Starting phenix.real_space_refine
on Fri Jul  3 05:57:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cdq_45484/07_2026/9cdq_45484_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cdq_45484/07_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_45484/07_2026/9cdq_45484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cdq_45484/07_2026/9cdq_45484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cdq_45484/07_2026/9cdq_45484_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cdq_45484/07_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 4
          Ad-hoc single atom residues: {' FE': 1}
          Unusual residues: {'BCT': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 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: 4.48, per 1000 atoms: 0.37
  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: 0.91
  Conformation dependent library (CDL) restraints added in 923.4 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: 0.36
  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: 2.05

  Time building geometry restraints manager: 1.24 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 3.000
  nonbonded pdb=" OD2 ASP F  82 "
            pdb="FE    FE F 702 "
     model   vdw
     2.074 3.000
  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 3.080
  nonbonded pdb=" O3  BCT F 701 "
            pdb="FE    FE F 702 "
     model   vdw
     2.133 3.000
  ... (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:             1.140
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.320
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
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/Z
  covalent geometry    : bond        0.00333 /  0.17 (12320)
  covalent geometry    : angle       0.86118 /  0.47 (16670)
  SS BOND              : bond        0.00211 /  0.13 (   22)
  SS BOND              : angle       0.94236 /  0.64 (   44)
  hydrogen bonds       : bond        0.14604 / 10.54 (  399)
  hydrogen bonds       : angle       7.68325 /  5.49 ( 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  : 0.396 
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: 0.0957
  time to fit residues: 18.9171
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  : 0.484 
-------------------------------------------------------------------------------
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...
F  33 HIS
** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3883 r_free = 0.3883 target = 0.114414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.088595 restraints weight = 62761.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.092107 restraints weight = 29167.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.094216 restraints weight = 14730.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.095025 restraints weight = 9563.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.095511 restraints weight = 8127.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    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 = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12342  Z= 0.236
  Angle     :  0.788  11.194  16714  Z= 0.403
  Chirality :  0.047   0.267   1754
  Planarity :  0.006   0.061   2197
  Dihedral  :  5.302  32.157   1717
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 10.38 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 31.96 %
    Favored  : 63.69 %
  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: -2.40 (0.20), residues: 1547
  helix: -0.82 (0.31), residues: 241
  sheet: -0.88 (0.24), residues: 461
  loop : -2.30 (0.20), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 286 
 TYR   0.020   0.002   TYR F 115 
 PHE   0.020   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/Z
  covalent geometry    : bond        0.00507 /  0.24 (12320)
  covalent geometry    : angle       0.78604 /  0.40 (16670)
  SS BOND              : bond        0.00280 /  0.18 (   22)
  SS BOND              : angle       1.26094 /  0.79 (   44)
  hydrogen bonds       : bond        0.04361 /  3.04 (  399)
  hydrogen bonds       : angle       6.85071 /  4.88 ( 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
  180 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 126
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  275 MET cc_start: 0.8510 (mpp) cc_final: 0.8158 (mpp)
REVERT: F  581 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8232 (mt)
  outliers start: 54
  outliers final: 33
  residues processed: 168
  average time/residue: 0.0805
  time to fit residues: 20.8043
Evaluate side-chains
  148 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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  337 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  646 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:    0.4980
   chunk 75 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0000
   chunk 50 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 150 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 125 optimal weight:    9.9990
   overall best weight:    1.4188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 430 ASN
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 807 ASN
A 859 HIS
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.119764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.093407 restraints weight = 57530.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.096745 restraints weight = 25836.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.098865 restraints weight = 14999.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.100249 restraints weight = 10176.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.101184 restraints weight = 7741.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1371

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= 0.140
  Angle     :  0.707  10.380  16714  Z= 0.356
  Chirality :  0.045   0.204   1754
  Planarity :  0.005   0.085   2197
  Dihedral  :  4.971  30.476   1717
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.57 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 32.44 %
    Favored  : 63.53 %
  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: -2.29 (0.20), residues: 1547
  helix: -0.81 (0.31), residues: 240
  sheet: -0.78 (0.25), residues: 438
  loop : -2.19 (0.20), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 286 
 TYR   0.013   0.001   TYR A 294 
 PHE   0.018   0.002   PHE F 695 
