Starting phenix.real_space_refine
on Sat Aug 23 00:37:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hbe_34623/08_2025/8hbe_34623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hbe_34623/08_2025/8hbe_34623.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hbe_34623/08_2025/8hbe_34623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hbe_34623/08_2025/8hbe_34623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hbe_34623/08_2025/8hbe_34623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hbe_34623/08_2025/8hbe_34623.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.185
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      60      5.16       5
     C    5534      2.51       5
     N    1457      2.21       5
     O    1558      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8610
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4120
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 542, 4117
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 175
          Unresolved non-hydrogen angles: 216
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 14, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 7, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 125
      Conformer: "B"
        Number of residues, atoms: 542, 4117
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 175
          Unresolved non-hydrogen angles: 216
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 14, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 7, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 125
          bond proxies already assigned to first conformer: 4196
    Chain: "B"
      Number of atoms: 4447
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 572, 4443
          Classifications: {'peptide': 572}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 548}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 104
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 81
      Conformer: "B"
        Number of residues, atoms: 572, 4443
          Classifications: {'peptide': 572}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 548}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 104
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 81
          bond proxies already assigned to first conformer: 4529
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.80, per 1000 atoms: 0.44
  Number of scatterers: 8610
  At special positions: 0
  Unit cell: (75.24, 95.095, 149.435, 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      60     16.00
     O    1558      8.00
     N    1457      7.00
     C    5534      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 630.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 9 sheets defined
      49.8% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  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 148
      removed outlier: 3.580A  pdb=" N   ASP A 148 " --> pdb=" O   CYS A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 4.900A  pdb=" N   SER A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   THR A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 228
      removed outlier: 3.712A  pdb=" N   TYR A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 242
      removed outlier: 4.039A  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 310
    Processing helix  chain 'A' and resid 334 through 340
    Processing helix  chain 'A' and resid 389 through 391
      No H-bonds generated for 'chain 'A' and resid 389 through 391'
    Processing helix  chain 'A' and resid 392 through 397
      removed outlier: 3.561A  pdb=" N   ARG A 396 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 4.398A  pdb=" N   ALA A 408 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 421
      removed outlier: 4.533A  pdb=" N   GLY A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   GLU A 417 " --> pdb=" O   VAL A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 425
      removed outlier: 4.240A  pdb=" N   LEU A 425 " --> pdb=" O   GLN A 422 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 422 through 425'
    Processing helix  chain 'A' and resid 426 through 458
      removed outlier: 3.965A  pdb=" N   GLY A 430 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS A 431 " --> pdb=" O   LYS A 427 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 469
    Processing helix  chain 'A' and resid 489 through 496
    Processing helix  chain 'A' and resid 498 through 521
    Processing helix  chain 'A' and resid 544 through 563
    Processing helix  chain 'A' and resid 598 through 610
      removed outlier: 3.759A  pdb=" N   THR A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 628
      removed outlier: 4.711A  pdb=" N   ASP A 628 " --> pdb=" O   ARG A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 642
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 3.566A  pdb=" N   ASN B   6 " --> pdb=" O   TYR B   2 " (cutoff:3.500A)
      Proline residue:  B  19  - end of helix
      removed outlier: 3.923A  pdb=" N   TRP B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 59
      removed outlier: 3.802A  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 109
      removed outlier: 4.679A  pdb=" N   ASP B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ALA B 103 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   HIS B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 157
      removed outlier: 3.862A  pdb=" N   VAL B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 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 249 through 252
