Starting phenix.real_space_refine
on Thu Jun  4 11:29:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/28pq_56721/06_2026/28pq_56721.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/28pq_56721/06_2026/28pq_56721.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/28pq_56721/06_2026/28pq_56721.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/28pq_56721/06_2026/28pq_56721.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/28pq_56721/06_2026/28pq_56721.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/28pq_56721/06_2026/28pq_56721.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Fe      6      7.16       5
     S      44      5.16       5
     C    7623      2.51       5
     N    1905      2.21       5
     O    2770      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12350
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5618
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 711, 5608
          Classifications: {'peptide': 711}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 676}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 711, 5608
          Classifications: {'peptide': 711}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 676}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 5777
    Chain: "B"
      Number of atoms: 5616
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 710, 5606
          Classifications: {'peptide': 710}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 674}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 710, 5606
          Classifications: {'peptide': 710}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 674}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 5776
    Chain: "A"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 119
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LMT': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 182
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LMT': 2, 'UQ5': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'UQ5:plan-2': 1, 'UQ5:plan-5': 1, 'UQ5:plan-6': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 384
          Classifications: {'water': 384}
          Link IDs: {None: 383}
    Chain: "B"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 431
          Classifications: {'water': 431}
          Link IDs: {None: 430}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AHIS A 224 " occ=0.58
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 224 " occ=0.42
    residue:
      pdb=" N  AHIS B 224 " occ=0.59
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 224 " occ=0.41
  Time building chain proxies: 4.77, per 1000 atoms: 0.39
  Number of scatterers: 12350
  At special positions: 0
  Unit cell: (107.3, 85.1, 108.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      6     26.01
     Ca      2     19.99
     S      44     16.00
     O    2770      8.00
     N    1905      7.00
     C    7623      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 866.6 milliseconds
  

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2576

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 4 sheets defined
      78.7% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 33
      removed outlier: 3.796A  pdb=" N   GLY A  23 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 82 through 104
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 112 through 128
    Processing helix  chain 'A' and resid 133 through 136
    Processing helix  chain 'A' and resid 142 through 161
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 173
    Processing helix  chain 'A' and resid 182 through 202
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 226 through 253
    Processing helix  chain 'A' and resid 268 through 272
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 282 through 307
    Processing helix  chain 'A' and resid 317 through 321
      removed outlier: 3.660A  pdb=" N   GLN A 320 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 355
      Proline residue:  A 352  - end of helix
      removed outlier: 3.971A  pdb=" N   ASN A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 390
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 397 through 402
    Processing helix  chain 'A' and resid 412 through 439
      removed outlier: 3.663A  pdb=" N   GLY A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      Proline residue:  A 436  - end of helix
    Processing helix  chain 'A' and resid 473 through 489
    Processing helix  chain 'A' and resid 491 through 509
    Processing helix  chain 'A' and resid 512 through 537
      removed outlier: 5.145A  pdb=" N   ILE A 532 " --> pdb=" O   MET A 528 " (cutoff:3.500A)
      Proline residue:  A 533  - end of helix
    Processing helix  chain 'A' and resid 545 through 555
      removed outlier: 3.634A  pdb=" N   MET A 549 " --> pdb=" O   THR A 545 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE A 555 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 576
    Processing helix  chain 'A' and resid 580 through 585
      removed outlier: 4.199A  pdb=" N   GLU A 584 " --> pdb=" O   PRO A 581 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASN A 585 " --> pdb=" O   TRP A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 603
