Starting phenix.real_space_refine
on Thu Jun  4 10:16:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sta_55214/06_2026/9sta_55214.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sta_55214/06_2026/9sta_55214.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sta_55214/06_2026/9sta_55214.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sta_55214/06_2026/9sta_55214.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9sta_55214/06_2026/9sta_55214.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sta_55214/06_2026/9sta_55214.cif"
  }
  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=   0.005
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    7685      2.51       5
     N    1911      2.21       5
     O    2319      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  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: 11967
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5641
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 711, 5617
          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, 5617
          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: 5771
    Chain: "B"
      Number of atoms: 5639
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 710, 5615
          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, 5615
          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: 5770
    Chain: "A"
      Number of atoms: 135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 135
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'HQE': 2, 'LMT': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 198
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'HQE': 2, 'LMT': 2, 'UQ5': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          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: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 178
          Classifications: {'water': 178}
          Link IDs: {None: 177}
    Chain: "B"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 176
          Classifications: {'water': 176}
          Link IDs: {None: 175}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AHIS A 224 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 224 " occ=0.50
    residue:
      pdb=" N  ATRP A 718 " occ=0.54
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 718 " occ=0.46
    residue:
      pdb=" N  AHIS B 224 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 224 " occ=0.50
    residue:
      pdb=" N  ATRP B 718 " occ=0.51
      ... (26 atoms not shown)
      pdb=" CH2BTRP B 718 " occ=0.49
  Time building chain proxies: 5.17, per 1000 atoms: 0.43
  Number of scatterers: 11967
  At special positions: 0
  Unit cell: (89.54, 104.34, 105.82, 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    2319      8.00
     N    1911      7.00
     C    7685      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: 1.15
  Conformation dependent library (CDL) restraints added in 788.7 milliseconds
  

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 6 sheets defined
      78.0% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 33
      removed outlier: 3.875A  pdb=" N   GLY A  23 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
      removed outlier: 3.866A  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 129
      removed outlier: 4.033A  pdb=" N   ALA A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
    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 319 through 321
      No H-bonds generated for 'chain 'A' and resid 319 through 321'
    Processing helix  chain 'A' and resid 323 through 355
      Proline residue:  A 352  - end of helix
      removed outlier: 4.083A  pdb=" N   ASN A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 390
    Processing helix  chain 'A' and resid 394 through 402
      removed outlier: 4.516A  pdb=" N   PHE A 399 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   TRP A 400 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 439
      removed outlier: 3.666A  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 486
    Processing helix  chain 'A' and resid 491 through 508
    Processing helix  chain 'A' and resid 512 through 537
      removed outlier: 5.151A  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: 3.568A  pdb=" N   MET A 549 " --> pdb=" O   THR A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 559
      removed outlier: 4.098A  pdb=" N   GLU A 559 " --> pdb=" O   SER A 556 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 556 through 559'
    Processing helix  chain 'A' and resid 560 through 568
      removed outlier: 3.733A  pdb=" N   ILE A 564 " --> pdb=" O   VAL A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 576
    Processing helix  chain 'A' and resid 580 through 585
      removed outlier: 3.739A  pdb=" N   GLU A 584 " --> pdb=" O   PRO A 581 " (cutoff:3.500A)