    Processing helix  chain 'B' and resid 264 through 271
    Processing helix  chain 'B' and resid 330 through 335
      removed outlier: 3.739A  pdb=" N   THR B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 355
      removed outlier: 4.098A  pdb=" N   ASP B 351 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 395
      removed outlier: 3.740A  pdb=" N   THR B 366 " --> pdb=" O   GLU B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 408
      removed outlier: 3.841A  pdb=" N   HIS B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 439 through 461
    Processing helix  chain 'B' and resid 491 through 507
    Processing helix  chain 'B' and resid 544 through 557
      removed outlier: 3.966A  pdb=" N   ASN B 548 " --> pdb=" O   GLY B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 573
    Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193
      removed outlier: 4.060A  pdb=" N   SER A 189 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 289 through 292
      removed outlier: 6.650A  pdb=" N   VAL A 347 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525
      removed outlier: 4.515A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   LYS A 476 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ALA A 584 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 523 through 525
      removed outlier: 4.515A  pdb=" N   CYS A 533 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   LYS A 476 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ALA A 584 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL A 582 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   ILE A 616 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124
      removed outlier: 6.563A  pdb=" N   GLN B 178 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU B 182 " --> pdb=" O   ASP B 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.691A  pdb=" N   VAL B 229 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ASP B 224 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   VAL B 277 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 470 through 472
      removed outlier: 4.469A  pdb=" N   MET B 480 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ARG B 416 " --> pdb=" O   THR B 530 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   THR B 530 " --> pdb=" O   ARG B 416 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   ASP B 418 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B 528 " --> pdb=" O   ASP B 418 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL B 529 " --> pdb=" O   PHE B 543 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 472
      removed outlier: 4.469A  pdb=" N   MET B 480 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ARG B 416 " --> pdb=" O   THR B 530 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   THR B 530 " --> pdb=" O   ARG B 416 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   ASP B 418 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B 528 " --> pdb=" O   ASP B 418 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 519 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ILE B 562 " --> pdb=" O   LEU B 604 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   MET B 599 " --> pdb=" O   VAL B 590 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL B 601 " --> pdb=" O   GLY B 588 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLY B 588 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   PHE B 603 " --> pdb=" O   HIS B 586 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   HIS B 586 " --> pdb=" O   PHE B 603 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   SER B 605 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LEU B 584 " --> pdb=" O   SER B 605 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 511 through 512

    519 hydrogen bonds defined for protein.
    1475 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.07 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: 3489
        1.38 -     1.56: 5206
        1.56 -     1.74: 0
        1.74 -     1.92: 93
        1.92 -     2.10: 3
  Bond restraints: 8791
  Sorted by residual:
  bond pdb=" CA  PHE B 359 "
       pdb=" C   PHE B 359 "
    ideal  model  delta    sigma   weight residual
    1.526  1.471  0.055 1.28e-02 6.10e+03 1.82e+01
  bond pdb=" C3B HEM B1000 "
       pdb=" CAB HEM B1000 "
    ideal  model  delta    sigma   weight residual
    1.544  1.468  0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" CA  ASN B 329 "
       pdb=" C   ASN B 329 "
    ideal  model  delta    sigma   weight residual
    1.523  1.475  0.048 1.31e-02 5.83e+03 1.36e+01
  bond pdb=" CA  ARG B 360 "
       pdb=" C   ARG B 360 "
    ideal  model  delta    sigma   weight residual
    1.523  1.473  0.050 1.42e-02 4.96e+03 1.23e+01
  bond pdb=" C3C HEM B1000 "
       pdb=" CAC HEM B1000 "
    ideal  model  delta    sigma   weight residual
    1.544  1.475  0.069 2.00e-02 2.50e+03 1.20e+01
  ... (remaining 8786 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.33: 11842
        3.33 -     6.67: 86
        6.67 -    10.00: 6
       10.00 -    13.34: 0
       13.34 -    16.67: 2
  Bond angle restraints: 11936
  Sorted by residual:
  angle pdb=" N   PHE B 359 "
        pdb=" CA  PHE B 359 "
        pdb=" C   PHE B 359 "
      ideal   model   delta    sigma   weight residual
     112.26  104.89    7.37 1.32e+00 5.74e-01 3.12e+01
  angle pdb=" N   ALA B 438 "
        pdb=" CA  ALA B 438 "
        pdb=" C   ALA B 438 "
      ideal   model   delta    sigma   weight residual