    Processing helix  chain 'A' and resid 605 through 612
    Processing helix  chain 'A' and resid 613 through 621
      removed outlier: 4.181A  pdb=" N   TYR A 619 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 654
      removed outlier: 4.808A  pdb=" N   PHE A 640 " --> pdb=" O   GLY A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 682
      removed outlier: 3.722A  pdb=" N   SER A 682 " --> pdb=" O   MET A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 697
    Processing helix  chain 'A' and resid 698 through 703
    Processing helix  chain 'A' and resid 704 through 709
    Processing helix  chain 'A' and resid 710 through 720
    Processing helix  chain 'A' and resid 720 through 744
    Processing helix  chain 'A' and resid 746 through 750
    Processing helix  chain 'B' and resid 19 through 33
      removed outlier: 3.793A  pdb=" N   GLY B  23 " --> pdb=" O   PHE B  19 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
      removed outlier: 3.551A  pdb=" N   ILE B  64 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 69
    Processing helix  chain 'B' and resid 82 through 104
    Processing helix  chain 'B' and resid 107 through 111
    Processing helix  chain 'B' and resid 112 through 128
    Processing helix  chain 'B' and resid 133 through 136
    Processing helix  chain 'B' and resid 142 through 161
    Processing helix  chain 'B' and resid 163 through 165
      No H-bonds generated for 'chain 'B' and resid 163 through 165'
    Processing helix  chain 'B' and resid 166 through 173
    Processing helix  chain 'B' and resid 182 through 202
    Processing helix  chain 'B' and resid 218 through 222
    Processing helix  chain 'B' and resid 226 through 253
    Processing helix  chain 'B' and resid 268 through 272
      removed outlier: 3.759A  pdb=" N   THR B 272 " --> pdb=" O   PRO B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 281
    Processing helix  chain 'B' and resid 282 through 307
    Processing helix  chain 'B' and resid 317 through 321
      removed outlier: 3.681A  pdb=" N   GLN B 320 " --> pdb=" O   ASP B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 355
      Proline residue:  B 352  - end of helix
      removed outlier: 3.954A  pdb=" N   ASN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 390
      removed outlier: 3.555A  pdb=" N   GLY B 366 " --> pdb=" O   TYR B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 396
      No H-bonds generated for 'chain 'B' and resid 394 through 396'
    Processing helix  chain 'B' and resid 397 through 402
    Processing helix  chain 'B' and resid 412 through 440
      removed outlier: 3.640A  pdb=" N   GLY B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
      Proline residue:  B 436  - end of helix
      removed outlier: 3.644A  pdb=" N   THR B 440 " --> pdb=" O   PRO B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 488
    Processing helix  chain 'B' and resid 494 through 509
    Processing helix  chain 'B' and resid 512 through 537
      removed outlier: 5.222A  pdb=" N   ILE B 532 " --> pdb=" O   MET B 528 " (cutoff:3.500A)
      Proline residue:  B 533  - end of helix
    Processing helix  chain 'B' and resid 545 through 555
      removed outlier: 3.638A  pdb=" N   MET B 549 " --> pdb=" O   THR B 545 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   PHE B 555 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 576
      removed outlier: 3.545A  pdb=" N   ARG B 575 " --> pdb=" O   TRP B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 585
      removed outlier: 3.995A  pdb=" N   MET B 583 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU B 584 " --> pdb=" O   PRO B 581 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ASN B 585 " --> pdb=" O   TRP B 582 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 580 through 585'
    Processing helix  chain 'B' and resid 586 through 603
    Processing helix  chain 'B' and resid 605 through 612
    Processing helix  chain 'B' and resid 613 through 621
      removed outlier: 4.207A  pdb=" N   TYR B 619 " --> pdb=" O   VAL B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 654
      removed outlier: 4.676A  pdb=" N   PHE B 640 " --> pdb=" O   GLY B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 682
      removed outlier: 3.711A  pdb=" N   SER B 682 " --> pdb=" O   MET B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 697
    Processing helix  chain 'B' and resid 698 through 703
    Processing helix  chain 'B' and resid 704 through 709
    Processing helix  chain 'B' and resid 710 through 720
    Processing helix  chain 'B' and resid 720 through 744
    Processing helix  chain 'B' and resid 746 through 750
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50
      removed outlier: 6.153A  pdb=" N   ARG A  47 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   SER A  42 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.229A  pdb=" N   ARG B  47 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   SER B  42 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72

    783 hydrogen bonds defined for protein.
