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.13   28.87     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  ASP B 262 "
           pdb=" C   ASP B 262 "
           pdb=" N   ILE B 263 "
           pdb=" CA  ILE B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.07  -24.93     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  HIS A 655 "
           pdb=" C   HIS A 655 "
           pdb=" N   PHE A 656 "
           pdb=" CA  PHE A 656 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.11   24.89     0      5.00e+00 4.00e-02 2.48e+01
  ... (remaining 5249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1037
       0.044 -    0.088: 264
       0.088 -    0.132: 82
       0.132 -    0.176: 6
       0.176 -    0.220: 1
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CG  LEU B   9 "
            pdb=" CB  LEU B   9 "
            pdb=" CD1 LEU B   9 "
            pdb=" CD2 LEU B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  PRO B 210 "
            pdb=" N   PRO B 210 "
            pdb=" C   PRO B 210 "
            pdb=" CB  PRO B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.65e-01
  chirality pdb=" CA  VAL B 564 "
            pdb=" N   VAL B 564 "
            pdb=" C   VAL B 564 "
            pdb=" CB  VAL B 564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 1387 not shown)

  Planarity restraints: 1515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 250 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.11e+00
        pdb=" N   PRO A 251 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 251 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 251 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 112 "   -0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO B 113 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 113 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 113 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 328 "    0.025 5.00e-02 4.00e+02   3.82e-02 2.34e+00
        pdb=" N   PRO A 329 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 329 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 329 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1512 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1258
        2.76 -     3.29: 8396
        3.29 -     3.83: 13964
        3.83 -     4.36: 15931
        4.36 -     4.90: 27305
  Nonbonded interactions: 66854
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 410 "
            pdb=" OD1 ASN B 100 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   THR B 392 "
            pdb=" OG  SER B 396 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   SER A 581 "
            pdb=" ND2 ASN A 600 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   LEU A  74 "
            pdb=" OG  SER A  77 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" ND1 HIS B 524 "
            pdb=" OG  SER B 565 "
     model   vdw
     2.335 3.120
  ... (remaining 66849 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=0.30 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:             0.690
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     28.120
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
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      :  0.004   0.100   8784  Z= 0.231
  Angle     :  0.710  10.228  11935  Z= 0.391
  Chirality :  0.043   0.220   1390
  Planarity :  0.004   0.057   1515
  Dihedral  : 12.208  87.630   3144
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.73 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  :  6.59 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.84 (0.22), residues: 1101
  helix: -1.01 (0.20), residues: 505
  sheet: -2.10 (0.31), residues: 211
  loop : -2.74 (0.27), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 602 
 HIS   0.004   0.001   HIS B 176 
 PHE   0.023   0.002   PHE A 458 
 TYR   0.016   0.002   TYR B 339 
 ARG   0.003   0.000   ARG B 360 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 178
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9551 (pp) cc_final: 0.9186 (tt)
REVERT: A  256 SER cc_start: 0.8985 (t) cc_final: 0.8331 (p)
REVERT: A  309 MET cc_start: 0.8928 (ttm) cc_final: 0.8504 (tmm)
