Starting phenix.real_space_refine
on Sun Apr  5 18:12:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cdq_45484/04_2026/9cdq_45484_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cdq_45484/04_2026/9cdq_45484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cdq_45484/04_2026/9cdq_45484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cdq_45484/04_2026/9cdq_45484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cdq_45484/04_2026/9cdq_45484_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cdq_45484/04_2026/9cdq_45484_neut.cif"
  }
  resolution = 3.76
  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=   0.002 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      57      5.16       5
     C    7536      2.51       5
     N    2148      2.21       5
     O    2306      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12048
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "F"
      Number of atoms: 5237
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 677, 5232
          Classifications: {'peptide': 677}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 645}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 11
      Conformer: "B"
        Number of residues, atoms: 677, 5232
          Classifications: {'peptide': 677}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 645}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 11
          bond proxies already assigned to first conformer: 5345
    Chain: "A"
      Number of atoms: 6806
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 868, 6795
          Classifications: {'peptide': 868}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 24, 'TRANS': 843}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
      Conformer: "B"
        Number of residues, atoms: 868, 6795
          Classifications: {'peptide': 868}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 24, 'TRANS': 843}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
          bond proxies already assigned to first conformer: 6936
    Chain: "F"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' FE': 1, 'BCT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AALA F 353 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA F 353 " occ=0.50
    residue:
      pdb=" N  AARG A 825 " occ=0.15
      ... (20 atoms not shown)
      pdb=" NH2BARG A 825 " occ=0.85
  Time building chain proxies: 4.28, per 1000 atoms: 0.36
  Number of scatterers: 12048
  At special positions: 0
  Unit cell: (75.46, 116.424, 150.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      57     16.00
     O    2306      8.00
     N    2148      7.00
     C    7536      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=22, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  28 " - pdb=" SG  CYS F  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  38 " - pdb=" SG  CYS F  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 137 " - pdb=" SG  CYS F 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 156 " - pdb=" SG  CYS F 350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 177 " - pdb=" SG  CYS F 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 180 " - pdb=" SG  CYS F 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 190 " - pdb=" SG  CYS F 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 246 " - pdb=" SG  CYS F 260 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 358 " - pdb=" SG  CYS F 615 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 364 " - pdb=" SG  CYS F 396 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 374 " - pdb=" SG  CYS F 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 421 " - pdb=" SG  CYS F 693 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 437 " - pdb=" SG  CYS F 656 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 469 " - pdb=" SG  CYS F 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 493 " - pdb=" SG  CYS F 684 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 503 " - pdb=" SG  CYS F 517 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 514 " - pdb=" SG  CYS F 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 582 " - pdb=" SG  CYS F 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 634 " - pdb=" SG  CYS F 639 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 264 " - pdb=" SG  CYS A 272 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 446 " - pdb=" SG  CYS A 455 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 562 " - pdb=" SG  CYS A 572 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 830.9 milliseconds
  

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2812

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 15 sheets defined
      20.9% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'F' and resid 31 through 49
      removed outlier: 3.624A  pdb=" N   VAL F  48 " --> pdb=" O   HIS F  44 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 63 through 73
    Processing helix  chain 'F' and resid 82 through 84
      No H-bonds generated for 'chain 'F' and resid 82 through 84'
    Processing helix  chain 'F' and resid 85 through 91
    Processing helix  chain 'F' and resid 127 through 131
      removed outlier: 3.895A  pdb=" N   LEU F 131 " --> pdb=" O   MET F 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 143 through 156
      removed outlier: 3.533A  pdb=" N   TRP F 147 " --> pdb=" O   ARG F 143 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   ILE F 149 " --> pdb=" O   ALA F 145 " (cutoff:3.500A)
      Proline residue:  F 150  - end of helix
      removed outlier: 4.346A  pdb=" N   CYS F 156 " --> pdb=" O   GLY F 152 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 165 through 173
    Processing helix  chain 'F' and resid 186 through 191
      removed outlier: 3.830A  pdb=" N   LEU F 189 " --> pdb=" O   PHE F 186 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 216
    Processing helix  chain 'F' and resid 227 through 232
    Processing helix  chain 'F' and resid 235 through 241
    Processing helix  chain 'F' and resid 278 through 294
    Processing helix  chain 'F' and resid 329 through 335
    Processing helix  chain 'F' and resid 335 through 348
      removed outlier: 4.033A  pdb=" N   ARG F 346 " --> pdb=" O   ILE F 342 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 367 through 381
    Processing helix  chain 'F' and resid 392 through 402
    Processing helix  chain 'F' and resid 411 through 421
      removed outlier: 4.055A  pdb=" N   ILE F 417 " --> pdb=" O   GLY F 413 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 436 through 440
    Processing helix  chain 'F' and resid 479 through 487
      removed outlier: 4.007A  pdb=" N   MET F 483 " --> pdb=" O   TRP F 479 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 494 through 499
      removed outlier: 3.512A  pdb=" N   PHE F 499 " --> pdb=" O   PHE F 495 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 535 through 546
    Processing helix  chain 'F' and resid 555 through 561