    2271 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: 1.93

  Time building geometry restraints manager: 1.49 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: 4630
        1.38 -     1.55: 7199
        1.55 -     1.72: 0
        1.72 -     1.90: 84
        1.90 -     2.07: 16
  Bond restraints: 11929
  Sorted by residual:
  bond pdb=" C   VAL B 561 "
       pdb=" N   PRO B 562 "
    ideal  model  delta    sigma   weight residual
    1.336  1.377 -0.041 1.20e-02 6.94e+03 1.17e+01
  bond pdb=" C   VAL A 561 "
       pdb=" N   PRO A 562 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.36e-02 5.41e+03 2.57e+00
  bond pdb=" CB  THR A 196 "
       pdb=" CG2 THR A 196 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.68e-01
  bond pdb=" CB  THR B 196 "
       pdb=" CG2 THR B 196 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 9.02e-01
  bond pdb=" CA  ARG A 720 "
       pdb=" C   ARG A 720 "
    ideal  model  delta    sigma   weight residual
    1.522  1.535 -0.014 1.45e-02 4.76e+03 8.91e-01
  ... (remaining 11924 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 16141
        2.36 -     4.73: 157
        4.73 -     7.09: 21
        7.09 -     9.45: 6
        9.45 -    11.82: 4
  Bond angle restraints: 16329
  Sorted by residual:
  angle pdb=" N   ILE A 392 "
        pdb=" CA  ILE A 392 "
        pdb=" C   ILE A 392 "
      ideal   model   delta    sigma   weight residual
     111.81  108.59    3.22 8.60e-01 1.35e+00 1.40e+01
  angle pdb=" C   LEU A 634 "
        pdb=" N   PHE A 635 "
        pdb=" CA  PHE A 635 "
      ideal   model   delta    sigma   weight residual
     120.65  116.83    3.82 1.32e+00 5.74e-01 8.36e+00
  angle pdb=" CA  TRP B 338 "
        pdb=" CB  TRP B 338 "
        pdb=" CG  TRP B 338 "
      ideal   model   delta    sigma   weight residual
     113.60  119.03   -5.43 1.90e+00 2.77e-01 8.18e+00
  angle pdb=" CA  TRP A 338 "
        pdb=" CB  TRP A 338 "
        pdb=" CG  TRP A 338 "
      ideal   model   delta    sigma   weight residual
     113.60  118.92   -5.32 1.90e+00 2.77e-01 7.85e+00
  angle pdb=" CB  MET A 477 "
        pdb=" CG  MET A 477 "
        pdb=" SD  MET A 477 "
      ideal   model   delta    sigma   weight residual
     112.70  120.88   -8.18 3.00e+00 1.11e-01 7.44e+00
  ... (remaining 16324 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 6003
       17.94 -    35.88: 537
       35.88 -    53.82: 162
       53.82 -    71.76: 36
       71.76 -    89.70: 25
  Dihedral angle restraints: 6763
    sinusoidal: 2714
      harmonic: 4049
  Sorted by residual:
  dihedral pdb=" CA  VAL B 560 "
           pdb=" C   VAL B 560 "
           pdb=" N   VAL B 561 "
           pdb=" CA  VAL B 561 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.51   28.49     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  GLU A 490 "
           pdb=" C   GLU A 490 "
           pdb=" N   GLY A 491 "
           pdb=" CA  GLY A 491 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.77  -22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  GLY B 491 "
           pdb=" C   GLY B 491 "
           pdb=" N   PHE B 492 "
           pdb=" CA  PHE B 492 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 6760 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1123
       0.030 -    0.059: 397
       0.059 -    0.089: 140
       0.089 -    0.119: 54
       0.119 -    0.148: 16
  Chirality restraints: 1730
  Sorted by residual:
  chirality pdb=" CB  VAL B 561 "
            pdb=" CA  VAL B 561 "
            pdb=" CG1 VAL B 561 "
            pdb=" CG2 VAL B 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  TRP B 588 "
            pdb=" N   TRP B 588 "
            pdb=" C   TRP B 588 "
            pdb=" CB  TRP B 588 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  THR B 546 "
            pdb=" N   THR B 546 "
            pdb=" C   THR B 546 "
            pdb=" CB  THR B 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 1727 not shown)

  Planarity restraints: 2023
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 420 "   -0.014 2.00e-02 2.50e+03   1.15e-02 2.31e+00
        pdb=" CG  PHE A 420 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 420 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 420 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 420 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 420 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 420 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 588 "    0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO A 589 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 589 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 589 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 147 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.04e+00
        pdb=" CD  GLN B 147 "    0.025 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 147 "   -0.009 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 147 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2020 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 222