REVERT: A  341 MET cc_start: 0.9062 (mmt) cc_final: 0.8707 (mmm)
REVERT: A  384 SER cc_start: 0.9182 (m) cc_final: 0.8978 (p)
REVERT: A  503 ILE cc_start: 0.9734 (mm) cc_final: 0.9468 (tt)
REVERT: A  520 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8777 (tt)
REVERT: A  557 MET cc_start: 0.9490 (mmt) cc_final: 0.9003 (tmm)
REVERT: B   65 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9073 (tp30)
REVERT: B   69 MET cc_start: 0.9468 (mtm) cc_final: 0.9091 (ptm)
REVERT: B  162 ILE cc_start: 0.9430 (pt) cc_final: 0.8938 (mm)
REVERT: B  164 MET cc_start: 0.9129 (ttm) cc_final: 0.8891 (ttm)
REVERT: B  243 LEU cc_start: 0.8978 (tt) cc_final: 0.8581 (pp)
REVERT: B  338 LEU cc_start: 0.9191 (mt) cc_final: 0.8910 (mt)
REVERT: B  373 THR cc_start: 0.9292 (m) cc_final: 0.9035 (p)
REVERT: B  388 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8615 (tppt)
REVERT: B  423 LEU cc_start: 0.9667 (tt) cc_final: 0.9438 (tp)
REVERT: B  424 PHE cc_start: 0.9273 (m-80) cc_final: 0.8741 (m-10)
REVERT: B  478 LYS cc_start: 0.9289 (mttm) cc_final: 0.8762 (mmtm)
REVERT: B  499 LEU cc_start: 0.9494 (tp) cc_final: 0.9061 (tp)
REVERT: B  503 MET cc_start: 0.9462 (mtp) cc_final: 0.9098 (mtm)
REVERT: B  505 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.9385 (mt-10)
REVERT: B  537 MET cc_start: 0.8906 (mmm) cc_final: 0.8503 (tmm)
REVERT: B  541 CYS cc_start: 0.9380 (m) cc_final: 0.8863 (m)
REVERT: B  572 LEU cc_start: 0.9692 (mm) cc_final: 0.9441 (mm)
REVERT: B  573 MET cc_start: 0.9467 (mmp) cc_final: 0.9226 (mmp)
  outliers start: 43
  outliers final: 11
  residues processed: 211
  average time/residue: 0.1871
  time to fit residues: 55.9272
Evaluate side-chains
  116 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  505 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
B 134 HIS
B 367 GLN
** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 518 GLN
B 563 ASN
B 581 GLN
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.057160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.045265 restraints weight = 85701.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.047375 restraints weight = 37884.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.048818 restraints weight = 22492.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8784  Z= 0.206
  Angle     :  0.779  14.874  11935  Z= 0.369
  Chirality :  0.045   0.195   1390
  Planarity :  0.005   0.094   1515
  Dihedral  :  7.609  86.399   1231
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.09 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.84 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.24), residues: 1101
  helix:  0.00 (0.21), residues: 520
  sheet: -1.29 (0.32), residues: 217
  loop : -2.41 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 602 
 HIS   0.005   0.001   HIS B 498 
 PHE   0.030   0.002   PHE A 646 
 TYR   0.026   0.002   TYR B 569 
 ARG   0.007   0.000   ARG B 464 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9462 (pp) cc_final: 0.9074 (tt)
REVERT: A  236 MET cc_start: 0.8329 (mmm) cc_final: 0.8036 (mmm)
REVERT: A  256 SER cc_start: 0.8872 (t) cc_final: 0.8374 (p)
REVERT: A  384 SER cc_start: 0.8957 (m) cc_final: 0.8696 (p)
REVERT: A  520 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8840 (tt)
REVERT: A  556 MET cc_start: 0.9500 (ttm) cc_final: 0.9216 (mpp)
REVERT: A  573 MET cc_start: 0.8910 (mmm) cc_final: 0.8428 (mmm)
REVERT: B    1 MET cc_start: 0.9228 (tpp) cc_final: 0.8832 (tpp)
REVERT: B   11 LEU cc_start: 0.9521 (tp) cc_final: 0.9275 (tp)
REVERT: B   69 MET cc_start: 0.9159 (mtm) cc_final: 0.8531 (ptm)
REVERT: B  320 LEU cc_start: 0.9308 (tp) cc_final: 0.9004 (tt)
REVERT: B  478 LYS cc_start: 0.9360 (mttm) cc_final: 0.8904 (mmtm)
REVERT: B  503 MET cc_start: 0.9324 (mtp) cc_final: 0.8997 (mtm)
REVERT: B  541 CYS cc_start: 0.8389 (m) cc_final: 0.7941 (m)
REVERT: B  572 LEU cc_start: 0.9393 (mm) cc_final: 0.9058 (mm)
  outliers start: 32
  outliers final: 16
  residues processed: 135
  average time/residue: 0.1953
  time to fit residues: 38.0664
Evaluate side-chains
  104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  563 ASN
Chi-restraints excluded: chain B residue  568 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0980