     111.55  117.05   -5.50 1.37e+00 5.33e-01 1.61e+01
  angle pdb=" C   PRO A 613 "
        pdb=" N   ARG A 614 "
        pdb=" CA  ARG A 614 "
      ideal   model   delta    sigma   weight residual
     121.54  128.61   -7.07 1.91e+00 2.74e-01 1.37e+01
  angle pdb=" N   LYS A 317 "
        pdb=" CA  LYS A 317 "
        pdb=" C   LYS A 317 "
      ideal   model   delta    sigma   weight residual
     111.00  119.53   -8.53 2.80e+00 1.28e-01 9.29e+00
  angle pdb=" C3D HEM B1000 "
        pdb=" CAD HEM B1000 "
        pdb=" CBD HEM B1000 "
      ideal   model   delta    sigma   weight residual
     109.50  118.26   -8.76 3.00e+00 1.11e-01 8.52e+00
  ... (remaining 11931 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 4633
       16.65 -    33.30: 464
       33.30 -    49.95: 136
       49.95 -    66.60: 18
       66.60 -    83.25: 15
  Dihedral angle restraints: 5266
    sinusoidal: 2022
      harmonic: 3244
  Sorted by residual:
  dihedral pdb=" C2B HEM B1000 "
           pdb=" C3B HEM B1000 "
           pdb=" CAB HEM B1000 "
           pdb=" CBB HEM B1000 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.48  -71.48     2      1.00e+01 1.00e-02 4.32e+01
  dihedral pdb=" CA  PHE A 301 "
           pdb=" C   PHE A 301 "
           pdb=" N   GLY A 302 "
           pdb=" CA  GLY A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.50   20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  GLY B  35 "
           pdb=" C   GLY B  35 "
           pdb=" N   GLN B  36 "
           pdb=" CA  GLN B  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.27  -18.73     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 5263 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 973
       0.044 -    0.087: 298
       0.087 -    0.131: 95
       0.131 -    0.174: 14
       0.174 -    0.218: 6
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  MET B 328 "
            pdb=" N   MET B 328 "
            pdb=" C   MET B 328 "
            pdb=" CB  MET B 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  MET B 444 "
            pdb=" N   MET B 444 "
            pdb=" C   MET B 444 "
            pdb=" CB  MET B 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1383 not shown)

  Planarity restraints: 1516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 466 "    0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO B 467 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B 467 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 467 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 442 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.98e+00
        pdb=" C   GLY B 442 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   GLY B 442 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA B 443 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 258 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.56e+00
        pdb=" N   PRO B 259 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1513 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1280
        2.75 -     3.29: 7984
        3.29 -     3.83: 14192
        3.83 -     4.36: 16730
        4.36 -     4.90: 29797
  Nonbonded interactions: 69983
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 473 "
            pdb=" NH1 ARG B 539 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   LEU B 251 "
            pdb=" NZ  LYS B 281 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OH  TYR A 510 "
            pdb=" O   GLY A 529 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OG1 THR A 168 "
            pdb=" O   ASN A 343 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" NH1 ARG B 121 "
            pdb=" OH  TYR B 136 "
     model   vdw
     2.318 3.120
  ... (remaining 69978 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.290
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
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      :  0.008   0.414   8792  Z= 0.294
  Angle     :  0.734  16.674  11936  Z= 0.366
  Chirality :  0.048   0.218   1386
  Planarity :  0.005   0.050   1516
  Dihedral  : 15.140  83.252   3166
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.25), residues: 1097
  helix:  0.45 (0.23), residues: 523
  sheet: -0.14 (0.32), residues: 247
  loop : -0.85 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 139 
 TYR   0.013   0.002   TYR B 135 
 PHE   0.017   0.002   PHE B 603 
 TRP   0.010   0.002   TRP B 602 
 HIS   0.013   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00677 ( 8791)
  covalent geometry    : angle       0.73416 (11936)
  hydrogen bonds       : bond        0.11333 (  485)
  hydrogen bonds       : angle       6.01594 ( 1475)
  Misc. bond           : bond        0.41360 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.279 
Fit side-chains
REVERT: B  355 LEU cc_start: 0.6425 (mp) cc_final: 0.6218 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0837
  time to fit residues: 12.4234
Evaluate side-chains
  103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.2980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 224 HIS
A 468 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.165289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.116223 restraints weight = 19171.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 3.35
r_work: 0.2950 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.0660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.228   8792  Z= 0.145
  Angle     :  0.591  13.154  11936  Z= 0.292
  Chirality :  0.043   0.165   1386
  Planarity :  0.004   0.040   1516
  Dihedral  :  5.878  86.211   1200