      removed outlier: 3.600A  pdb=" N   THR F 561 " --> pdb=" O   VAL F 557 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 574 through 576
      No H-bonds generated for 'chain 'F' and resid 574 through 576'
    Processing helix  chain 'F' and resid 591 through 593
      No H-bonds generated for 'chain 'F' and resid 591 through 593'
    Processing helix  chain 'F' and resid 612 through 627
      removed outlier: 3.999A  pdb=" N   ARG F 621 " --> pdb=" O   HIS F 617 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   HIS F 625 " --> pdb=" O   ARG F 621 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 665 through 671
    Processing helix  chain 'F' and resid 671 through 681
      removed outlier: 3.931A  pdb=" N   LEU F 681 " --> pdb=" O   ALA F 677 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 687 through 695
      removed outlier: 3.640A  pdb=" N   GLU F 691 " --> pdb=" O   SER F 687 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE F 695 " --> pdb=" O   GLU F 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 71
    Processing helix  chain 'A' and resid 75 through 79
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 292 through 294
      No H-bonds generated for 'chain 'A' and resid 292 through 294'
    Processing helix  chain 'A' and resid 350 through 362
      removed outlier: 3.799A  pdb=" N   GLN A 360 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 378
    Processing helix  chain 'A' and resid 817 through 820
      removed outlier: 3.537A  pdb=" N   GLU A 820 " --> pdb=" O   GLU A 817 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 817 through 820'
    Processing helix  chain 'A' and resid 876 through 882
      removed outlier: 3.754A  pdb=" N   GLN A 882 " --> pdb=" O   GLU A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 901
      removed outlier: 4.052A  pdb=" N   ARG A 899 " --> pdb=" O   VAL A 896 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA A 901 " --> pdb=" O   ASN A 898 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 30
      removed outlier: 5.658A  pdb=" N   VAL F  25 " --> pdb=" O   ALA F  57 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL F  59 " --> pdb=" O   VAL F  25 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   TRP F  27 " --> pdb=" O   VAL F  59 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   LYS F  61 " --> pdb=" O   TRP F  27 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ALA F  29 " --> pdb=" O   LYS F  61 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'F' and resid 78 through 81
      removed outlier: 6.491A  pdb=" N   VAL F 270 " --> pdb=" O   VAL F  99 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS F  97 " --> pdb=" O   ALA F 272 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 110 through 111
      removed outlier: 6.129A  pdb=" N   PHE F 103 " --> pdb=" O   HIS F 319 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 113 through 121
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 113 through 121
    current: chain 'F' and resid 176 through 177
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 176 through 177
    current: chain 'F' and resid 251 through 252
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 361 through 365
    Processing sheet with id=AA6, first strand: chain 'F' and resid 408 through 410
      removed outlier: 3.954A  pdb=" N   MET F 408 " --> pdb=" O   VAL F 607 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU F 427 " --> pdb=" O   VAL F 606 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 444 through 447
      removed outlier: 4.061A  pdb=" N   ALA F 599 " --> pdb=" O   ALA F 447 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 450 through 452
    Processing sheet with id=AA9, first strand: chain 'F' and resid 468 through 469
    Processing sheet with id=AB1, first strand: chain 'A' and resid 63 through 64
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 63 through 64
    current: chain 'A' and resid 116 through 117
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 116 through 117
    current: chain 'A' and resid 169 through 175
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 87 through 90
      removed outlier: 6.708A  pdb=" N   ALA A  87 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   TYR A  99 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   VAL A  89 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 188 through 197
      removed outlier: 4.735A  pdb=" N   VAL A 397 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 493 through 513
    current: chain 'A' and resid 555 through 560
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 555 through 560
    current: chain 'A' and resid 596 through 599
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 596 through 599
    current: chain 'A' and resid 638 through 645
      removed outlier: 3.747A  pdb=" N   SER A 645 " --> pdb=" O   ASN A 677 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TRP A 695 " --> pdb=" O   ALA A 680 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   LEU A 691 " --> pdb=" O   LYS A 741 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   LYS A 741 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   ALA A 693 " --> pdb=" O   LEU A 739 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LEU A 739 " --> pdb=" O   ALA A 693 " (cutoff:3.500A)
      removed outlier: 5.460A  pdb=" N   TRP A 695 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASN A 737 " --> pdb=" O   TRP A 695 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   ASN A 697 " --> pdb=" O   GLY A 735 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   GLY A 735 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   ALA A 699 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE A 733 " --> pdb=" O   ALA A 699 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   ARG A 701 " --> pdb=" O   ALA A 731 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ALA A 731 " --> pdb=" O   ARG A 701 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   VAL A 705 " --> pdb=" O   ASN A 727 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   ASN A 727 " --> pdb=" O   VAL A 705 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   GLY A 707 " --> pdb=" O   TYR A 725 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   TYR A 725 " --> pdb=" O   GLY A 707 " (cutoff:3.500A)
      removed outlier: 8.568A  pdb=" N   GLU A 709 " --> pdb=" O   PRO A 723 " (cutoff:3.500A)
      removed outlier: 10.176A  pdb=" N   GLN A 711 " --> pdb=" O   GLY A 721 " (cutoff:3.500A)
      removed outlier: 10.337A  pdb=" N   GLY A 721 " --> pdb=" O   GLN A 711 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   SER A 730 " --> pdb=" O   ILE A 769 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ILE A 769 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ARG A 732 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ARG A 863 " --> pdb=" O   SER A 910 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 240 through 250
    Processing sheet with id=AB5, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779