        2.56 -     3.15: 9893
        3.15 -     3.73: 21284
        3.73 -     4.32: 30376
        4.32 -     4.90: 47967
  Nonbonded interactions: 109742
  Sorted by model distance:
  nonbonded pdb="FE    FE A 804 "
            pdb=" O   HOH A 976 "
     model   vdw
     1.978 2.260
  nonbonded pdb="FE    FE B 805 "
            pdb=" O   HOH B1064 "
     model   vdw
     1.980 2.260
  nonbonded pdb=" NE2 HIS B 537 "
            pdb="FE    FE B 805 "
     model   vdw
     2.200 2.340
  nonbonded pdb=" NE2 HIS A 537 "
            pdb="FE    FE A 804 "
     model   vdw
     2.205 2.340
  nonbonded pdb=" O   GLU B 494 "
            pdb=" OG1 THR B 498 "
     model   vdw
     2.222 3.040
  ... (remaining 109737 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 18 through 223 or resid 225 through 439 or resid 465 throu \ 
gh 750))
  selection = (chain 'B' and (resid 18 through 223 or resid 225 through 439 or resid 465 throu \ 
gh 750))
}

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=0.41 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:             5.980
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.660
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11933  Z= 0.135
  Angle     :  0.605  11.817  16329  Z= 0.294
  Chirality :  0.038   0.148   1730
  Planarity :  0.004   0.037   2023
  Dihedral  : 16.368  89.697   4187
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.97 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.98 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.23), residues: 1419
  helix:  2.08 (0.17), residues: 983
  sheet:  None (None), residues: 0
  loop : -0.67 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 267 
 TYR   0.016   0.002   TYR A 324 
 PHE   0.026   0.001   PHE A 420 
 TRP   0.023   0.002   TRP B 251 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.13 (11929)
  covalent geometry    : angle       0.60493 /  0.29 (16329)
  hydrogen bonds       : bond        0.13757 /  9.61 (  783)
  hydrogen bonds       : angle       5.11965 /  3.73 ( 2271)
  Misc. bond           : bond        0.00958 /  0.47 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.410 
Fit side-chains
REVERT: B  584 GLU cc_start: 0.7815 (pp20) cc_final: 0.7235 (tm-30)
  outliers start: 14
  outliers final: 0
  residues processed: 129
  average time/residue: 0.6770
  time to fit residues: 93.8148
Evaluate side-chains
  94 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A 710 GLN
B  58 GLN
B  62 GLN
B 213 ASN
B 568 HIS
B 621 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.097981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.063990 restraints weight = 42485.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.2683 rms_B_bonded: 3.28
r_work: 0.2519 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2519
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  11933  Z= 0.139
  Angle     :  0.612  12.700  16329  Z= 0.289
  Chirality :  0.039   0.139   1730
  Planarity :  0.004   0.055   2023
  Dihedral  :  7.505  83.424   1766
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.04 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.77 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.23), residues: 1419
  helix:  2.28 (0.17), residues: 994
  sheet: -1.21 (1.07), residues: 10
  loop : -0.55 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 513 
 TYR   0.013   0.001   TYR B 324 
 PHE   0.013   0.001   PHE A 420 
 TRP   0.021   0.001   TRP B 338 
 HIS   0.008   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 (11929)
  covalent geometry    : angle       0.61153 /  0.29 (16329)
  hydrogen bonds       : bond        0.05017 /  3.42 (  783)
  hydrogen bonds       : angle       4.18455 /  3.06 ( 2271)
  Misc. bond           : bond        0.05557 /  2.71 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8545 (tt0)
REVERT: A  508 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8480 (mp)
REVERT: A  584 GLU cc_start: 0.8246 (pm20) cc_final: 0.7903 (mm-30)
REVERT: B  168 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8010 (tpt-90)
REVERT: B  508 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8436 (mp)
REVERT: B  514 ARG cc_start: 0.7390 (ttp80) cc_final: 0.7100 (ppp80)
REVERT: B  584 GLU cc_start: 0.8699 (pp20) cc_final: 0.7984 (tm-30)
  outliers start: 32
  outliers final: 5
  residues processed: 114
  average time/residue: 0.6071
  time to fit residues: 75.0174
Evaluate side-chains
  102 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  583 MET
Chi-restraints excluded: chain B residue  168 ARG
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  510 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 105 optimal weight:    0.0070
   chunk 88 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 134 optimal weight:    3.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
A 217 HIS
A 710 GLN
B 217 HIS