      removed outlier: 3.682A  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 611
      removed outlier: 3.569A  pdb=" N   MET A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE A 611 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 621
      removed outlier: 4.101A  pdb=" N   TYR A 619 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 654
      removed outlier: 4.386A  pdb=" N   PHE A 640 " --> pdb=" O   GLY A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 682
      removed outlier: 3.772A  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: 4.005A  pdb=" N   GLY B  23 " --> pdb=" O   PHE B  19 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 65 through 69
    Processing helix  chain 'B' and resid 82 through 104
    Processing helix  chain 'B' and resid 112 through 129
      removed outlier: 3.941A  pdb=" N   ALA B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 136
    Processing helix  chain 'B' and resid 142 through 160
    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
    Processing helix  chain 'B' and resid 276 through 281
    Processing helix  chain 'B' and resid 282 through 307
    Processing helix  chain 'B' and resid 319 through 321
      No H-bonds generated for 'chain 'B' and resid 319 through 321'
    Processing helix  chain 'B' and resid 323 through 355
      Proline residue:  B 352  - end of helix
      removed outlier: 4.079A  pdb=" N   ASN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 390
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 4.509A  pdb=" N   PHE B 399 " --> pdb=" O   PRO B 395 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   TRP B 400 " --> pdb=" O   ASP B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 440
      removed outlier: 3.659A  pdb=" N   GLY B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
      Proline residue:  B 436  - end of helix
      removed outlier: 3.568A  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 508
    Processing helix  chain 'B' and resid 512 through 537
      removed outlier: 5.161A  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: 3.560A  pdb=" N   MET B 549 " --> pdb=" O   THR B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 576
    Processing helix  chain 'B' and resid 580 through 585
      removed outlier: 3.881A  pdb=" N   MET B 583 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ASN B 585 " --> pdb=" O   TRP B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 603
    Processing helix  chain 'B' and resid 604 through 612
    Processing helix  chain 'B' and resid 613 through 621
      removed outlier: 4.022A  pdb=" N   TYR B 619 " --> pdb=" O   VAL B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 654
      removed outlier: 4.402A  pdb=" N   PHE B 640 " --> pdb=" O   GLY B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 682
      removed outlier: 3.737A  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: 6.190A  pdb=" N   ARG A  47 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   SER A  42 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   GLU A  39 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   LEU A 141 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ALA A  41 " --> pdb=" O   LEU A 141 " (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 'A' and resid 312 through 313
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.210A  pdb=" N   ARG B  47 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   SER B  42 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU B  39 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   LEU B 141 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ALA B  41 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313

    778 hydrogen bonds defined for protein.
    2258 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.47 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: 4626
        1.38 -     1.55: 7291
        1.55 -     1.72: 0
        1.72 -     1.90: 84
        1.90 -     2.07: 16
  Bond restraints: 12017
  Sorted by residual:
  bond pdb=" C  BHIS B 224 "
       pdb=" N   PRO B 225 "
    ideal  model  delta    sigma   weight residual
    1.332  1.376 -0.045 1.30e-02 5.92e+03 1.18e+01
  bond pdb=" N   VAL A 637 "
       pdb=" CA  VAL A 637 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 1.19e-02 7.06e+03 1.12e+01
  bond pdb=" N   LEU A 634 "
       pdb=" CA  LEU A 634 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.16e-02 7.43e+03 1.08e+01
  bond pdb=" N   TYR A 638 "
       pdb=" CA  TYR A 638 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.28e-02 6.10e+03 9.02e+00
  bond pdb=" N   GLU A 559 "
       pdb=" CA  GLU A 559 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.31e-02 5.83e+03 8.83e+00
  ... (remaining 12012 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 16193
        2.39 -     4.79: 227