      removed outlier: 3.660A  pdb=" N   ILE A 778 " --> pdb=" O   ALA A 826 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1117 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: 2.15

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4043
        1.34 -     1.46: 2917
        1.46 -     1.58: 5290
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 12320
  Sorted by residual:
  bond pdb=" CA  ASP A 293 "
       pdb=" CB  ASP A 293 "
    ideal  model  delta    sigma   weight residual
    1.528  1.568 -0.040 1.49e-02 4.50e+03 7.24e+00
  bond pdb=" C   LYS F 163 "
       pdb=" N   PRO F 164 "
    ideal  model  delta    sigma   weight residual
    1.330  1.353 -0.023 1.23e-02 6.61e+03 3.57e+00
  bond pdb=" CB  GLU A 753 "
       pdb=" CG  GLU A 753 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 3.00e-02 1.11e+03 2.27e+00
  bond pdb=" CA  GLU A 753 "
       pdb=" CB  GLU A 753 "
    ideal  model  delta    sigma   weight residual
    1.530  1.555 -0.025 1.69e-02 3.50e+03 2.15e+00
  bond pdb=" CA  ASN A 298 "
       pdb=" CB  ASN A 298 "
    ideal  model  delta    sigma   weight residual
    1.526  1.550 -0.024 1.76e-02 3.23e+03 1.92e+00
  ... (remaining 12315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 16328
        2.50 -     5.01: 290
        5.01 -     7.51: 36
        7.51 -    10.01: 11
       10.01 -    12.51: 5
  Bond angle restraints: 16670
  Sorted by residual:
  angle pdb=" C   LEU F 649 "
        pdb=" CA  LEU F 649 "
        pdb=" CB  LEU F 649 "
      ideal   model   delta    sigma   weight residual
     117.23  109.96    7.27 1.36e+00 5.41e-01 2.86e+01
  angle pdb=" CA  GLU A 753 "
        pdb=" CB  GLU A 753 "
        pdb=" CG  GLU A 753 "
      ideal   model   delta    sigma   weight residual
     114.10  124.78  -10.68 2.00e+00 2.50e-01 2.85e+01
  angle pdb=" N   TYR A  82 "
        pdb=" CA  TYR A  82 "
        pdb=" C   TYR A  82 "
      ideal   model   delta    sigma   weight residual
     114.75  108.80    5.95 1.26e+00 6.30e-01 2.23e+01
  angle pdb=" N   ASP A 105 "
        pdb=" CA  ASP A 105 "
        pdb=" C   ASP A 105 "
      ideal   model   delta    sigma   weight residual
     108.45  113.62   -5.17 1.26e+00 6.30e-01 1.69e+01
  angle pdb=" CA  GLN A 531 "
        pdb=" CB  GLN A 531 "
        pdb=" CG  GLN A 531 "
      ideal   model   delta    sigma   weight residual
     114.10  122.26   -8.16 2.00e+00 2.50e-01 1.67e+01
  ... (remaining 16665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 6164
       18.00 -    35.99: 898
       35.99 -    53.99: 238
       53.99 -    71.98: 47
       71.98 -    89.98: 20
  Dihedral angle restraints: 7367
    sinusoidal: 2928
      harmonic: 4439
  Sorted by residual:
  dihedral pdb=" CB  CYS F 374 "
           pdb=" SG  CYS F 374 "
           pdb=" SG  CYS F 387 "
           pdb=" CB  CYS F 387 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.86  -80.86     1      1.00e+01 1.00e-02 8.08e+01
  dihedral pdb=" CB  CYS F 514 "
           pdb=" SG  CYS F 514 "
           pdb=" SG  CYS F 525 "
           pdb=" CB  CYS F 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.47   70.47     1      1.00e+01 1.00e-02 6.39e+01
  dihedral pdb=" CB  CYS F 177 "
           pdb=" SG  CYS F 177 "
           pdb=" SG  CYS F 193 "
           pdb=" CB  CYS F 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.97   68.97     1      1.00e+01 1.00e-02 6.15e+01
  ... (remaining 7364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1301
       0.045 -    0.091: 352
       0.091 -    0.136: 89
       0.136 -    0.182: 10
       0.182 -    0.227: 2
  Chirality restraints: 1754
  Sorted by residual:
  chirality pdb=" CB  VAL F 382 "
            pdb=" CA  VAL F 382 "
            pdb=" CG1 VAL F 382 "
            pdb=" CG2 VAL F 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  THR A 544 "
            pdb=" CA  THR A 544 "
            pdb=" OG1 THR A 544 "
            pdb=" CG2 THR A 544 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" CA  ARG A 286 "
            pdb=" N   ARG A 286 "
            pdb=" C   ARG A 286 "
            pdb=" CB  ARG A 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.19e-01
  ... (remaining 1751 not shown)

  Planarity restraints: 2197
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 163 "   -0.052 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO F 164 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO F 164 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO F 164 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F 697 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO F 698 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO F 698 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO F 698 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 751 "    0.038 5.00e-02 4.00e+02   5.80e-02 5.39e+00
        pdb=" N   PRO A 752 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 752 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 752 "    0.033 5.00e-02 4.00e+02
  ... (remaining 2194 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 187
        2.61 -     3.18: 10801
        3.18 -     3.76: 19200
        3.76 -     4.33: 25411
        4.33 -     4.90: 40830
  Nonbonded interactions: 96429
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F 114 "
            pdb="FE    FE F 702 "
     model   vdw
     2.041 2.260
  nonbonded pdb=" OD2 ASP F  82 "
            pdb="FE    FE F 702 "
     model   vdw
     2.074 2.260
  nonbonded pdb=" OH  TYR A 269 "
            pdb=" O   PRO A 546 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" NE2 HIS F 268 "
            pdb="FE    FE F 702 "
     model   vdw
     2.124 2.340
  nonbonded pdb=" O3  BCT F 701 "
            pdb="FE    FE F 702 "
     model   vdw
     2.133 2.260
  ... (remaining 96424 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.15 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     14.250
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12342  Z= 0.174
  Angle     :  0.861  12.513  16714  Z= 0.471
  Chirality :  0.045   0.227   1754
  Planarity :  0.005   0.079   2197
  Dihedral  : 18.146  89.975   4489
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.31 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 35.52 %
    Favored  : 64.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.20), residues: 1547
  helix: -0.76 (0.31), residues: 240
  sheet: -0.83 (0.23), residues: 484
  loop : -2.19 (0.20), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 587 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.024   0.002   PHE A 441 
 TRP   0.029   0.002   TRP A 312 
 HIS   0.006   0.001   HIS F 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (12320)
  covalent geometry    : angle       0.86118 (16670)
  SS BOND              : bond        0.00211 (   22)
  SS BOND              : angle       0.94236 (   44)
  hydrogen bonds       : bond        0.14604 (  399)