 TRP   0.024   0.001   TRP F 363 
 HIS   0.008   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.14 (12320)
  covalent geometry    : angle       0.70525 /  0.36 (16670)
  SS BOND              : bond        0.00220 /  0.15 (   22)
  SS BOND              : angle       1.10846 /  0.65 (   44)
  hydrogen bonds       : bond        0.03560 /  2.48 (  399)
  hydrogen bonds       : angle       6.41979 /  4.57 ( 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
  174 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.7915 (m-80) cc_final: 0.6812 (m-80)
REVERT: F  264 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6988 (mm-40)
REVERT: F  275 MET cc_start: 0.8540 (mpp) cc_final: 0.8301 (mpp)
REVERT: A  104 MET cc_start: 0.8410 (mpp) cc_final: 0.8204 (mpp)
REVERT: A  262 GLU cc_start: 0.7783 (pm20) cc_final: 0.7477 (mm-30)
REVERT: A  753 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7075 (pm20)
REVERT: A  779 GLN cc_start: 0.7390 (tp-100) cc_final: 0.7070 (tp-100)
REVERT: A  791 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5442 (t80)
  outliers start: 49
  outliers final: 31
  residues processed: 162
  average time/residue: 0.0992
  time to fit residues: 23.9074
Evaluate side-chains
  146 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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  388 VAL
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  409 SER
Chi-restraints excluded: chain F residue  430 ASN
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  432 ASN
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 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  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  345 VAL
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 124 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 116 optimal weight:   20.0000
   chunk 13 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 147 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 GLN
A 357 ASN
A 382 ASN
A 433 GLN
** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 ASN
** 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 = 0.3857 r_free = 0.3857 target = 0.112756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.088133 restraints weight = 40306.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.091437 restraints weight = 21857.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.092935 restraints weight = 11572.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.093371 restraints weight = 8242.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.093768 restraints weight = 7594.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (14 function evaluations)
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  12342  Z= 0.305
  Angle     :  0.826  11.091  16714  Z= 0.428
  Chirality :  0.048   0.256   1754
  Planarity :  0.006   0.064   2197
  Dihedral  :  5.549  32.521   1717
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 19.17
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 12.26 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 31.57 %
    Favored  : 62.50 %
  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: -2.65 (0.20), residues: 1547
  helix: -0.98 (0.31), residues: 239
  sheet: -1.09 (0.24), residues: 440
  loop : -2.42 (0.20), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 286 
 TYR   0.028   0.002   TYR F 207 
 PHE   0.019   0.003   PHE A 648 
 TRP   0.020   0.003   TRP A 626 
 HIS   0.007   0.002   HIS F 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00657 /  0.31 (12320)
  covalent geometry    : angle       0.82382 /  0.43 (16670)
  SS BOND              : bond        0.00358 /  0.24 (   22)
  SS BOND              : angle       1.37027 /  0.82 (   44)
  hydrogen bonds       : bond        0.04511 /  3.15 (  399)
  hydrogen bonds       : angle       7.00357 /  4.99 ( 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
  188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 115
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.8152 (m-80) cc_final: 0.7822 (m-80)
REVERT: F  264 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7274 (pm20)
REVERT: F  275 MET cc_start: 0.8567 (mpp) cc_final: 0.8276 (mpp)
REVERT: F  442 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.4532 (tt0)
REVERT: A  357 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8327 (t0)
REVERT: A  412 TYR cc_start: 0.6091 (OUTLIER) cc_final: 0.4389 (t80)
REVERT: A  475 GLU cc_start: 0.6563 (tt0) cc_final: 0.6275 (tt0)
REVERT: A  791 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.5764 (t80)
  outliers start: 73
  outliers final: 50
  residues processed: 177
  average time/residue: 0.0922
  time to fit residues: 24.5581
Evaluate side-chains
  166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 111
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
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  158 LEU
Chi-restraints excluded: chain F residue  229 ILE
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  388 VAL
Chi-restraints excluded: chain F residue  396 CYS
Chi-restraints excluded: chain F residue  408 MET
Chi-restraints excluded: chain F residue  409 SER
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  442 GLU
Chi-restraints excluded: chain F residue  561 THR
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 F residue  664 ASN
Chi-restraints excluded: chain F residue  688 SER
Chi-restraints excluded: chain F residue  689 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   86 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  194 THR
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  345 VAL
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  412 TYR
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  446 CYS
Chi-restraints excluded: chain A residue  472 ILE
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  755 TRP
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
Chi-restraints excluded: chain A residue  883 THR
Chi-restraints excluded: chain A residue  896 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 13 optimal weight:    0.0170
   chunk 133 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 100 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0980
   chunk 50 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.1620

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 268 HIS
F 402 ASN
F 432 ASN