        4.79 -     7.18: 25
        7.18 -     9.58: 4
        9.58 -    11.97: 4
  Bond angle restraints: 16453
  Sorted by residual:
  angle pdb=" O  BHIS A 224 "
        pdb=" C  BHIS A 224 "
        pdb=" N   PRO A 225 "
      ideal   model   delta    sigma   weight residual
     121.71  117.65    4.06 6.40e-01 2.44e+00 4.02e+01
  angle pdb=" O  BHIS B 224 "
        pdb=" C  BHIS B 224 "
        pdb=" N   PRO B 225 "
      ideal   model   delta    sigma   weight residual
     121.65  125.49   -3.84 7.30e-01 1.88e+00 2.77e+01
  angle pdb=" C   GLY A 636 "
        pdb=" N   VAL A 637 "
        pdb=" CA  VAL A 637 "
      ideal   model   delta    sigma   weight residual
     122.66  117.86    4.80 9.70e-01 1.06e+00 2.45e+01
  angle pdb=" CA BHIS A 224 "
        pdb=" C  BHIS A 224 "
        pdb=" N   PRO A 225 "
      ideal   model   delta    sigma   weight residual
     117.71  122.15   -4.44 9.20e-01 1.18e+00 2.33e+01
  angle pdb=" CA BHIS B 224 "
        pdb=" C  BHIS B 224 "
        pdb=" N   PRO B 225 "
      ideal   model   delta    sigma   weight residual
     117.95  114.36    3.59 7.70e-01 1.69e+00 2.17e+01
  ... (remaining 16448 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 6008
       17.73 -    35.45: 554
       35.45 -    53.18: 160
       53.18 -    70.90: 35
       70.90 -    88.63: 22
  Dihedral angle restraints: 6779
    sinusoidal: 2722
      harmonic: 4057
  Sorted by residual:
  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 -153.46  -26.54     0      5.00e+00 4.00e-02 2.82e+01
  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  153.91   26.09     0      5.00e+00 4.00e-02 2.72e+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  159.43   20.57     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 6776 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1610
       0.074 -    0.149: 118
       0.149 -    0.223: 2
       0.223 -    0.297: 0
       0.297 -    0.371: 2
  Chirality restraints: 1732
  Sorted by residual:
  chirality pdb=" CB  VAL A 637 "
            pdb=" CA  VAL A 637 "
            pdb=" CG1 VAL A 637 "
            pdb=" CG2 VAL A 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.26   -0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CB  VAL B 637 "
            pdb=" CA  VAL B 637 "
            pdb=" CG1 VAL B 637 "
            pdb=" CG2 VAL B 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" CA  VAL A 560 "
            pdb=" N   VAL A 560 "
            pdb=" C   VAL A 560 "
            pdb=" CB  VAL A 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 1729 not shown)

  Planarity restraints: 2035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 632 "   -0.018 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   ALA B 632 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ALA B 632 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ALA B 633 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 357 "   -0.009 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   GLY A 357 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLY A 357 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A 358 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 558 "    0.008 2.00e-02 2.50e+03   1.51e-02 2.29e+00
        pdb=" C   LEU A 558 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A 558 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLU A 559 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2032 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 52
        2.43 -     3.05: 7595
        3.05 -     3.66: 18935
        3.66 -     4.28: 30106
        4.28 -     4.90: 48410
  Nonbonded interactions: 105098
  Sorted by model distance:
  nonbonded pdb="FE    FE A 804 "
            pdb=" O   HOH A 928 "
     model   vdw
     1.809 2.260
  nonbonded pdb="FE    FE B 803 "
            pdb=" O   HOH B 924 "
     model   vdw
     1.853 2.260
  nonbonded pdb=" O   HOH A 901 "
            pdb=" O   HOH A1057 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   HOH B 940 "
            pdb=" O   HOH B 951 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   HOH A 941 "
            pdb=" O   HOH A 957 "
     model   vdw
     2.214 3.040
  ... (remaining 105093 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 717 or resid 719 through 750))
  selection = (chain 'B' and (resid 18 through 223 or resid 225 through 439 or resid 465 throu \ 
gh 717 or resid 719 through 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=0.46 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:                  0.010
  Normalize map: mean=0, sd=1:             4.890
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     14.740
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  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:7.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