B 568 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.097321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.063479 restraints weight = 39032.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.2679 rms_B_bonded: 3.20
r_work: 0.2516 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2528 r_free = 0.2528    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2528 r_free = 0.2528    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106  11933  Z= 0.137
  Angle     :  0.598  13.031  16329  Z= 0.278
  Chirality :  0.039   0.140   1730
  Planarity :  0.004   0.045   2023
  Dihedral  :  7.377  82.928   1766
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.83 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.13 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.23), residues: 1419
  helix:  2.35 (0.17), residues: 1002
  sheet: -2.10 (0.73), residues: 20
  loop : -0.56 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 267 
 TYR   0.018   0.001   TYR A  30 
 PHE   0.013   0.001   PHE B 555 
 TRP   0.021   0.001   TRP B 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 (11929)
  covalent geometry    : angle       0.59790 /  0.28 (16329)
  hydrogen bonds       : bond        0.04821 /  3.28 (  783)
  hydrogen bonds       : angle       4.00969 /  2.93 ( 2271)
  Misc. bond           : bond        0.07533 /  3.75 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  302 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7504 (t80)
REVERT: A  467 PHE cc_start: 0.7369 (m-80) cc_final: 0.7069 (m-80)
REVERT: A  508 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8441 (mp)
REVERT: B  494 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8023 (mm-30)
REVERT: B  508 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: B  584 GLU cc_start: 0.8658 (pp20) cc_final: 0.7983 (tm-30)
  outliers start: 20
  outliers final: 7
  residues processed: 109
  average time/residue: 0.5930
  time to fit residues: 70.1319
Evaluate side-chains
  108 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  506 SER
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  528 MET
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 114 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.063782 restraints weight = 33187.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.2684 rms_B_bonded: 2.98
r_work: 0.2528 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098  11933  Z= 0.137
  Angle     :  0.595  13.032  16329  Z= 0.276
  Chirality :  0.039   0.163   1730
  Planarity :  0.004   0.063   2023
  Dihedral  :  7.331  82.006   1766
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.18 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.13 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.23), residues: 1419
  helix:  2.38 (0.17), residues: 1004
  sheet: -2.25 (0.74), residues: 20
  loop : -0.50 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 267 
 TYR   0.018   0.001   TYR B  30 
 PHE   0.012   0.001   PHE A 635 
 TRP   0.020   0.001   TRP B 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 (11929)
  covalent geometry    : angle       0.59456 /  0.28 (16329)
  hydrogen bonds       : bond        0.04732 /  3.22 (  783)
  hydrogen bonds       : angle       3.94913 /  2.89 ( 2271)
  Misc. bond           : bond        0.07021 /  3.47 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8555 (tt0)
REVERT: A  467 PHE cc_start: 0.7368 (m-80) cc_final: 0.7023 (m-80)
REVERT: A  508 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8435 (mp)
REVERT: A  584 GLU cc_start: 0.8405 (pm20) cc_final: 0.7961 (mm-30)
REVERT: B  126 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8546 (tt0)
REVERT: B  302 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7540 (t80)
REVERT: B  494 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7942 (mm-30)
REVERT: B  508 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (mp)
REVERT: B  584 GLU cc_start: 0.8623 (pp20) cc_final: 0.7940 (tm-30)
  outliers start: 22
  outliers final: 9
  residues processed: 107
  average time/residue: 0.5790
  time to fit residues: 67.3498
Evaluate side-chains
  107 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  302 PHE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 127 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.095234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.062392 restraints weight = 30828.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.2665 rms_B_bonded: 2.90
r_work: 0.2512 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2506 r_free = 0.2506    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2506 r_free = 0.2506    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.127  11933  Z= 0.151
  Angle     :  0.613  13.655  16329  Z= 0.283
  Chirality :  0.039   0.140   1730
  Planarity :  0.004   0.078   2023
  Dihedral  :  7.389  81.020   1766
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.97 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.22 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.23), residues: 1419