  hydrogen bonds       : angle       7.68325 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   69 ARG cc_start: 0.8336 (tpp-160) cc_final: 0.8102 (mmp-170)
REVERT: F  257 TYR cc_start: 0.8188 (p90) cc_final: 0.7784 (p90)
REVERT: F  697 ARG cc_start: 0.8882 (tpt90) cc_final: 0.8665 (mtm180)
REVERT: A  262 GLU cc_start: 0.8206 (pm20) cc_final: 0.7834 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1078
  time to fit residues: 21.1013
Evaluate side-chains
  120 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.4980
   chunk 149 optimal weight:    6.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
F  33 HIS
** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
A 357 ASN
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 ASN
** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 859 HIS
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 893 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.114479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.088766 restraints weight = 62961.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.092398 restraints weight = 28753.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.094147 restraints weight = 14477.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.094946 restraints weight = 9877.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.095539 restraints weight = 8540.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3548
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12342  Z= 0.232
  Angle     :  0.786  11.137  16714  Z= 0.402
  Chirality :  0.047   0.265   1754
  Planarity :  0.006   0.062   2197
  Dihedral  :  5.297  32.360   1717
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 10.71 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 31.88 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.41 (0.20), residues: 1547
  helix: -0.85 (0.31), residues: 243
  sheet: -0.87 (0.24), residues: 461
  loop : -2.32 (0.20), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 286 
 TYR   0.017   0.002   TYR A 408 
 PHE   0.019   0.002   PHE F 695 
 TRP   0.018   0.002   TRP A 312 
 HIS   0.007   0.001   HIS F 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 (12320)
  covalent geometry    : angle       0.78442 (16670)
  SS BOND              : bond        0.00288 (   22)
  SS BOND              : angle       1.23405 (   44)
  hydrogen bonds       : bond        0.04573 (  399)
  hydrogen bonds       : angle       6.86165 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 122
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  275 MET cc_start: 0.8512 (mpp) cc_final: 0.8213 (mpp)
REVERT: F  581 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8223 (mt)
  outliers start: 53
  outliers final: 31
  residues processed: 162
  average time/residue: 0.0971
  time to fit residues: 23.7948
Evaluate side-chains
  143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain F residue  229 ILE
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  364 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  409 SER
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  581 LEU
Chi-restraints excluded: chain F residue  590 VAL
Chi-restraints excluded: chain F residue  607 VAL
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  660 LEU
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  677 ASN
Chi-restraints excluded: chain A residue  703 LEU
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  883 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0010
   chunk 50 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 150 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 10 optimal weight:    0.1980
   chunk 125 optimal weight:   10.0000
   overall best weight:    0.7588

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

Flipped N/Q/H residues before XYZ refinement:
F 432 ASN
A 118 GLN
A 357 ASN
A 360 GLN
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 ASN
** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 807 ASN
A 859 HIS
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.120959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.094511 restraints weight = 57776.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.097908 restraints weight = 25337.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.100076 restraints weight = 14533.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.101510 restraints weight = 9770.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.102482 restraints weight = 7384.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12342  Z= 0.129
  Angle     :  0.706  10.284  16714  Z= 0.354
  Chirality :  0.045   0.203   1754
  Planarity :  0.005   0.075   2197
  Dihedral  :  4.912  29.938   1717
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.31 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 33.15 %
    Favored  : 63.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.20 (0.20), residues: 1547
  helix: -0.77 (0.31), residues: 240
  sheet: -0.68 (0.24), residues: 446
  loop : -2.17 (0.20), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 273 
 TYR   0.013   0.001   TYR A 294 
 PHE   0.018   0.001   PHE F 695 
 TRP   0.026   0.001   TRP F 363 
 HIS   0.008   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12320)
  covalent geometry    : angle       0.70466 (16670)
  SS BOND              : bond        0.00314 (   22)
  SS BOND              : angle       1.08388 (   44)
  hydrogen bonds       : bond        0.03459 (  399)
  hydrogen bonds       : angle       6.33804 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 131
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.7873 (m-80) cc_final: 0.6717 (m-80)
REVERT: F  264 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6856 (mm-40)
REVERT: F  275 MET cc_start: 0.8558 (mpp) cc_final: 0.8339 (mpp)
REVERT: A  262 GLU cc_start: 0.7771 (pm20) cc_final: 0.7473 (mm-30)
REVERT: A  475 GLU cc_start: 0.6435 (tt0) cc_final: 0.6213 (tt0)
REVERT: A  753 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7067 (pm20)
REVERT: A  779 GLN cc_start: 0.7236 (tp-100) cc_final: 0.6948 (tp-100)
  outliers start: 41
  outliers final: 25
  residues processed: 163
  average time/residue: 0.0997
  time to fit residues: 24.0894
Evaluate side-chains
  143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  264 GLN
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  400 ILE
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  432 ASN
Chi-restraints excluded: chain F residue  607 VAL
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  660 LEU
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain F residue  695 PHE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  677 ASN
Chi-restraints excluded: chain A residue  753 GLU
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  880 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 99 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 116 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 147 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0040
   overall best weight:    1.5796