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      :  0.005   0.287  12021  Z= 0.195
  Angle     :  0.663  11.973  16453  Z= 0.369
  Chirality :  0.040   0.371   1732
  Planarity :  0.004   0.036   2035
  Dihedral  : 16.235  88.626   4199
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.82 %
    Favored  : 83.38 %
  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:  1.71 (0.23), residues: 1425
  helix:  1.82 (0.17), residues: 1010
  sheet: -0.51 (0.88), residues: 20
  loop : -0.52 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 267 
 TYR   0.020   0.002   TYR A 468 
 PHE   0.013   0.001   PHE B 492 
 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        0.00324 /  0.19 (12017)
  covalent geometry    : angle       0.66261 /  0.37 (16453)
  hydrogen bonds       : bond        0.14649 /  9.50 (  778)
  hydrogen bonds       : angle       5.60278 /  4.03 ( 2258)
  Misc. bond           : bond        0.19990 /  9.02 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 112
  average time/residue: 0.6506
  time to fit residues: 78.5164
Evaluate side-chains
  90 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain B residue  637 VAL
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:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A 184 ASN
B  62 GLN
B 184 ASN
B 217 HIS
B 624 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.091828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.064177 restraints weight = 59608.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 3.82
r_work: 0.2595 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2640 r_free = 0.2640    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.160  12021  Z= 0.143
  Angle     :  0.613  12.043  16453  Z= 0.291
  Chirality :  0.040   0.246   1732
  Planarity :  0.004   0.041   2035
  Dihedral  :  7.615  85.532   1772
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.37 %
    Favored  : 82.66 %
  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:  2.31 (0.23), residues: 1425
  helix:  2.26 (0.17), residues: 1013
  sheet: -0.95 (1.13), residues: 10
  loop : -0.32 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 267 
 TYR   0.019   0.001   TYR B  30 
 PHE   0.016   0.001   PHE B 466 
 TRP   0.019   0.001   TRP B 338 
 HIS   0.008   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 (12017)
  covalent geometry    : angle       0.61278 /  0.29 (16453)
  hydrogen bonds       : bond        0.04783 /  3.26 (  778)
  hydrogen bonds       : angle       4.17689 /  3.00 ( 2258)
  Misc. bond           : bond        0.10972 /  5.49 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  494 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: A  583 MET cc_start: 0.8950 (mpp) cc_final: 0.8472 (mpp)
REVERT: A  734 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8570 (tpp)
REVERT: B  494 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8005 (tm-30)
  outliers start: 22
  outliers final: 6
  residues processed: 104
  average time/residue: 0.6171
  time to fit residues: 69.7035
Evaluate side-chains
  91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  734 MET
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  563 LEU
Chi-restraints excluded: chain B residue  637 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 133 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 217 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.090063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.062867 restraints weight = 61021.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 3.80
r_work: 0.2586 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2607 r_free = 0.2607    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.193  12021  Z= 0.149
  Angle     :  0.605  13.251  16453  Z= 0.283
  Chirality :  0.040   0.266   1732
  Planarity :  0.004   0.038   2035
  Dihedral  :  7.491  85.107   1772
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 16.09 %
    Favored  : 82.75 %
  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:  2.39 (0.23), residues: 1425
  helix:  2.38 (0.17), residues: 1010
  sheet: -0.91 (1.19), residues: 10
  loop : -0.42 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 187 
 TYR   0.012   0.001   TYR B 638 
 PHE   0.009   0.001   PHE B 635 
 TRP   0.019   0.001   TRP B 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 (12017)
  covalent geometry    : angle       0.60480 /  0.28 (16453)
  hydrogen bonds       : bond        0.04982 /  3.39 (  778)
  hydrogen bonds       : angle       4.10180 /  2.95 ( 2258)
  Misc. bond           : bond        0.13497 /  6.69 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 PHE cc_start: 0.7155 (m-80) cc_final: 0.6942 (m-80)
REVERT: A  487 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7872 (mp)
REVERT: A  494 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: A  528 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6168 (ttt)