   chunk 5 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN
B 563 ASN
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 600 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 = 0.3141 r_free = 0.3141 target = 0.055589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.044683 restraints weight = 59401.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.046459 restraints weight = 30178.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.047710 restraints weight = 19198.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   8784  Z= 0.269
  Angle     :  0.775  12.993  11935  Z= 0.371
  Chirality :  0.045   0.189   1390
  Planarity :  0.005   0.064   1515
  Dihedral  :  6.961  79.575   1225
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.55 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.59 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1101
  helix:  0.63 (0.22), residues: 517
  sheet: -1.15 (0.33), residues: 219
  loop : -2.00 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  22 
 HIS   0.004   0.001   HIS A 578 
 PHE   0.027   0.002   PHE A 141 
 TYR   0.018   0.002   TYR A 399 
 ARG   0.005   0.001   ARG B 464 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9493 (pp) cc_final: 0.9099 (tt)
REVERT: A  236 MET cc_start: 0.8410 (mmm) cc_final: 0.8074 (mmm)
REVERT: A  256 SER cc_start: 0.8968 (t) cc_final: 0.8429 (p)
REVERT: A  520 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8822 (tt)
REVERT: A  556 MET cc_start: 0.9498 (ttm) cc_final: 0.9151 (mpp)
REVERT: A  573 MET cc_start: 0.8811 (mmm) cc_final: 0.8525 (mmm)
REVERT: B    1 MET cc_start: 0.9228 (tpp) cc_final: 0.8864 (tpp)
REVERT: B   11 LEU cc_start: 0.9538 (tp) cc_final: 0.9236 (tp)
REVERT: B  478 LYS cc_start: 0.9456 (mttm) cc_final: 0.8896 (mmtm)
REVERT: B  541 CYS cc_start: 0.8344 (m) cc_final: 0.7966 (m)
REVERT: B  572 LEU cc_start: 0.9393 (mm) cc_final: 0.9161 (mm)
REVERT: B  592 MET cc_start: 0.7733 (mmm) cc_final: 0.7298 (mmm)
  outliers start: 26
  outliers final: 20
  residues processed: 112
  average time/residue: 0.1753
  time to fit residues: 29.1783
Evaluate side-chains
  105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  343 ILE
Chi-restraints excluded: chain B residue  389 LYS
Chi-restraints excluded: chain B residue  528 VAL
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 106 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.055917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.044901 restraints weight = 60758.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.046733 restraints weight = 31137.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.047921 restraints weight = 19618.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8784  Z= 0.202
  Angle     :  0.730  12.656  11935  Z= 0.345
  Chirality :  0.043   0.188   1390
  Planarity :  0.004   0.049   1515
  Dihedral  :  6.485  79.513   1225
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.27 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.02 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.25), residues: 1101
  helix:  1.13 (0.23), residues: 514
  sheet: -0.88 (0.34), residues: 219
  loop : -1.75 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  22 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.027   0.002   PHE A 141 
 TYR   0.021   0.002   TYR B 569 
 ARG   0.004   0.000   ARG B 464 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9479 (pp) cc_final: 0.9105 (tt)
REVERT: A  236 MET cc_start: 0.8555 (mmm) cc_final: 0.8267 (mmm)
REVERT: A  256 SER cc_start: 0.9004 (t) cc_final: 0.8481 (p)
REVERT: A  482 MET cc_start: 0.8201 (tpp) cc_final: 0.7983 (tpp)
REVERT: A  520 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8814 (tt)
REVERT: A  556 MET cc_start: 0.9466 (ttm) cc_final: 0.9179 (mtt)
REVERT: B    1 MET cc_start: 0.9163 (tpp) cc_final: 0.8792 (tpp)
REVERT: B   11 LEU cc_start: 0.9557 (tp) cc_final: 0.9222 (tp)
REVERT: B  320 LEU cc_start: 0.9386 (tp) cc_final: 0.9131 (tt)
REVERT: B  541 CYS cc_start: 0.8407 (m) cc_final: 0.7991 (m)
REVERT: B  569 TYR cc_start: 0.9165 (t80) cc_final: 0.8864 (t80)
REVERT: B  592 MET cc_start: 0.7660 (mmm) cc_final: 0.7178 (mmm)
  outliers start: 27