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.98 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.25), residues: 1097
  helix:  0.77 (0.22), residues: 523
  sheet: -0.20 (0.31), residues: 247
  loop : -0.61 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 539 
 TYR   0.014   0.001   TYR B  49 
 PHE   0.016   0.001   PHE A 141 
 TRP   0.008   0.001   TRP A 467 
 HIS   0.008   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8791)
  covalent geometry    : angle       0.59102 (11936)
  hydrogen bonds       : bond        0.03995 (  485)
  hydrogen bonds       : angle       4.74471 ( 1475)
  Misc. bond           : bond        0.22846 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: B  404 ASN cc_start: 0.7078 (t0) cc_final: 0.6820 (t0)
REVERT: B  527 GLU cc_start: 0.7275 (pp20) cc_final: 0.7071 (pp20)
REVERT: B  599 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6355 (ptt)
  outliers start: 12
  outliers final: 8
  residues processed: 118
  average time/residue: 0.0857
  time to fit residues: 14.8305
Evaluate side-chains
  112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  599 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 468 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.163196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.109370 restraints weight = 19878.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 3.35
r_work: 0.2886 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.0726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.230   8792  Z= 0.200
  Angle     :  0.628  13.577  11936  Z= 0.308
  Chirality :  0.044   0.158   1386
  Planarity :  0.004   0.042   1516
  Dihedral  :  5.901  86.150   1200
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.62 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.25), residues: 1097
  helix:  0.78 (0.22), residues: 522
  sheet: -0.14 (0.31), residues: 245
  loop : -0.65 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 139 
 TYR   0.017   0.002   TYR B  49 
 PHE   0.016   0.002   PHE A 141 
 TRP   0.009   0.002   TRP B 602 
 HIS   0.009   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 8791)
  covalent geometry    : angle       0.62768 (11936)
  hydrogen bonds       : bond        0.04144 (  485)
  hydrogen bonds       : angle       4.63024 ( 1475)
  Misc. bond           : bond        0.23031 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6431 (mp)
REVERT: B  404 ASN cc_start: 0.7005 (t0) cc_final: 0.6804 (t0)
REVERT: B  527 GLU cc_start: 0.7297 (pp20) cc_final: 0.7066 (pp20)
REVERT: B  599 MET cc_start: 0.6880 (ptp) cc_final: 0.6311 (ptt)
  outliers start: 17
  outliers final: 11
  residues processed: 123
  average time/residue: 0.0865
  time to fit residues: 15.4187
Evaluate side-chains
  120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 76 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 468 GLN
A 548 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.165702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.113958 restraints weight = 15649.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 3.05
r_work: 0.2955 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.217   8792  Z= 0.137
  Angle     :  0.569  12.966  11936  Z= 0.279
  Chirality :  0.042   0.149   1386
  Planarity :  0.004   0.041   1516
  Dihedral  :  5.671  82.768   1200
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.83 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.25), residues: 1097
  helix:  1.03 (0.23), residues: 522
  sheet: -0.18 (0.31), residues: 247
  loop : -0.51 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 539 
 TYR   0.018   0.001   TYR B  49 
 PHE   0.015   0.001   PHE A 141 
 TRP   0.008   0.001   TRP B 602 
 HIS   0.008   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8791)
  covalent geometry    : angle       0.56946 (11936)
  hydrogen bonds       : bond        0.03669 (  485)
  hydrogen bonds       : angle       4.42756 ( 1475)
  Misc. bond           : bond        0.21724 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6384 (mp)
REVERT: A  344 MET cc_start: 0.8582 (mmm) cc_final: 0.8341 (mmt)
REVERT: B  384 GLU cc_start: 0.7934 (tp30) cc_final: 0.7176 (tt0)
REVERT: B  404 ASN cc_start: 0.7043 (t0) cc_final: 0.6833 (t0)
REVERT: B  527 GLU cc_start: 0.7222 (pp20) cc_final: 0.6971 (pp20)
REVERT: B  599 MET cc_start: 0.6819 (ptp) cc_final: 0.6258 (ptt)
  outliers start: 18
  outliers final: 12
  residues processed: 124
  average time/residue: 0.0845
  time to fit residues: 15.2814
Evaluate side-chains
  117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0370
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0770
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
A 468 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.166829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.113560 restraints weight = 18837.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 3.24
r_work: 0.2956 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.209   8792  Z= 0.121
  Angle     :  0.551  12.270  11936  Z= 0.270
  Chirality :  0.041   0.142   1386
  Planarity :  0.004   0.040   1516
  Dihedral  :  5.530  82.613   1200
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.60 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.25), residues: 1097
  helix:  1.22 (0.23), residues: 522
  sheet: -0.02 (0.31), residues: 244
  loop : -0.45 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 593 
 TYR   0.020   0.001   TYR B  49 
 PHE   0.015   0.001   PHE A 141 
 TRP   0.008   0.001   TRP B 602 