  helix:  2.48 (0.17), residues: 989
  sheet: -2.44 (0.73), residues: 20
  loop : -0.52 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 267 
 TYR   0.020   0.001   TYR A  30 
 PHE   0.014   0.001   PHE A 635 
 TRP   0.019   0.001   TRP A 338 
 HIS   0.008   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.15 (11929)
  covalent geometry    : angle       0.61283 /  0.28 (16329)
  hydrogen bonds       : bond        0.05063 /  3.44 (  783)
  hydrogen bonds       : angle       3.97431 /  2.91 ( 2271)
  Misc. bond           : bond        0.09293 /  4.59 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  467 PHE cc_start: 0.7413 (m-80) cc_final: 0.7030 (m-80)
REVERT: A  508 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: B  487 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7703 (mp)
REVERT: B  508 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8338 (mp)
REVERT: B  584 GLU cc_start: 0.8608 (pp20) cc_final: 0.7950 (tm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 108
  average time/residue: 0.5803
  time to fit residues: 68.2207
Evaluate side-chains
  110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  506 SER
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 30 optimal weight:    0.0770
   chunk 17 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0040
   chunk 123 optimal weight:    5.9990
   chunk 113 optimal weight:    8.9990
   chunk 112 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 133 optimal weight:    0.5980
   overall best weight:    0.3950

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
B 568 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.098617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.065398 restraints weight = 37943.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 3.16
r_work: 0.2562 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11933  Z= 0.109
  Angle     :  0.567  10.722  16329  Z= 0.265
  Chirality :  0.037   0.135   1730
  Planarity :  0.004   0.061   2023
  Dihedral  :  7.167  83.849   1766
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.90 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.04 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.23), residues: 1419
  helix:  2.55 (0.17), residues: 995
  sheet: -2.24 (1.09), residues: 10
  loop : -0.54 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 267 
 TYR   0.018   0.001   TYR B  30 
 PHE   0.012   0.001   PHE B 492 
 TRP   0.022   0.001   TRP B 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 (11929)
  covalent geometry    : angle       0.56653 /  0.26 (16329)
  hydrogen bonds       : bond        0.04033 /  2.75 (  783)
  hydrogen bonds       : angle       3.81675 /  2.79 ( 2271)
  Misc. bond           : bond        0.02105 /  1.01 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8514 (tt0)
REVERT: A  302 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7515 (t80)
REVERT: A  467 PHE cc_start: 0.7293 (m-80) cc_final: 0.6893 (m-80)
REVERT: A  508 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8379 (mp)
REVERT: A  584 GLU cc_start: 0.8395 (pm20) cc_final: 0.7931 (mm-30)
REVERT: B  123 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8247 (tp)
REVERT: B  302 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7516 (t80)
REVERT: B  362 TYR cc_start: 0.8227 (m-80) cc_final: 0.7961 (m-80)
REVERT: B  508 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8361 (mp)
REVERT: B  584 GLU cc_start: 0.8581 (pp20) cc_final: 0.7969 (tm-30)
  outliers start: 23
  outliers final: 7
  residues processed: 114
  average time/residue: 0.5909
  time to fit residues: 73.3135
Evaluate side-chains
  110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  302 PHE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  528 MET
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 19 optimal weight:    0.3980
   chunk 115 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 136 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.096427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.063095 restraints weight = 36178.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.2656 rms_B_bonded: 3.10
r_work: 0.2497 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2497
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2507 r_free = 0.2507    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2507 r_free = 0.2507    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106  11933  Z= 0.145
  Angle     :  0.603  13.720  16329  Z= 0.278
  Chirality :  0.039   0.137   1730
  Planarity :  0.004   0.059   2023
  Dihedral  :  7.305  83.204   1766
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.97 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.58 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.23), residues: 1419
  helix:  2.51 (0.17), residues: 995
  sheet: -2.44 (0.74), residues: 20
  loop : -0.43 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 267 