A 357 ASN
A 540 ASN
A 677 ASN
** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.118962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.093216 restraints weight = 54966.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.097571 restraints weight = 25298.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.100114 restraints weight = 11437.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.100060 restraints weight = 7937.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.100288 restraints weight = 7156.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3631 r_free = 0.3631    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 = 0.3631 r_free = 0.3631    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)
r_final: 0.3631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12342  Z= 0.136
  Angle     :  0.717   9.714  16714  Z= 0.361
  Chirality :  0.045   0.240   1754
  Planarity :  0.004   0.054   2197
  Dihedral  :  5.066  31.100   1717
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.18 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 33.07 %
    Favored  : 62.58 %
  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: -2.44 (0.20), residues: 1547
  helix: -0.91 (0.31), residues: 239
  sheet: -0.89 (0.25), residues: 442
  loop : -2.29 (0.20), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 186 
 TYR   0.019   0.001   TYR F 207 
 PHE   0.017   0.001   PHE F 695 
 TRP   0.020   0.001   TRP F 363 
 HIS   0.008   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 (12320)
  covalent geometry    : angle       0.71535 /  0.36 (16670)
  SS BOND              : bond        0.00202 /  0.14 (   22)
  SS BOND              : angle       1.11734 /  0.65 (   44)
  hydrogen bonds       : bond        0.03420 /  2.39 (  399)
  hydrogen bonds       : angle       6.42390 /  4.58 ( 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
  174 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 121
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.7998 (m-80) cc_final: 0.6970 (m-80)
REVERT: F  167 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7638 (pttt)
REVERT: F  264 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7010 (mm-40)
REVERT: F  432 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6806 (m-40)
REVERT: A  357 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8185 (t0)
REVERT: A  753 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7130 (pm20)
REVERT: A  791 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.5399 (t80)
  outliers start: 53
  outliers final: 36
  residues processed: 163
  average time/residue: 0.0927
  time to fit residues: 22.6717
Evaluate side-chains
  157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 116
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
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  158 LEU
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  549 VAL
Chi-restraints excluded: chain F residue  561 THR
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  688 SER
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  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  295 THR
Chi-restraints excluded: chain A residue  345 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  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  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:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 137 optimal weight:    0.2980
   chunk 131 optimal weight:    6.9990
   chunk 138 optimal weight:    3.9990
   chunk 133 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 49 optimal weight:   30.0000
   chunk 147 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    2.0386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 357 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.117801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091442 restraints weight = 69724.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.095567 restraints weight = 29276.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.097799 restraints weight = 13888.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.098549 restraints weight = 8806.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.099115 restraints weight = 7529.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (6 function evaluations)
r_final: 0.3611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12342  Z= 0.158
  Angle     :  0.711  10.074  16714  Z= 0.357
  Chirality :  0.045   0.245   1754
  Planarity :  0.004   0.055   2197
  Dihedral  :  4.980  31.647   1717
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.99 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 33.15 %
    Favored  : 62.42 %
  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: -2.44 (0.20), residues: 1547
  helix: -0.91 (0.31), residues: 241
  sheet: -0.88 (0.25), residues: 442
  loop : -2.30 (0.20), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 905 
 TYR   0.018   0.001   TYR F 207 
 PHE   0.016   0.001   PHE F 695 
 TRP   0.022   0.002   TRP F 363 
 HIS   0.007   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 (12320)
  covalent geometry    : angle       0.70917 /  0.36 (16670)
  SS BOND              : bond        0.00216 /  0.14 (   22)
  SS BOND              : angle       1.11210 /  0.65 (   44)
  hydrogen bonds       : bond        0.03463 /  2.41 (  399)
  hydrogen bonds       : angle       6.37085 /  4.56 ( 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
  173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 119
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.8096 (m-80) cc_final: 0.7034 (m-80)
REVERT: F  167 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7655 (pttt)
REVERT: F  264 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7076 (mm-40)
REVERT: F  435 ASP cc_start: 0.7185 (m-30) cc_final: 0.6815 (m-30)
REVERT: A  357 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8199 (t0)
REVERT: A  478 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7503 (mtm110)
REVERT: A  515 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.7036 (t80)
REVERT: A  753 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7129 (pm20)
REVERT: A  791 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.5538 (t80)
  outliers start: 54
  outliers final: 42
  residues processed: 161
  average time/residue: 0.0885
  time to fit residues: 21.1772