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

Flipped N/Q/H residues before XYZ refinement:
F 430 ASN
F 432 ASN
A 357 ASN
A 382 ASN
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.119221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.095765 restraints weight = 44010.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.097575 restraints weight = 22699.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.099462 restraints weight = 13509.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.099831 restraints weight = 9294.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.100204 restraints weight = 8753.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12342  Z= 0.141
  Angle     :  0.705  10.811  16714  Z= 0.353
  Chirality :  0.045   0.213   1754
  Planarity :  0.004   0.053   2197
  Dihedral  :  4.821  30.478   1717
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.34 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 32.99 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.20), residues: 1547
  helix: -0.79 (0.32), residues: 239
  sheet: -0.79 (0.24), residues: 454
  loop : -2.12 (0.20), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 594 
 TYR   0.025   0.001   TYR F 207 
 PHE   0.017   0.001   PHE F 695 
 TRP   0.021   0.002   TRP F 569 
 HIS   0.007   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (12320)
  covalent geometry    : angle       0.70344 (16670)
  SS BOND              : bond        0.00203 (   22)
  SS BOND              : angle       1.07070 (   44)
  hydrogen bonds       : bond        0.03441 (  399)
  hydrogen bonds       : angle       6.22934 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 120
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.7964 (m-80) cc_final: 0.6924 (m-80)
REVERT: F  167 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7568 (pttt)
REVERT: F  264 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6980 (mm-40)
REVERT: A  161 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7599 (mt-10)
REVERT: A  262 GLU cc_start: 0.8153 (pm20) cc_final: 0.7828 (mm-30)
REVERT: A  357 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8216 (t0)
REVERT: A  475 GLU cc_start: 0.6428 (tt0) cc_final: 0.6200 (tt0)
REVERT: A  753 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6973 (pm20)
REVERT: A  779 GLN cc_start: 0.7404 (tp-100) cc_final: 0.7114 (tp-100)
REVERT: A  791 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.5360 (t80)
REVERT: A  816 LYS cc_start: 0.7958 (tppt) cc_final: 0.7696 (tppt)
  outliers start: 51
  outliers final: 35
  residues processed: 159
  average time/residue: 0.0938
  time to fit residues: 22.6977
Evaluate side-chains
  156 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 117
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain F residue  128 MET
Chi-restraints excluded: chain F residue  264 GLN
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  364 CYS
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  432 ASN
Chi-restraints excluded: chain F residue  561 THR
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  660 LEU
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain F residue  689 LEU
Chi-restraints excluded: chain F residue  695 PHE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  357 ASN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  677 ASN
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  753 GLU
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  880 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 13 optimal weight:    0.0070
   chunk 133 optimal weight:    7.9990
   chunk 135 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 62 optimal weight:    0.0980
   chunk 50 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.5600

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

Flipped N/Q/H residues before XYZ refinement:
** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 402 ASN
A 357 ASN
A 540 ASN
A 677 ASN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.121904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.097515 restraints weight = 54650.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.100252 restraints weight = 23794.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.102048 restraints weight = 13509.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.102180 restraints weight = 10018.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.102426 restraints weight = 8772.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3663 r_free = 0.3663    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3663 r_free = 0.3663    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
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   0.040  12342  Z= 0.116
  Angle     :  0.683   9.517  16714  Z= 0.339
  Chirality :  0.044   0.217   1754
  Planarity :  0.004   0.050   2197
  Dihedral  :  4.625  29.147   1717
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.11 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 33.15 %
    Favored  : 63.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.15 (0.20), residues: 1547
  helix: -0.82 (0.31), residues: 239
  sheet: -0.67 (0.24), residues: 448
  loop : -2.07 (0.20), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 594 
 TYR   0.021   0.001   TYR F  87 
 PHE   0.018   0.001   PHE F 695 
 TRP   0.021   0.001   TRP F 283 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (12320)
  covalent geometry    : angle       0.68189 (16670)
  SS BOND              : bond        0.00175 (   22)
  SS BOND              : angle       0.99664 (   44)
  hydrogen bonds       : bond        0.03090 (  399)
  hydrogen bonds       : angle       5.97178 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 137
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8347 (mm)
REVERT: F  155 TYR cc_start: 0.7970 (m-80) cc_final: 0.6975 (m-80)
REVERT: F  167 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7573 (pttt)
REVERT: F  264 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6773 (mm-40)
REVERT: F  378 SER cc_start: 0.9283 (t) cc_final: 0.8647 (p)
REVERT: A  262 GLU cc_start: 0.8084 (pm20) cc_final: 0.7796 (mm-30)
REVERT: A  357 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8137 (t0)
REVERT: A  475 GLU cc_start: 0.6260 (tt0) cc_final: 0.6058 (tt0)
REVERT: A  515 TYR cc_start: 0.7223 (t80) cc_final: 0.6813 (t80)
REVERT: A  677 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8524 (m-40)
REVERT: A  747 VAL cc_start: 0.6985 (t) cc_final: 0.6662 (t)
REVERT: A  753 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6998 (pm20)
REVERT: A  791 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5504 (t80)
  outliers start: 46
  outliers final: 28
  residues processed: 174
  average time/residue: 0.1016
  time to fit residues: 26.0925
Evaluate side-chains
  161 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  128 MET
Chi-restraints excluded: chain F residue  154 LEU
Chi-restraints excluded: chain F residue  264 GLN
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  400 ILE