REVERT: A  583 MET cc_start: 0.8972 (mpp) cc_final: 0.8456 (mpp)
REVERT: B  494 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7957 (tm-30)
REVERT: B  528 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5932 (ttt)
  outliers start: 13
  outliers final: 2
  residues processed: 95
  average time/residue: 0.6139
  time to fit residues: 63.5003
Evaluate side-chains
  91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain B residue  528 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 138 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.092468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.065012 restraints weight = 75813.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.13
r_work: 0.2679 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.096  12021  Z= 0.115
  Angle     :  0.565  11.137  16453  Z= 0.266
  Chirality :  0.038   0.199   1732
  Planarity :  0.004   0.039   2035
  Dihedral  :  7.255  85.603   1771
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.00 %
    Favored  : 82.57 %
  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:  2.48 (0.23), residues: 1425
  helix:  2.48 (0.17), residues: 1010
  sheet:  None (None), residues: 0
  loop : -0.51 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 267 
 TYR   0.013   0.001   TYR B 638 
 PHE   0.010   0.001   PHE B 527 
 TRP   0.019   0.001   TRP B 338 
 HIS   0.008   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.11 (12017)
  covalent geometry    : angle       0.56509 /  0.27 (16453)
  hydrogen bonds       : bond        0.04219 /  2.89 (  778)
  hydrogen bonds       : angle       3.92461 /  2.82 ( 2258)
  Misc. bond           : bond        0.06390 /  3.16 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 PHE cc_start: 0.7052 (m-80) cc_final: 0.6807 (m-80)
REVERT: A  487 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7866 (mp)
REVERT: A  494 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7669 (tm-30)
REVERT: A  528 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6123 (ttt)
REVERT: A  583 MET cc_start: 0.8992 (mpp) cc_final: 0.8472 (mpp)
REVERT: B   19 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5515 (p90)
REVERT: B  487 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7696 (tt)
REVERT: B  494 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: B  528 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5826 (ttt)
  outliers start: 16
  outliers final: 3
  residues processed: 95
  average time/residue: 0.5670
  time to fit residues: 58.6538
Evaluate side-chains
  91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  528 MET
Chi-restraints excluded: chain B residue  563 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 138 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.089931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.062946 restraints weight = 60924.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 3.78
r_work: 0.2624 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2624 r_free = 0.2624    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 = 0.2624 r_free = 0.2624    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.206  12021  Z= 0.149
  Angle     :  0.598  14.111  16453  Z= 0.275
  Chirality :  0.039   0.146   1732
  Planarity :  0.004   0.037   2035
  Dihedral  :  7.289  84.733   1771
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.73 %
    Favored  : 82.84 %
  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:  2.48 (0.23), residues: 1425
  helix:  2.48 (0.17), residues: 1011
  sheet: -1.12 (1.37), residues: 10
  loop : -0.51 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 267 
 TYR   0.018   0.001   TYR B 638 
 PHE   0.011   0.001   PHE B 635 
 TRP   0.017   0.001   TRP B 251 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 (12017)
  covalent geometry    : angle       0.59837 /  0.27 (16453)
  hydrogen bonds       : bond        0.04899 /  3.34 (  778)
  hydrogen bonds       : angle       3.99003 /  2.87 ( 2258)
  Misc. bond           : bond        0.14774 /  7.35 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 PHE cc_start: 0.7040 (m-80) cc_final: 0.6759 (m-80)
REVERT: A  487 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7856 (mp)
REVERT: A  494 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7760 (tm-30)
REVERT: A  528 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6133 (ttt)
REVERT: A  583 MET cc_start: 0.9018 (tpp) cc_final: 0.8460 (mpp)
REVERT: B   19 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5424 (p90)
REVERT: B  251 TRP cc_start: 0.7319 (t60) cc_final: 0.6788 (t60)
REVERT: B  487 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7544 (tt)
REVERT: B  494 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: B  515 MET cc_start: 0.8374 (tpp) cc_final: 0.8147 (tpp)
REVERT: B  528 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5816 (ttt)