Evaluate side-chains
  166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 118
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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  138 HIS
Chi-restraints excluded: chain F residue  158 LEU
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  549 VAL
Chi-restraints excluded: chain F residue  561 THR
Chi-restraints excluded: chain F residue  590 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  688 SER
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   76 ILE
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  345 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  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  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:    0.8980
   chunk 115 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 121 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 111 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   overall best weight:    2.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 432 ASN
A 357 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.117457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.091443 restraints weight = 68784.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.095513 restraints weight = 29219.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.097713 restraints weight = 13922.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.098413 restraints weight = 8885.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.099154 restraints weight = 7565.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    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 = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (6 function evaluations)
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12342  Z= 0.161
  Angle     :  0.713  10.008  16714  Z= 0.359
  Chirality :  0.045   0.241   1754
  Planarity :  0.005   0.056   2197
  Dihedral  :  4.984  30.702   1717
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.47 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 32.83 %
    Favored  : 62.34 %
  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: -2.40 (0.20), residues: 1547
  helix: -0.88 (0.31), residues: 241
  sheet: -0.86 (0.25), residues: 444
  loop : -2.28 (0.20), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 587 
 TYR   0.017   0.001   TYR F 207 
 PHE   0.016   0.002   PHE F 695 
 TRP   0.023   0.002   TRP F 283 
 HIS   0.008   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 (12320)
  covalent geometry    : angle       0.71138 /  0.36 (16670)
  SS BOND              : bond        0.00227 /  0.15 (   22)
  SS BOND              : angle       1.13067 /  0.66 (   44)
  hydrogen bonds       : bond        0.03504 /  2.44 (  399)
  hydrogen bonds       : angle       6.36731 /  4.55 ( 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
  176 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 117
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.8075 (m-80) cc_final: 0.7032 (m-80)
REVERT: F  167 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7649 (pttt)
REVERT: F  264 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7027 (mm-40)
REVERT: F  432 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6811 (m-40)
REVERT: F  553 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6287 (mtpp)
REVERT: A  357 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8125 (t0)
REVERT: A  478 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7512 (mtm110)
REVERT: A  515 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.7040 (t80)
REVERT: A  753 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7182 (pm20)
REVERT: A  791 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.5596 (t80)
  outliers start: 59
  outliers final: 45
  residues processed: 166
  average time/residue: 0.0916
  time to fit residues: 22.4462
Evaluate side-chains
  165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 112
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
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  138 HIS
Chi-restraints excluded: chain F residue  154 LEU
Chi-restraints excluded: chain F residue  158 LEU
Chi-restraints excluded: chain F residue  229 ILE
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  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  432 ASN
Chi-restraints excluded: chain F residue  549 VAL
Chi-restraints excluded: chain F residue  553 LYS
Chi-restraints excluded: chain F residue  561 THR
Chi-restraints excluded: chain F residue  590 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  688 SER
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  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  345 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  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  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  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
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:    6.9990
   chunk 90 optimal weight:    0.9990
   chunk 138 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 143 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0470
   chunk 119 optimal weight:    5.9990
   chunk 147 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   overall best weight:    1.4084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 268 HIS
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 = 0.3973 r_free = 0.3973 target = 0.119146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.092584 restraints weight = 70444.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.096941 restraints weight = 29385.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.099104 restraints weight = 13833.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.099873 restraints weight = 8860.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.100377 restraints weight = 7593.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
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 = 0.00   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 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (6 function evaluations)
r_final: 0.3630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12342  Z= 0.135
  Angle     :  0.703  10.046  16714  Z= 0.351
  Chirality :  0.045   0.254   1754
  Planarity :  0.004   0.054   2197
  Dihedral  :  4.844  30.166   1717