  outliers final: 21
  residues processed: 116
  average time/residue: 0.1741
  time to fit residues: 29.7325
Evaluate side-chains
  109 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  343 ILE
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    0.0170
   chunk 99 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 87 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.2222

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

Flipped N/Q/H residues before XYZ refinement:
A 303 ASN
B 563 ASN
** B 600 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 = 0.3155 r_free = 0.3155 target = 0.055901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.044913 restraints weight = 58833.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.046724 restraints weight = 29627.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.048001 restraints weight = 18713.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8784  Z= 0.210
  Angle     :  0.728  12.615  11935  Z= 0.343
  Chirality :  0.043   0.201   1390
  Planarity :  0.004   0.050   1515
  Dihedral  :  6.265  76.896   1225
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.09 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.47 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.26), residues: 1101
  helix:  1.33 (0.23), residues: 514
  sheet: -0.72 (0.34), residues: 221
  loop : -1.55 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  22 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.027   0.002   PHE B  75 
 TYR   0.023   0.002   TYR B 569 
 ARG   0.003   0.000   ARG B 464 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9488 (pp) cc_final: 0.9115 (tt)
REVERT: A  236 MET cc_start: 0.8638 (mmm) cc_final: 0.8344 (mmm)
REVERT: A  256 SER cc_start: 0.9046 (t) cc_final: 0.8494 (p)
REVERT: A  301 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7396 (m-80)
REVERT: A  399 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8402 (m-10)
REVERT: A  520 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8826 (tt)
REVERT: B    1 MET cc_start: 0.9161 (tpp) cc_final: 0.8813 (tpp)
REVERT: B   11 LEU cc_start: 0.9582 (tp) cc_final: 0.9221 (tp)
REVERT: B  478 LYS cc_start: 0.9528 (mttm) cc_final: 0.9000 (mmtm)
REVERT: B  541 CYS cc_start: 0.8419 (m) cc_final: 0.8024 (m)
REVERT: B  569 TYR cc_start: 0.9092 (t80) cc_final: 0.8863 (t80)
REVERT: B  592 MET cc_start: 0.7579 (mmm) cc_final: 0.7167 (mmm)
  outliers start: 32
  outliers final: 22
  residues processed: 116
  average time/residue: 0.1777
  time to fit residues: 30.6985
Evaluate side-chains
  108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  399 TYR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  343 ILE
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   chunk 79 optimal weight:    0.0970
   chunk 102 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 ASN
** B 600 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 = 0.3170 r_free = 0.3170 target = 0.056438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.045201 restraints weight = 65955.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.047123 restraints weight = 32001.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.048455 restraints weight = 19729.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8784  Z= 0.185
  Angle     :  0.746  12.350  11935  Z= 0.343
  Chirality :  0.044   0.338   1390
  Planarity :  0.004   0.046   1515
  Dihedral  :  5.942  74.504   1223
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.73 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.24 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.26), residues: 1101
  helix:  1.40 (0.23), residues: 513
  sheet: -0.50 (0.34), residues: 223
  loop : -1.49 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  22 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.025   0.002   PHE A 141 
 TYR   0.021   0.001   TYR A 399 
 ARG   0.003   0.000   ARG B 464 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9479 (pp) cc_final: 0.9127 (tt)
REVERT: A  236 MET cc_start: 0.8584 (mmm) cc_final: 0.8316 (mmm)
REVERT: A  256 SER cc_start: 0.9090 (t) cc_final: 0.8598 (p)
REVERT: A  301 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7484 (m-80)