  outliers start: 16
  outliers final: 0
  residues processed: 94
  average time/residue: 0.5630
  time to fit residues: 58.0046
Evaluate side-chains
  89 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  528 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 131 optimal weight:    4.9990
   chunk 127 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3315 r_free = 0.3315 target = 0.090324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.063170 restraints weight = 65461.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 3.89
r_work: 0.2632 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    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 = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.158  12021  Z= 0.136
  Angle     :  0.576  12.113  16453  Z= 0.268
  Chirality :  0.038   0.144   1732
  Planarity :  0.004   0.037   2035
  Dihedral  :  7.169  84.743   1770
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 16.35 %
    Favored  : 82.75 %
  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:  2.51 (0.23), residues: 1425
  helix:  2.51 (0.17), residues: 1012
  sheet: -1.18 (1.38), residues: 10
  loop : -0.52 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 267 
 TYR   0.019   0.001   TYR B 638 
 PHE   0.011   0.001   PHE B 527 
 TRP   0.020   0.001   TRP A 251 
 HIS   0.008   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.13 (12017)
  covalent geometry    : angle       0.57621 /  0.27 (16453)
  hydrogen bonds       : bond        0.04610 /  3.15 (  778)
  hydrogen bonds       : angle       3.94827 /  2.84 ( 2258)
  Misc. bond           : bond        0.10971 /  5.44 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5958 (p90)
REVERT: A  251 TRP cc_start: 0.7305 (t60) cc_final: 0.6723 (t60)
REVERT: A  467 PHE cc_start: 0.7017 (m-80) cc_final: 0.6722 (m-80)
REVERT: A  487 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7880 (mp)
REVERT: A  494 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: A  528 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.5997 (ttt)
REVERT: A  583 MET cc_start: 0.9025 (tpp) cc_final: 0.8459 (mpp)
REVERT: B   19 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5417 (p90)
REVERT: B  251 TRP cc_start: 0.7309 (t60) cc_final: 0.6755 (t60)
REVERT: B  487 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7514 (tt)
REVERT: B  494 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: B  515 MET cc_start: 0.8375 (tpp) cc_final: 0.8136 (tpp)
REVERT: B  528 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5715 (ttt)
  outliers start: 10
  outliers final: 0
  residues processed: 94
  average time/residue: 0.5746
  time to fit residues: 59.1305
Evaluate side-chains
  91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  528 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 126 optimal weight:    0.7980
   chunk 135 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 90 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 130 ASN
B 568 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.089097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.061114 restraints weight = 78673.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 4.20
r_work: 0.2593 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.183  12021  Z= 0.141
  Angle     :  0.585  13.247  16453  Z= 0.270
  Chirality :  0.038   0.149   1732
  Planarity :  0.004   0.037   2035
  Dihedral  :  7.183  84.952   1770
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 16.18 %
    Favored  : 82.66 %
  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:  2.54 (0.23), residues: 1425
  helix:  2.56 (0.17), residues: 1007
  sheet: -1.24 (1.39), residues: 10
  loop : -0.56 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 267 
 TYR   0.022   0.001   TYR B 638 
 PHE   0.011   0.001   PHE B 527 
 TRP   0.017   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.14 (12017)
  covalent geometry    : angle       0.58504 /  0.27 (16453)
  hydrogen bonds       : bond        0.04727 /  3.22 (  778)
  hydrogen bonds       : angle       3.95361 /  2.85 ( 2258)
  Misc. bond           : bond        0.12909 /  6.40 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.5955 (p90)
REVERT: A  467 PHE cc_start: 0.7043 (m-80) cc_final: 0.6753 (m-80)
REVERT: A  487 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7855 (mp)
REVERT: A  494 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: A  528 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.5947 (ttt)
REVERT: A  583 MET cc_start: 0.9020 (tpp) cc_final: 0.8493 (mpp)
REVERT: B   19 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5424 (p90)
REVERT: B  251 TRP cc_start: 0.7309 (t60) cc_final: 0.6776 (t60)
REVERT: B  487 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7467 (tt)
REVERT: B  494 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8017 (tm-30)