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.15 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 32.99 %
    Favored  : 62.58 %
  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: -2.35 (0.20), residues: 1547
  helix: -0.85 (0.31), residues: 241
  sheet: -0.82 (0.25), residues: 444
  loop : -2.24 (0.20), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 587 
 TYR   0.017   0.001   TYR F 207 
 PHE   0.016   0.001   PHE F 695 
 TRP   0.027   0.001   TRP F 283 
 HIS   0.007   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 (12320)
  covalent geometry    : angle       0.70161 /  0.35 (16670)
  SS BOND              : bond        0.00220 /  0.15 (   22)
  SS BOND              : angle       1.19364 /  0.70 (   44)
  hydrogen bonds       : bond        0.03275 /  2.27 (  399)
  hydrogen bonds       : angle       6.22014 /  4.44 ( 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
  170 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 116
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (mm)
REVERT: F  155 TYR cc_start: 0.8145 (m-80) cc_final: 0.7036 (m-80)
REVERT: F  167 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7536 (pttt)
REVERT: F  264 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7195 (pm20)
REVERT: F  435 ASP cc_start: 0.7106 (m-30) cc_final: 0.6766 (m-30)
REVERT: F  553 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.6243 (mtpp)
REVERT: A  161 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7758 (mt-10)
REVERT: A  357 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8297 (t0)
REVERT: A  463 PHE cc_start: 0.7484 (m-10) cc_final: 0.7166 (m-10)
REVERT: A  478 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7402 (mtm110)
REVERT: A  515 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.7013 (t80)
REVERT: A  753 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7405 (pm20)
REVERT: A  791 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.5383 (t80)
  outliers start: 54
  outliers final: 39
  residues processed: 160
  average time/residue: 0.0852
  time to fit residues: 20.4406
Evaluate side-chains
  159 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 112
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  138 HIS
Chi-restraints excluded: chain F residue  154 LEU
Chi-restraints excluded: chain F residue  158 LEU
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  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  549 VAL
Chi-restraints excluded: chain F residue  553 LYS
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  688 SER
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   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  295 THR
Chi-restraints excluded: chain A residue  345 VAL
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  478 ARG
Chi-restraints excluded: chain A residue  515 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  733 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 134 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 142 optimal weight:    6.9990
   chunk 144 optimal weight:    0.6980
   chunk 120 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 137 optimal weight:    4.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 432 ASN
A 187 GLN
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3930 r_free = 0.3930 target = 0.116447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.092985 restraints weight = 46039.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.094767 restraints weight = 25346.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.096232 restraints weight = 15233.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.096755 restraints weight = 11309.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.097109 restraints weight = 9885.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)
r_final: 0.3581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12342  Z= 0.187
  Angle     :  0.725  10.230  16714  Z= 0.368
  Chirality :  0.046   0.255   1754
  Planarity :  0.005   0.056   2197
  Dihedral  :  4.998  30.300   1717
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.45 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 32.59 %
    Favored  : 62.42 %
  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: -2.45 (0.20), residues: 1547
  helix: -0.93 (0.31), residues: 242
  sheet: -0.88 (0.25), residues: 441
  loop : -2.31 (0.20), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 587 
 TYR   0.018   0.002   TYR F 207 
 PHE   0.016   0.002   PHE F 695 
 TRP   0.028   0.002   TRP F 283 
 HIS   0.008   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.19 (12320)
  covalent geometry    : angle       0.72323 /  0.37 (16670)
  SS BOND              : bond        0.00257 /  0.17 (   22)
  SS BOND              : angle       1.22250 /  0.74 (   44)
  hydrogen bonds       : bond        0.03659 /  2.55 (  399)
  hydrogen bonds       : angle       6.38112 /  4.58 ( 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
  173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 112
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: F  155 TYR cc_start: 0.8116 (m-80) cc_final: 0.7830 (m-80)
REVERT: F  167 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7455 (pttt)
REVERT: F  264 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7273 (pm20)
REVERT: F  553 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.6357 (mtpp)
REVERT: A  478 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7405 (mtm110)
REVERT: A  515 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.7137 (t80)
REVERT: A  753 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7153 (pm20)
REVERT: A  791 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5693 (t80)
  outliers start: 61
  outliers final: 46
  residues processed: 164
  average time/residue: 0.0878
  time to fit residues: 21.4728
Evaluate side-chains
  165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 112
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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  138 HIS
Chi-restraints excluded: chain F residue  154 LEU
Chi-restraints excluded: chain F residue  158 LEU
Chi-restraints excluded: chain F residue  229 ILE
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  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  549 VAL
Chi-restraints excluded: chain F residue  553 LYS
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  688 SER