 HIS   0.007   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8791)
  covalent geometry    : angle       0.55140 (11936)
  hydrogen bonds       : bond        0.03485 (  485)
  hydrogen bonds       : angle       4.31983 ( 1475)
  Misc. bond           : bond        0.20913 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6440 (mp)
REVERT: B  404 ASN cc_start: 0.7012 (t0) cc_final: 0.6781 (t0)
REVERT: B  454 TYR cc_start: 0.7830 (m-10) cc_final: 0.7580 (m-10)
REVERT: B  527 GLU cc_start: 0.7354 (pp20) cc_final: 0.7106 (pp20)
REVERT: B  599 MET cc_start: 0.6764 (ptp) cc_final: 0.6221 (ptt)
  outliers start: 17
  outliers final: 15
  residues processed: 123
  average time/residue: 0.0842
  time to fit residues: 15.1505
Evaluate side-chains
  123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  572 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0470
   chunk 102 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 468 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.167561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.133750 restraints weight = 26482.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 6.36
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.209   8792  Z= 0.121
  Angle     :  0.545  12.283  11936  Z= 0.267
  Chirality :  0.041   0.139   1386
  Planarity :  0.004   0.039   1516
  Dihedral  :  5.470  82.501   1200
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.71 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1097
  helix:  1.33 (0.23), residues: 522
  sheet: -0.12 (0.31), residues: 249
  loop : -0.31 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 593 
 TYR   0.011   0.001   TYR B 237 
 PHE   0.014   0.001   PHE A 141 
 TRP   0.008   0.001   TRP B 602 
 HIS   0.005   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8791)
  covalent geometry    : angle       0.54490 (11936)
  hydrogen bonds       : bond        0.03437 (  485)
  hydrogen bonds       : angle       4.27766 ( 1475)
  Misc. bond           : bond        0.20934 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7416 (mp)
REVERT: B  539 ARG cc_start: 0.7957 (ptm160) cc_final: 0.7670 (ttt-90)
REVERT: B  599 MET cc_start: 0.6974 (ptp) cc_final: 0.6508 (ptt)
  outliers start: 18
  outliers final: 12
  residues processed: 125
  average time/residue: 0.0898
  time to fit residues: 16.2099
Evaluate side-chains
  122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 224 HIS
A 468 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.164258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.123513 restraints weight = 11500.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.75
r_work: 0.2959 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.225   8792  Z= 0.195
  Angle     :  0.602  13.163  11936  Z= 0.295
  Chirality :  0.043   0.155   1386
  Planarity :  0.004   0.040   1516
  Dihedral  :  5.653  84.548   1200
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.69 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1097
  helix:  1.11 (0.22), residues: 520
  sheet: -0.12 (0.31), residues: 249
  loop : -0.45 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 593 
 TYR   0.013   0.001   TYR B 135 
 PHE   0.014   0.002   PHE A 141 
 TRP   0.010   0.002   TRP B 602 
 HIS   0.010   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 8791)
  covalent geometry    : angle       0.60153 (11936)
  hydrogen bonds       : bond        0.03836 (  485)
  hydrogen bonds       : angle       4.40919 ( 1475)
  Misc. bond           : bond        0.22495 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6358 (mp)
REVERT: B  328 MET cc_start: 0.7992 (ptp) cc_final: 0.7776 (mtt)
REVERT: B  384 GLU cc_start: 0.7848 (tp30) cc_final: 0.7068 (tt0)
REVERT: B  599 MET cc_start: 0.6665 (ptp) cc_final: 0.6140 (ptt)
  outliers start: 19
  outliers final: 16
  residues processed: 125
  average time/residue: 0.0906
  time to fit residues: 16.0096
Evaluate side-chains
  123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue    2 TYR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  475 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 102 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 224 HIS
A 468 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.163805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.112599 restraints weight = 14668.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.77
r_work: 0.2946 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.220   8792  Z= 0.190
  Angle     :  0.609  13.450  11936  Z= 0.298
  Chirality :  0.044   0.152   1386
  Planarity :  0.004   0.041   1516
  Dihedral  :  5.707  84.260   1200
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.67 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.25), residues: 1097
  helix:  1.03 (0.22), residues: 520
  sheet: -0.13 (0.31), residues: 246
  loop : -0.52 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 139 
 TYR   0.013   0.001   TYR B 135 
 PHE   0.014   0.002   PHE A 141 
 TRP   0.010   0.002   TRP B 602 
 HIS   0.011   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 8791)
  covalent geometry    : angle       0.60901 (11936)
  hydrogen bonds       : bond        0.03898 (  485)
  hydrogen bonds       : angle       4.44259 ( 1475)
  Misc. bond           : bond        0.22023 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6508 (mp)
REVERT: A  344 MET cc_start: 0.8614 (mmm) cc_final: 0.8357 (mmt)
REVERT: B  384 GLU cc_start: 0.7926 (tp30) cc_final: 0.7158 (tt0)
REVERT: B  599 MET cc_start: 0.6726 (ptp) cc_final: 0.6167 (ptt)
  outliers start: 18