REVERT: B  515 MET cc_start: 0.8388 (tpp) cc_final: 0.8149 (tpp)
REVERT: B  528 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5740 (ttt)
  outliers start: 13
  outliers final: 1
  residues processed: 94
  average time/residue: 0.6017
  time to fit residues: 61.6020
Evaluate side-chains
  90 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain B residue  487 LEU
Chi-restraints excluded: chain B residue  528 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 139 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 96 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN
A 151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.088913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.061242 restraints weight = 70395.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.2674 rms_B_bonded: 4.09
r_work: 0.2496 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2493 r_free = 0.2493    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2493 r_free = 0.2493    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.129  12021  Z= 0.123
  Angle     :  0.567  11.846  16453  Z= 0.265
  Chirality :  0.038   0.144   1732
  Planarity :  0.004   0.037   2035
  Dihedral  :  7.069  85.449   1770
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 16.35 %
    Favored  : 82.75 %
  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:  2.55 (0.23), residues: 1425
  helix:  2.56 (0.17), residues: 1013
  sheet:  None (None), residues: 0
  loop : -0.59 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 267 
 TYR   0.022   0.001   TYR B 638 
 PHE   0.012   0.001   PHE B 527 
 TRP   0.018   0.001   TRP B 338 
 HIS   0.008   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.12 (12017)
  covalent geometry    : angle       0.56746 /  0.26 (16453)
  hydrogen bonds       : bond        0.04333 /  2.96 (  778)
  hydrogen bonds       : angle       3.88606 /  2.80 ( 2258)
  Misc. bond           : bond        0.08921 /  4.41 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.5962 (p90)
REVERT: A  121 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8336 (pp20)
REVERT: A  467 PHE cc_start: 0.7023 (m-80) cc_final: 0.6691 (m-80)
REVERT: A  487 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7684 (mp)
REVERT: A  494 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: A  528 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5858 (ttt)
REVERT: A  583 MET cc_start: 0.8930 (tpp) cc_final: 0.8335 (mpp)
REVERT: B   19 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5390 (p90)
REVERT: B  251 TRP cc_start: 0.7238 (t60) cc_final: 0.6703 (t60)
REVERT: B  487 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7335 (tt)
REVERT: B  494 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7975 (tm-30)
REVERT: B  515 MET cc_start: 0.8335 (tpp) cc_final: 0.8108 (tpp)
  outliers start: 10
  outliers final: 2
  residues processed: 93
  average time/residue: 0.5654
  time to fit residues: 57.5746
Evaluate side-chains
  93 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  121 GLU
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0270
   chunk 135 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   chunk 136 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A 585 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.090406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.062462 restraints weight = 72788.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 4.19
r_work: 0.2533 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  12021  Z= 0.108
  Angle     :  0.549  11.432  16453  Z= 0.257
  Chirality :  0.037   0.143   1732
  Planarity :  0.004   0.040   2035
  Dihedral  :  6.937  87.459   1770
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 16.35 %
    Favored  : 82.84 %
  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:  2.63 (0.24), residues: 1425
  helix:  2.63 (0.17), residues: 1013
  sheet:  None (None), residues: 0
  loop : -0.58 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 267 
 TYR   0.019   0.001   TYR A 638 
 PHE   0.015   0.001   PHE A 492 
 TRP   0.022   0.001   TRP A 251 
 HIS   0.008   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 (12017)
  covalent geometry    : angle       0.54900 /  0.26 (16453)
  hydrogen bonds       : bond        0.03895 /  2.67 (  778)
  hydrogen bonds       : angle       3.79821 /  2.74 ( 2258)
  Misc. bond           : bond        0.05772 /  2.84 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5956 (p90)
REVERT: A  251 TRP cc_start: 0.7176 (t60) cc_final: 0.6735 (t60)
REVERT: A  487 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7654 (mp)
REVERT: A  494 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: A  528 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5814 (ttt)
REVERT: A  583 MET cc_start: 0.8885 (tpp) cc_final: 0.8284 (mpp)
REVERT: B   19 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5428 (p90)