REVERT: A  384 SER cc_start: 0.8956 (m) cc_final: 0.8651 (p)
REVERT: A  520 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8672 (tt)
REVERT: A  548 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8946 (mp10)
REVERT: A  573 MET cc_start: 0.7892 (mmm) cc_final: 0.7495 (mpp)
REVERT: B    1 MET cc_start: 0.9166 (tpp) cc_final: 0.8801 (tpp)
REVERT: B   11 LEU cc_start: 0.9591 (tp) cc_final: 0.9252 (tp)
REVERT: B  424 PHE cc_start: 0.8997 (m-80) cc_final: 0.8533 (m-10)
REVERT: B  478 LYS cc_start: 0.9492 (mttm) cc_final: 0.8886 (mmtm)
REVERT: B  504 MET cc_start: 0.8633 (tpp) cc_final: 0.8426 (tpp)
REVERT: B  541 CYS cc_start: 0.8299 (m) cc_final: 0.7936 (m)
REVERT: B  592 MET cc_start: 0.7526 (mmm) cc_final: 0.7103 (mmm)
  outliers start: 32
  outliers final: 21
  residues processed: 116
  average time/residue: 0.1840
  time to fit residues: 31.7588
Evaluate side-chains
  111 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  343 ILE
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0000
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 134 HIS
** B 600 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 = 0.3182 r_free = 0.3182 target = 0.056791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.044981 restraints weight = 76388.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.047066 restraints weight = 35046.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.048470 restraints weight = 21107.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8784  Z= 0.180
  Angle     :  0.763  13.729  11935  Z= 0.345
  Chirality :  0.045   0.377   1390
  Planarity :  0.004   0.040   1515
  Dihedral  :  5.540  74.020   1218
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.91 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.34 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.16 (0.26), residues: 1101
  helix:  1.43 (0.23), residues: 514
  sheet: -0.38 (0.35), residues: 217
  loop : -1.45 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  22 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.024   0.001   PHE A 141 
 TYR   0.019   0.001   TYR A 399 
 ARG   0.003   0.000   ARG B 464 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9449 (pp) cc_final: 0.9112 (tt)
REVERT: A  236 MET cc_start: 0.8608 (mmm) cc_final: 0.8330 (mmm)
REVERT: A  256 SER cc_start: 0.9095 (t) cc_final: 0.8610 (p)
REVERT: A  301 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7633 (m-80)
REVERT: A  384 SER cc_start: 0.8932 (m) cc_final: 0.8619 (p)
REVERT: A  556 MET cc_start: 0.9416 (tpp) cc_final: 0.8902 (tpt)
REVERT: A  573 MET cc_start: 0.7987 (mmm) cc_final: 0.7583 (mpp)
REVERT: B    1 MET cc_start: 0.9168 (tpp) cc_final: 0.8811 (tpp)
REVERT: B   11 LEU cc_start: 0.9586 (tp) cc_final: 0.9265 (tp)
REVERT: B  340 LEU cc_start: 0.8694 (tt) cc_final: 0.8323 (tt)
REVERT: B  424 PHE cc_start: 0.9013 (m-80) cc_final: 0.8554 (m-10)
REVERT: B  478 LYS cc_start: 0.9478 (mttm) cc_final: 0.8929 (mmtm)
REVERT: B  504 MET cc_start: 0.8643 (tpp) cc_final: 0.8417 (tpp)
REVERT: B  541 CYS cc_start: 0.8222 (m) cc_final: 0.7857 (m)
REVERT: B  592 MET cc_start: 0.7389 (mmm) cc_final: 0.7006 (mmm)
  outliers start: 23
  outliers final: 21
  residues processed: 108
  average time/residue: 0.1948
  time to fit residues: 30.8528
Evaluate side-chains
  103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  263 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0270
   overall best weight:    0.7844

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

Flipped N/Q/H residues before XYZ refinement:
B 563 ASN
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 600 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 = 0.3174 r_free = 0.3174 target = 0.056782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.045463 restraints weight = 65492.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.047413 restraints weight = 32116.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.048738 restraints weight = 19825.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.4041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8784  Z= 0.182
  Angle     :  0.755  12.997  11935  Z= 0.340
  Chirality :  0.043   0.182   1390
  Planarity :  0.004   0.039   1515