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  561 THR
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain F residue  695 PHE
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  357 ASN
Chi-restraints excluded: chain A residue  446 CYS
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  677 ASN
Chi-restraints excluded: chain A residue  753 GLU
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  909 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0050
   chunk 52 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9990
   chunk 138 optimal weight:    6.9990
   chunk 133 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 147 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    1.5600

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
A 357 ASN
A 540 ASN
A 677 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.120402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.093787 restraints weight = 70053.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.098308 restraints weight = 29092.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.099886 restraints weight = 13761.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.101251 restraints weight = 9007.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.101323 restraints weight = 7364.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12342  Z= 0.140
  Angle     :  0.686   9.809  16714  Z= 0.344
  Chirality :  0.044   0.231   1754
  Planarity :  0.004   0.052   2197
  Dihedral  :  4.662  29.712   1717
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.34 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 32.28 %
    Favored  : 63.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.14 (0.20), residues: 1547
  helix: -0.76 (0.31), residues: 239
  sheet: -0.79 (0.24), residues: 456
  loop : -2.02 (0.20), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 594 
 TYR   0.016   0.001   TYR F  87 
 PHE   0.024   0.001   PHE A 441 
 TRP   0.022   0.001   TRP F 283 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (12320)
  covalent geometry    : angle       0.68534 (16670)
  SS BOND              : bond        0.00197 (   22)
  SS BOND              : angle       1.03042 (   44)
  hydrogen bonds       : bond        0.03214 (  399)
  hydrogen bonds       : angle       6.05939 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 125
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8322 (mm)
REVERT: F  155 TYR cc_start: 0.8056 (m-80) cc_final: 0.6973 (m-80)
REVERT: F  167 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7594 (pttt)
REVERT: F  264 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6818 (mm-40)
REVERT: F  300 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6581 (tm-30)
REVERT: A  262 GLU cc_start: 0.8022 (pm20) cc_final: 0.7729 (mm-30)
REVERT: A  357 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8130 (t0)
REVERT: A  475 GLU cc_start: 0.6491 (tt0) cc_final: 0.6264 (tt0)
REVERT: A  515 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6923 (t80)
REVERT: A  677 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8018 (t0)
REVERT: A  747 VAL cc_start: 0.7007 (t) cc_final: 0.6700 (t)
REVERT: A  753 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6983 (pm20)
REVERT: A  791 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5567 (t80)
REVERT: A  816 LYS cc_start: 0.8007 (tppt) cc_final: 0.7632 (tppt)
  outliers start: 56
  outliers final: 40
  residues processed: 167
  average time/residue: 0.0936
  time to fit residues: 23.7771
Evaluate side-chains
  168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 120
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain F residue  128 MET
Chi-restraints excluded: chain F residue  154 LEU
Chi-restraints excluded: chain F residue  229 ILE
Chi-restraints excluded: chain F residue  264 GLN
Chi-restraints excluded: chain F residue  300 GLU
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  364 CYS
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  389 SER
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  561 THR
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain F residue  695 PHE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  357 ASN
Chi-restraints excluded: chain A residue  446 CYS
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  515 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  677 ASN
Chi-restraints excluded: chain A residue  753 GLU
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  909 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 115 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 121 optimal weight:    0.7980
   chunk 124 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 357 ASN
A 677 ASN
** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.119449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.092543 restraints weight = 69954.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.097147 restraints weight = 29055.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.099106 restraints weight = 13358.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.100227 restraints weight = 8714.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.100498 restraints weight = 7348.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12342  Z= 0.152
  Angle     :  0.693   9.947  16714  Z= 0.349
  Chirality :  0.044   0.231   1754
  Planarity :  0.004   0.052   2197
  Dihedral  :  4.739  29.338   1717
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.02 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 32.28 %
    Favored  : 63.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.22 (0.20), residues: 1547
  helix: -0.88 (0.31), residues: 243
  sheet: -0.78 (0.25), residues: 442
  loop : -2.09 (0.20), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 286 
 TYR   0.015   0.001   TYR F 207 
 PHE   0.021   0.001   PHE A 441 
 TRP   0.022   0.002   TRP F 283 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12320)
  covalent geometry    : angle       0.69157 (16670)
  SS BOND              : bond        0.00210 (   22)
  SS BOND              : angle       1.06066 (   44)
  hydrogen bonds       : bond        0.03290 (  399)
  hydrogen bonds       : angle       6.12352 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 123
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8360 (mm)
REVERT: F  155 TYR cc_start: 0.8123 (m-80) cc_final: 0.7029 (m-80)
REVERT: F  167 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7592 (pttt)
REVERT: F  264 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6833 (mm-40)
REVERT: F  300 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6739 (tm-30)
REVERT: A   58 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: A  262 GLU cc_start: 0.7998 (pm20) cc_final: 0.7723 (mm-30)
REVERT: A  357 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8192 (t0)
REVERT: A  515 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.7016 (t80)
REVERT: A  747 VAL cc_start: 0.7040 (t) cc_final: 0.6733 (t)