REVERT: B  487 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7295 (tt)
REVERT: B  494 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: B  515 MET cc_start: 0.8322 (tpp) cc_final: 0.8071 (tpp)
  outliers start: 9
  outliers final: 2
  residues processed: 93
  average time/residue: 0.5979
  time to fit residues: 60.6298
Evaluate side-chains
  90 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 101 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0000
   overall best weight:    0.5762

-------------------------------------------------------------------------------
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 = 0.3303 r_free = 0.3303 target = 0.090939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.063155 restraints weight = 73139.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 4.20
r_work: 0.2539 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2536 r_free = 0.2536    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2536 r_free = 0.2536    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  12021  Z= 0.108
  Angle     :  0.550  11.241  16453  Z= 0.257
  Chirality :  0.037   0.143   1732
  Planarity :  0.004   0.067   2035
  Dihedral  :  6.934  88.388   1770
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 16.35 %
    Favored  : 82.84 %
  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:  2.66 (0.24), residues: 1425
  helix:  2.65 (0.17), residues: 1013
  sheet:  None (None), residues: 0
  loop : -0.59 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 267 
 TYR   0.020   0.001   TYR A 638 
 PHE   0.011   0.001   PHE B 527 
 TRP   0.021   0.001   TRP B 251 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 (12017)
  covalent geometry    : angle       0.54954 /  0.26 (16453)
  hydrogen bonds       : bond        0.03872 /  2.65 (  778)
  hydrogen bonds       : angle       3.77121 /  2.72 ( 2258)
  Misc. bond           : bond        0.06222 /  3.08 (    4)

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

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

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2850 Ramachandran restraints generated.
    1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5965 (p90)
REVERT: A  251 TRP cc_start: 0.7191 (t60) cc_final: 0.6794 (t60)
REVERT: A  487 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7592 (mp)
REVERT: A  494 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7671 (tm-30)
REVERT: A  528 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5796 (ttt)
REVERT: A  583 MET cc_start: 0.8900 (tpp) cc_final: 0.8295 (mpp)
REVERT: B   19 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5459 (p90)
REVERT: B  251 TRP cc_start: 0.7163 (t60) cc_final: 0.6684 (t60)
REVERT: B  487 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7274 (tt)
REVERT: B  494 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: B  515 MET cc_start: 0.8328 (tpp) cc_final: 0.8076 (tpp)
  outliers start: 9
  outliers final: 1
  residues processed: 95
  average time/residue: 0.5615
  time to fit residues: 58.3428
Evaluate side-chains
  89 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   chunk 138 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.3188

-------------------------------------------------------------------------------
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 = 0.3248 r_free = 0.3248 target = 0.087841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.060267 restraints weight = 63606.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.2658 rms_B_bonded: 3.92
r_work: 0.2484 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2482 r_free = 0.2482    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2482 r_free = 0.2482    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.202  12021  Z= 0.145
  Angle     :  0.590  13.668  16453  Z= 0.271
  Chirality :  0.038   0.148   1732
  Planarity :  0.004   0.037   2035
  Dihedral  :  7.089  86.691   1770
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 16.98 %
    Favored  : 82.57 %
  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:  2.61 (0.24), residues: 1425
  helix:  2.61 (0.17), residues: 1013
  sheet: -1.00 (1.59), residues: 10
  loop : -0.57 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 267 
 TYR   0.022   0.001   TYR A 638 
 PHE   0.011   0.001   PHE B 635 
 TRP   0.019   0.001   TRP A 251 
 HIS   0.007   0.001   HIS A 537 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.14 (12017)
  covalent geometry    : angle       0.59024 /  0.27 (16453)
  hydrogen bonds       : bond        0.04691 /  3.20 (  778)
  hydrogen bonds       : angle       3.89022 /  2.80 ( 2258)
  Misc. bond           : bond        0.14359 /  7.14 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4467.25 seconds
wall clock time: 76 minutes 43.63 seconds (4603.63 seconds total)