  Dihedral  :  5.419  73.628   1217
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.73 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.12 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.28 (0.26), residues: 1101
  helix:  1.47 (0.23), residues: 514
  sheet: -0.29 (0.35), residues: 215
  loop : -1.32 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  22 
 HIS   0.003   0.001   HIS B 105 
 PHE   0.024   0.001   PHE A 141 
 TYR   0.018   0.001   TYR A 399 
 ARG   0.006   0.000   ARG B 552 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9435 (pp) cc_final: 0.9159 (tt)
REVERT: A  236 MET cc_start: 0.8569 (mmm) cc_final: 0.8267 (mmm)
REVERT: A  256 SER cc_start: 0.9106 (t) cc_final: 0.8574 (p)
REVERT: A  301 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7634 (m-80)
REVERT: A  384 SER cc_start: 0.8927 (m) cc_final: 0.8604 (p)
REVERT: A  455 CYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8938 (p)
REVERT: A  573 MET cc_start: 0.8055 (mmm) cc_final: 0.7627 (mpp)
REVERT: B    1 MET cc_start: 0.9112 (tpp) cc_final: 0.8773 (tpp)
REVERT: B   73 MET cc_start: 0.9188 (tpp) cc_final: 0.8914 (tpp)
REVERT: B  478 LYS cc_start: 0.9487 (mttm) cc_final: 0.8987 (mmtm)
REVERT: B  504 MET cc_start: 0.8588 (tpp) cc_final: 0.8348 (tpp)
REVERT: B  541 CYS cc_start: 0.8178 (m) cc_final: 0.7849 (m)
REVERT: B  592 MET cc_start: 0.7484 (mmm) cc_final: 0.7098 (mmm)
  outliers start: 26
  outliers final: 21
  residues processed: 106
  average time/residue: 0.1835
  time to fit residues: 28.5272
Evaluate side-chains
  105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    0.0030
   chunk 26 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 109 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 70 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.8392

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

Flipped N/Q/H residues before XYZ refinement:
** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.056799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.045025 restraints weight = 77728.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.047083 restraints weight = 35436.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.048479 restraints weight = 21331.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2926
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8784  Z= 0.190
  Angle     :  0.775  12.955  11935  Z= 0.347
  Chirality :  0.044   0.256   1390
  Planarity :  0.004   0.039   1515
  Dihedral  :  5.402  73.337   1215
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.73 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.12 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.31 (0.26), residues: 1101
  helix:  1.45 (0.23), residues: 518
  sheet: -0.21 (0.36), residues: 215
  loop : -1.29 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  22 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.036   0.002   PHE A 513 
 TYR   0.025   0.001   TYR B 363 
 ARG   0.007   0.000   ARG B 552 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 82
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9423 (pp) cc_final: 0.9146 (tt)
REVERT: A  191 LEU cc_start: 0.9326 (tt) cc_final: 0.8910 (mm)
REVERT: A  236 MET cc_start: 0.8615 (mmm) cc_final: 0.8304 (mmm)
REVERT: A  256 SER cc_start: 0.9108 (t) cc_final: 0.8586 (p)
REVERT: A  301 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7693 (m-80)
REVERT: A  384 SER cc_start: 0.8932 (m) cc_final: 0.8612 (p)
REVERT: A  455 CYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8970 (p)
REVERT: A  573 MET cc_start: 0.8115 (mmm) cc_final: 0.7670 (mpp)
REVERT: B    1 MET cc_start: 0.9112 (tpp) cc_final: 0.8773 (tpp)
REVERT: B  424 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8546 (m-10)
REVERT: B  478 LYS cc_start: 0.9391 (mttm) cc_final: 0.8987 (mmtm)
REVERT: B  504 MET cc_start: 0.8617 (tpp) cc_final: 0.8362 (tpp)
REVERT: B  541 CYS cc_start: 0.8176 (m) cc_final: 0.7836 (m)
REVERT: B  592 MET cc_start: 0.7445 (mmm) cc_final: 0.7086 (mmm)
  outliers start: 30
  outliers final: 25
  residues processed: 105
  average time/residue: 0.1758
  time to fit residues: 27.5473
Evaluate side-chains
  111 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  343 ILE