REVERT: A  791 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5432 (t80)
  outliers start: 55
  outliers final: 42
  residues processed: 164
  average time/residue: 0.0953
  time to fit residues: 23.6418
Evaluate side-chains
  167 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 118
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  115 TYR
Chi-restraints excluded: chain F residue  128 MET
Chi-restraints excluded: chain F residue  154 LEU
Chi-restraints excluded: chain F residue  229 ILE
Chi-restraints excluded: chain F residue  264 GLN
Chi-restraints excluded: chain F residue  300 GLU
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  364 CYS
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  389 SER
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  561 THR
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  660 LEU
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  357 ASN
Chi-restraints excluded: chain A residue  446 CYS
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  515 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  677 ASN
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  909 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 90 optimal weight:    0.7980
   chunk 138 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 143 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0970
   chunk 119 optimal weight:    0.0980
   chunk 147 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 ASN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.121773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.094865 restraints weight = 72720.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.099219 restraints weight = 30328.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.101060 restraints weight = 14568.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.102651 restraints weight = 9253.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.102776 restraints weight = 7222.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12342  Z= 0.118
  Angle     :  0.691  11.014  16714  Z= 0.342
  Chirality :  0.044   0.239   1754
  Planarity :  0.004   0.050   2197
  Dihedral  :  4.605  28.719   1717
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 33.23 %
    Favored  : 62.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.18 (0.20), residues: 1547
  helix: -0.92 (0.31), residues: 242
  sheet: -0.65 (0.25), residues: 437
  loop : -2.08 (0.20), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 594 
 TYR   0.013   0.001   TYR F 207 
 PHE   0.025   0.001   PHE A 441 
 TRP   0.026   0.001   TRP F 283 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12320)
  covalent geometry    : angle       0.68995 (16670)
  SS BOND              : bond        0.00182 (   22)
  SS BOND              : angle       1.00240 (   44)
  hydrogen bonds       : bond        0.03001 (  399)
  hydrogen bonds       : angle       5.98087 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 121
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   87 TYR cc_start: 0.9051 (t80) cc_final: 0.8832 (t80)
REVERT: F  155 TYR cc_start: 0.8057 (m-80) cc_final: 0.7753 (m-80)
REVERT: F  167 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7584 (pttt)
REVERT: F  264 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6701 (mm-40)
REVERT: F  300 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6662 (tm-30)
REVERT: A   58 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8059 (mm)
REVERT: A  262 GLU cc_start: 0.7971 (pm20) cc_final: 0.7703 (mm-30)
REVERT: A  515 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6877 (t80)
REVERT: A  747 VAL cc_start: 0.6929 (t) cc_final: 0.6624 (t)
REVERT: A  753 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7208 (pm20)
REVERT: A  791 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5462 (t80)
  outliers start: 46
  outliers final: 34
  residues processed: 156
  average time/residue: 0.0991
  time to fit residues: 23.2832
Evaluate side-chains
  159 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 119
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  128 MET
Chi-restraints excluded: chain F residue  264 GLN
Chi-restraints excluded: chain F residue  300 GLU
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  364 CYS
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  389 SER
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain F residue  689 LEU
Chi-restraints excluded: chain F residue  695 PHE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  446 CYS
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  515 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  638 LEU
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  753 GLU
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  909 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 134 optimal weight:    0.7980
   chunk 0 optimal weight:   30.0000
   chunk 142 optimal weight:   10.0000
   chunk 144 optimal weight:    0.9990
   chunk 120 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 GLN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.121204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.096718 restraints weight = 46463.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.099343 restraints weight = 23667.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.100783 restraints weight = 13123.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.101524 restraints weight = 9896.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.101870 restraints weight = 8512.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12342  Z= 0.124
  Angle     :  0.681  10.074  16714  Z= 0.339
  Chirality :  0.044   0.243   1754
  Planarity :  0.004   0.050   2197
  Dihedral  :  4.519  28.443   1717
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 33.15 %
    Favored  : 62.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.14 (0.20), residues: 1547
  helix: -0.90 (0.31), residues: 241
  sheet: -0.63 (0.24), residues: 442
  loop : -2.06 (0.20), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 587 
 TYR   0.012   0.001   TYR F 207 
 PHE   0.022   0.001   PHE A 441 
 TRP   0.032   0.001   TRP F 283 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12320)
  covalent geometry    : angle       0.67993 (16670)
  SS BOND              : bond        0.00189 (   22)
  SS BOND              : angle       0.99896 (   44)
  hydrogen bonds       : bond        0.03013 (  399)
  hydrogen bonds       : angle       5.93404 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 121
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.8079 (m-80) cc_final: 0.7825 (m-80)
REVERT: F  167 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7548 (pttt)
REVERT: F  264 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6762 (mm-40)
REVERT: F  300 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6668 (tm-30)
REVERT: A   58 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8132 (mm)
REVERT: A  262 GLU cc_start: 0.8003 (pm20) cc_final: 0.7743 (mm-30)