  outliers final: 17
  residues processed: 123
  average time/residue: 0.0906
  time to fit residues: 15.8766
Evaluate side-chains
  121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  224 HIS
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue    2 TYR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  475 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 4 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 224 HIS
A 468 GLN
B 367 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.164983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.123842 restraints weight = 11021.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.51
r_work: 0.2990 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2982
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2982
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.216   8792  Z= 0.149
  Angle     :  0.581  12.976  11936  Z= 0.285
  Chirality :  0.042   0.141   1386
  Planarity :  0.004   0.040   1516
  Dihedral  :  5.640  83.055   1200
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.78 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.25), residues: 1097
  helix:  1.14 (0.23), residues: 520
  sheet: -0.17 (0.31), residues: 249
  loop : -0.42 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 593 
 TYR   0.011   0.001   TYR B 135 
 PHE   0.015   0.001   PHE A 141 
 TRP   0.010   0.002   TRP B 602 
 HIS   0.014   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8791)
  covalent geometry    : angle       0.58085 (11936)
  hydrogen bonds       : bond        0.03710 (  485)
  hydrogen bonds       : angle       4.39361 ( 1475)
  Misc. bond           : bond        0.21580 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6186 (mp)
REVERT: A  344 MET cc_start: 0.8479 (mmm) cc_final: 0.8224 (mmt)
REVERT: B  384 GLU cc_start: 0.7723 (tp30) cc_final: 0.6916 (tt0)
REVERT: B  599 MET cc_start: 0.6679 (ptp) cc_final: 0.6117 (ptt)
  outliers start: 18
  outliers final: 15
  residues processed: 119
  average time/residue: 0.0875
  time to fit residues: 14.8923
Evaluate side-chains
  118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue    2 TYR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  475 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 7 optimal weight:    0.0030
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:   30.0000
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.4930

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

Flipped N/Q/H residues before XYZ refinement:
A 468 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.167387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.124600 restraints weight = 9327.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.92
r_work: 0.3102 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.200   8792  Z= 0.116
  Angle     :  0.549  12.222  11936  Z= 0.269
  Chirality :  0.041   0.136   1386
  Planarity :  0.004   0.039   1516
  Dihedral  :  5.468  81.711   1200
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.99 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.25), residues: 1097
  helix:  1.33 (0.23), residues: 519
  sheet: -0.17 (0.31), residues: 249
  loop : -0.32 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 593 
 TYR   0.010   0.001   TYR B 237 
 PHE   0.015   0.001   PHE A 141 
 TRP   0.010   0.001   TRP B 602 
 HIS   0.009   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8791)
  covalent geometry    : angle       0.54942 (11936)
  hydrogen bonds       : bond        0.03405 (  485)
  hydrogen bonds       : angle       4.28756 ( 1475)
  Misc. bond           : bond        0.20036 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6399 (mp)
REVERT: A  344 MET cc_start: 0.8412 (mmm) cc_final: 0.8196 (mmt)
REVERT: B  384 GLU cc_start: 0.7939 (tp30) cc_final: 0.7142 (tt0)
REVERT: B  599 MET cc_start: 0.6694 (ptp) cc_final: 0.6192 (ptt)
  outliers start: 15
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1006
  time to fit residues: 17.0344
Evaluate side-chains
  122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  301 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain B residue    2 TYR
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  475 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 94 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 468 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.165604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.113917 restraints weight = 15529.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 3.06
r_work: 0.2959 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.213   8792  Z= 0.146
  Angle     :  0.571  12.762  11936  Z= 0.280
  Chirality :  0.042   0.139   1386
  Planarity :  0.004   0.039   1516
  Dihedral  :  5.523  83.178   1200
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.88 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.25), residues: 1097
  helix:  1.27 (0.23), residues: 519
  sheet: -0.16 (0.31), residues: 249
  loop : -0.36 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 593 
 TYR   0.011   0.001   TYR B 135 
 PHE   0.014   0.001   PHE A 141 
 TRP   0.011   0.002   TRP B 602 
 HIS   0.010   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8791)
  covalent geometry    : angle       0.57064 (11936)
  hydrogen bonds       : bond        0.03583 (  485)
  hydrogen bonds       : angle       4.31917 ( 1475)
  Misc. bond           : bond        0.21306 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2343.84 seconds
wall clock time: 40 minutes 54.67 seconds (2454.67 seconds total)