 TYR   0.019   0.001   TYR A  30 
 PHE   0.014   0.001   PHE A 635 
 TRP   0.018   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.14 (11929)
  covalent geometry    : angle       0.60302 /  0.28 (16329)
  hydrogen bonds       : bond        0.04748 /  3.22 (  783)
  hydrogen bonds       : angle       3.89040 /  2.84 ( 2271)
  Misc. bond           : bond        0.07871 /  3.88 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8519 (tt0)
REVERT: A  467 PHE cc_start: 0.7298 (m-80) cc_final: 0.6870 (m-80)
REVERT: A  508 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: A  584 GLU cc_start: 0.8342 (pm20) cc_final: 0.7934 (mm-30)
REVERT: B  123 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8189 (tp)
REVERT: B  508 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8333 (mp)
REVERT: B  584 GLU cc_start: 0.8598 (pp20) cc_final: 0.7953 (tm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 106
  average time/residue: 0.5948
  time to fit residues: 68.8601
Evaluate side-chains
  113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  506 SER
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  528 MET
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.096905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.063232 restraints weight = 42598.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.2661 rms_B_bonded: 3.31
r_work: 0.2498 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2509 r_free = 0.2509    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2509 r_free = 0.2509    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  11933  Z= 0.131
  Angle     :  0.592  12.647  16329  Z= 0.273
  Chirality :  0.038   0.136   1730
  Planarity :  0.004   0.061   2023
  Dihedral  :  7.280  83.100   1766
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.11 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.31 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.23), residues: 1419
  helix:  2.57 (0.17), residues: 990
  sheet: -2.54 (0.74), residues: 20
  loop : -0.46 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 267 
 TYR   0.020   0.001   TYR B  30 
 PHE   0.013   0.001   PHE B 492 
 TRP   0.019   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.13 (11929)
  covalent geometry    : angle       0.59229 /  0.27 (16329)
  hydrogen bonds       : bond        0.04559 /  3.10 (  783)
  hydrogen bonds       : angle       3.86624 /  2.82 ( 2271)
  Misc. bond           : bond        0.06328 /  3.12 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8505 (tt0)
REVERT: A  467 PHE cc_start: 0.7285 (m-80) cc_final: 0.6849 (m-80)
REVERT: A  508 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8355 (mp)
REVERT: A  584 GLU cc_start: 0.8358 (pm20) cc_final: 0.7972 (mm-30)
REVERT: B  508 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8306 (mp)
REVERT: B  584 GLU cc_start: 0.8607 (pp20) cc_final: 0.8029 (tm-30)
  outliers start: 20
  outliers final: 11
  residues processed: 108
  average time/residue: 0.5751
  time to fit residues: 67.7601
Evaluate side-chains
  112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain B residue  302 PHE
Chi-restraints excluded: chain B residue  506 SER
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  528 MET
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 80 optimal weight:    0.1980
   chunk 97 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 64 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.097228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.063223 restraints weight = 50044.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2663 rms_B_bonded: 3.53
r_work: 0.2495 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2505
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2505 r_free = 0.2505    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2505 r_free = 0.2505    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2505
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  11933  Z= 0.125
  Angle     :  0.589  12.748  16329  Z= 0.272
  Chirality :  0.038   0.135   1730
  Planarity :  0.004   0.060   2023
  Dihedral  :  7.256  84.042   1766
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.18 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.49 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.23), residues: 1419
  helix:  2.58 (0.17), residues: 991
  sheet: -2.56 (0.74), residues: 20
  loop : -0.44 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B 267 
 TYR   0.023   0.001   TYR A  30 
 PHE   0.012   0.001   PHE A 635 
 TRP   0.020   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.12 (11929)
  covalent geometry    : angle       0.58939 /  0.27 (16329)
  hydrogen bonds       : bond        0.04433 /  3.02 (  783)
  hydrogen bonds       : angle       3.84375 /  2.80 ( 2271)
  Misc. bond           : bond        0.05721 /  2.80 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8508 (tt0)
REVERT: A  302 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7513 (t80)