REVERT: A  478 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7362 (mtm110)
REVERT: A  515 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6862 (t80)
REVERT: A  747 VAL cc_start: 0.6948 (t) cc_final: 0.6650 (t)
REVERT: A  753 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7262 (pm20)
REVERT: A  791 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5466 (t80)
REVERT: A  809 MET cc_start: 0.7715 (mmm) cc_final: 0.6979 (mmm)
  outliers start: 47
  outliers final: 36
  residues processed: 159
  average time/residue: 0.1020
  time to fit residues: 24.1426
Evaluate side-chains
  161 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 118
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  113 PHE
Chi-restraints excluded: chain F residue  128 MET
Chi-restraints excluded: chain F residue  264 GLN
Chi-restraints excluded: chain F residue  300 GLU
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  364 CYS
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  389 SER
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  440 THR
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain F residue  689 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  446 CYS
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  478 ARG
Chi-restraints excluded: chain A residue  515 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  753 GLU
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  909 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 141 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0170
   chunk 99 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 834 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.122213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.095208 restraints weight = 79312.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.099761 restraints weight = 32190.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.101990 restraints weight = 15046.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.103173 restraints weight = 9352.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.103602 restraints weight = 7589.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12342  Z= 0.114
  Angle     :  0.699  15.020  16714  Z= 0.343
  Chirality :  0.044   0.246   1754
  Planarity :  0.004   0.049   2197
  Dihedral  :  4.438  27.751   1717
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 33.94 %
    Favored  : 63.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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: -2.06 (0.20), residues: 1547
  helix: -0.91 (0.30), residues: 241
  sheet: -0.60 (0.24), residues: 454
  loop : -1.98 (0.20), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 587 
 TYR   0.011   0.001   TYR F 207 
 PHE   0.024   0.001   PHE A 441 
 TRP   0.037   0.002   TRP F 283 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (12320)
  covalent geometry    : angle       0.69810 (16670)
  SS BOND              : bond        0.00172 (   22)
  SS BOND              : angle       0.96903 (   44)
  hydrogen bonds       : bond        0.02895 (  399)
  hydrogen bonds       : angle       5.82188 ( 1117)

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

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

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3094 Ramachandran restraints generated.
    1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   61 LYS cc_start: 0.7771 (ptpt) cc_final: 0.7544 (ptpt)
REVERT: F  155 TYR cc_start: 0.8067 (m-80) cc_final: 0.7808 (m-80)
REVERT: F  167 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7420 (pttt)
REVERT: A   58 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (mm)
REVERT: A  262 GLU cc_start: 0.7944 (pm20) cc_final: 0.7707 (mm-30)
REVERT: A  515 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6809 (t80)
REVERT: A  747 VAL cc_start: 0.6847 (t) cc_final: 0.6554 (t)
REVERT: A  753 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7387 (pm20)
REVERT: A  791 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5533 (t80)
REVERT: A  809 MET cc_start: 0.7594 (mmm) cc_final: 0.6902 (mmm)
  outliers start: 36
  outliers final: 29
  residues processed: 152
  average time/residue: 0.0901
  time to fit residues: 20.7258
Evaluate side-chains
  154 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  128 MET
Chi-restraints excluded: chain F residue  338 TYR
Chi-restraints excluded: chain F residue  364 CYS
Chi-restraints excluded: chain F residue  374 CYS
Chi-restraints excluded: chain F residue  388 VAL
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  440 THR
Chi-restraints excluded: chain F residue  625 HIS
Chi-restraints excluded: chain F residue  664 ASN
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  446 CYS
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  515 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  753 GLU
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain A residue  804 TRP
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  896 VAL
Chi-restraints excluded: chain A residue  909 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 64 optimal weight:    0.7980
   chunk 118 optimal weight:   10.0000
   chunk 151 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 130 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 148 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 572 ASN
A 357 ASN
** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.119496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.095092 restraints weight = 48056.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.097637 restraints weight = 23011.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.099562 restraints weight = 13089.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.099677 restraints weight = 9696.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.100006 restraints weight = 8509.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12342  Z= 0.152
  Angle     :  0.705  13.526  16714  Z= 0.352
  Chirality :  0.044   0.239   1754
  Planarity :  0.004   0.050   2197
  Dihedral  :  4.585  31.829   1717
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.09 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 33.78 %
    Favored  : 63.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.20), residues: 1547
  helix: -0.90 (0.31), residues: 242
  sheet: -0.70 (0.24), residues: 461
  loop : -1.99 (0.21), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 587 
 TYR   0.013   0.001   TYR A 516 
 PHE   0.019   0.001   PHE A 441 
 TRP   0.033   0.002   TRP F 283 
 HIS   0.006   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (12320)
  covalent geometry    : angle       0.70441 (16670)
  SS BOND              : bond        0.00204 (   22)
  SS BOND              : angle       1.02602 (   44)
  hydrogen bonds       : bond        0.03242 (  399)
  hydrogen bonds       : angle       5.97239 ( 1117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2027.58 seconds
wall clock time: 35 minutes 54.60 seconds (2154.60 seconds total)