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 101 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 563 ASN
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 600 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 = 0.3167 r_free = 0.3167 target = 0.056303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.044615 restraints weight = 78066.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.046654 restraints weight = 35497.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.048072 restraints weight = 21350.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8784  Z= 0.213
  Angle     :  0.805  20.019  11935  Z= 0.358
  Chirality :  0.045   0.399   1390
  Planarity :  0.004   0.038   1515
  Dihedral  :  5.437  73.565   1215
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.00 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.23 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.37 (0.26), residues: 1101
  helix:  1.47 (0.23), residues: 517
  sheet: -0.16 (0.36), residues: 215
  loop : -1.22 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  22 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.032   0.002   PHE A 513 
 TYR   0.019   0.002   TYR A 399 
 ARG   0.007   0.000   ARG B 552 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LEU cc_start: 0.9417 (pp) cc_final: 0.9150 (tt)
REVERT: A  191 LEU cc_start: 0.9322 (tt) cc_final: 0.8956 (mm)
REVERT: A  236 MET cc_start: 0.8680 (mmm) cc_final: 0.8359 (mmm)
REVERT: A  256 SER cc_start: 0.9117 (t) cc_final: 0.8610 (p)
REVERT: A  301 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7673 (m-80)
REVERT: A  384 SER cc_start: 0.8967 (m) cc_final: 0.8667 (p)
REVERT: A  455 CYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8957 (p)
REVERT: A  556 MET cc_start: 0.9104 (tpp) cc_final: 0.8846 (tpp)
REVERT: A  557 MET cc_start: 0.9239 (mmt) cc_final: 0.9010 (tpp)
REVERT: A  573 MET cc_start: 0.8212 (mmm) cc_final: 0.7748 (mpp)
REVERT: B    1 MET cc_start: 0.9120 (tpp) cc_final: 0.8796 (tpp)
REVERT: B  504 MET cc_start: 0.8616 (tpp) cc_final: 0.8371 (tpp)
REVERT: B  541 CYS cc_start: 0.8181 (m) cc_final: 0.7890 (m)
REVERT: B  592 MET cc_start: 0.7395 (mmm) cc_final: 0.7065 (mmm)
  outliers start: 29
  outliers final: 24
  residues processed: 105
  average time/residue: 0.1681
  time to fit residues: 26.5545
Evaluate side-chains
  106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  455 CYS
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  520 LEU
Chi-restraints excluded: chain A residue  533 CYS
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  343 ILE
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain B residue  503 MET
Chi-restraints excluded: chain B residue  563 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0470
   chunk 30 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0770
   chunk 63 optimal weight:    0.0040
   chunk 81 optimal weight:    7.9990
   overall best weight:    0.3048

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

Flipped N/Q/H residues before XYZ refinement:
** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.057386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.045688 restraints weight = 71592.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.047740 restraints weight = 34017.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.049117 restraints weight = 20641.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.4348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8784  Z= 0.174
  Angle     :  0.795  13.408  11935  Z= 0.354
  Chirality :  0.044   0.200   1390
  Planarity :  0.004   0.038   1515
  Dihedral  :  5.337  72.050   1215
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.89 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.43 (0.26), residues: 1101
  helix:  1.52 (0.24), residues: 517
  sheet: -0.02 (0.36), residues: 214
  loop : -1.29 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 545 
 PHE   0.030   0.002   PHE A 513 
 TYR   0.018   0.001   TYR A 399 
 ARG   0.007   0.000   ARG B 552 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2923.57 seconds
wall clock time: 53 minutes 5.89 seconds (3185.89 seconds total)