REVERT: A  467 PHE cc_start: 0.7271 (m-80) cc_final: 0.6826 (m-80)
REVERT: A  508 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8349 (mp)
REVERT: A  584 GLU cc_start: 0.8378 (pm20) cc_final: 0.8015 (mm-30)
REVERT: B  508 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8308 (mp)
REVERT: B  584 GLU cc_start: 0.8602 (pp20) cc_final: 0.7963 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 108
  average time/residue: 0.5670
  time to fit residues: 66.8933
Evaluate side-chains
  114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  493 PHE
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain B residue  302 PHE
Chi-restraints excluded: chain B residue  506 SER
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  528 MET
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0060
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.097328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.063859 restraints weight = 39810.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2676 rms_B_bonded: 3.24
r_work: 0.2516 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2524 r_free = 0.2524    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2524 r_free = 0.2524    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  11933  Z= 0.123
  Angle     :  0.590  12.756  16329  Z= 0.271
  Chirality :  0.038   0.136   1730
  Planarity :  0.004   0.065   2023
  Dihedral  :  7.249  84.482   1766
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.04 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.21 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.53 (0.23), residues: 1419
  helix:  2.59 (0.17), residues: 990
  sheet: -2.56 (0.74), residues: 20
  loop : -0.44 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 267 
 TYR   0.018   0.001   TYR B  30 
 PHE   0.014   0.001   PHE B 492 
 TRP   0.019   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.12 (11929)
  covalent geometry    : angle       0.58950 /  0.27 (16329)
  hydrogen bonds       : bond        0.04388 /  2.99 (  783)
  hydrogen bonds       : angle       3.82945 /  2.79 ( 2271)
  Misc. bond           : bond        0.05604 /  2.75 (    4)

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

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

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2838 Ramachandran restraints generated.
    1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  126 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8500 (tt0)
REVERT: A  302 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7509 (t80)
REVERT: A  467 PHE cc_start: 0.7284 (m-80) cc_final: 0.6801 (m-80)
REVERT: A  508 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8378 (mp)
REVERT: A  584 GLU cc_start: 0.8363 (pm20) cc_final: 0.8023 (mm-30)
REVERT: B  508 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8310 (mp)
REVERT: B  584 GLU cc_start: 0.8609 (pp20) cc_final: 0.7997 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 109
  average time/residue: 0.5763
  time to fit residues: 68.4769
Evaluate side-chains
  112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  302 PHE
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  506 SER
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain B residue  302 PHE
Chi-restraints excluded: chain B residue  506 SER
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  582 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 136 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0370
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.8062

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

Flipped N/Q/H residues before XYZ refinement:
** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.097114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.064638 restraints weight = 31565.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.2686 rms_B_bonded: 2.93
r_work: 0.2532 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  11933  Z= 0.127
  Angle     :  0.593  12.977  16329  Z= 0.273
  Chirality :  0.038   0.136   1730
  Planarity :  0.004   0.064   2023
  Dihedral  :  7.270  84.437   1766
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.26 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 18.48 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.23), residues: 1419
  helix:  2.53 (0.17), residues: 996
  sheet: -2.57 (0.73), residues: 20
  loop : -0.40 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 267 
 TYR   0.024   0.001   TYR A  30 
 PHE   0.013   0.001   PHE A 635 
 TRP   0.019   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 (11929)
  covalent geometry    : angle       0.59286 /  0.27 (16329)
  hydrogen bonds       : bond        0.04466 /  3.04 (  783)
  hydrogen bonds       : angle       3.84459 /  2.80 ( 2271)
  Misc. bond           : bond        0.06258 /  3.07 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4610.02 seconds
wall clock time: 79 minutes 9.57 seconds (4749.57 seconds total)