Chi-restraints excluded: chain F residue  689 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  181 VAL
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  194 THR
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  301 LEU
Chi-restraints excluded: chain A residue  345 VAL
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  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  668 VAL
Chi-restraints excluded: chain A residue  733 ILE
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  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:    0.9980
   chunk 141 optimal weight:    0.5980
   chunk 0 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 60 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 99 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 430 ASN
F 432 ASN
A 357 ASN
A 540 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 = 0.3979 r_free = 0.3979 target = 0.119248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.092404 restraints weight = 79734.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.096876 restraints weight = 31713.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.098845 restraints weight = 14880.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.099724 restraints weight = 9746.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.100168 restraints weight = 8899.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3637
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    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 = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (6 function evaluations)
r_final: 0.3637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2350

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= 0.123
  Angle     :  0.715  14.050  16714  Z= 0.354
  Chirality :  0.045   0.256   1754
  Planarity :  0.004   0.053   2197
  Dihedral  :  4.814  28.929   1717
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.50 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 33.62 %
    Favored  : 62.26 %
  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: -2.36 (0.20), residues: 1547
  helix: -0.92 (0.31), residues: 242
  sheet: -0.73 (0.25), residues: 437
  loop : -2.29 (0.20), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 587 
 TYR   0.015   0.001   TYR F 207 
 PHE   0.014   0.001   PHE A 484 
 TRP   0.030   0.002   TRP F 363 
 HIS   0.008   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (12320)
  covalent geometry    : angle       0.71390 /  0.35 (16670)
  SS BOND              : bond        0.00200 /  0.14 (   22)
  SS BOND              : angle       1.14469 /  0.67 (   44)
  hydrogen bonds       : bond        0.03154 /  2.17 (  399)
  hydrogen bonds       : angle       6.14404 /  4.41 ( 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
  168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 118
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  155 TYR cc_start: 0.8138 (m-80) cc_final: 0.7834 (m-80)
REVERT: F  167 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7517 (pttt)
REVERT: F  264 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7150 (pm20)
REVERT: A  357 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8150 (t0)
REVERT: A  463 PHE cc_start: 0.7416 (m-10) cc_final: 0.7135 (m-10)
REVERT: A  478 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7355 (mtm110)
REVERT: A  515 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6966 (t80)
REVERT: A  753 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7440 (pm20)
REVERT: A  791 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5409 (t80)
  outliers start: 50
  outliers final: 38
  residues processed: 159
  average time/residue: 0.0996
  time to fit residues: 23.7069
Evaluate side-chains
  156 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 112
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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  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  430 ASN
Chi-restraints excluded: chain F residue  431 TYR
Chi-restraints excluded: chain F residue  432 ASN
Chi-restraints excluded: chain F residue  440 THR
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  688 SER
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  295 THR
Chi-restraints excluded: chain A residue  301 LEU
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  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  733 ILE
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   chunk 151 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 130 optimal weight:    7.9990
   chunk 96 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 148 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   overall best weight:    2.3188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 432 ASN
A 357 ASN
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3963 r_free = 0.3963 target = 0.118160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.094133 restraints weight = 48340.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.096518 restraints weight = 23013.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.098103 restraints weight = 13222.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.098562 restraints weight = 10011.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.098848 restraints weight = 8916.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    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 = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (8 function evaluations)
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12342  Z= 0.167
  Angle     :  0.720  13.533  16714  Z= 0.360
  Chirality :  0.045   0.260   1754
  Planarity :  0.004   0.053   2197
  Dihedral  :  4.811  29.763   1717
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.47 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 33.54 %
    Favored  : 62.50 %
  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: -2.36 (0.20), residues: 1547
  helix: -0.90 (0.31), residues: 242
  sheet: -0.82 (0.24), residues: 450
  loop : -2.25 (0.20), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 587 
 TYR   0.016   0.001   TYR F 207 
 PHE   0.026   0.001   PHE A 441 
 TRP   0.029   0.002   TRP F 283 
 HIS   0.008   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.17 (12320)
  covalent geometry    : angle       0.71854 /  0.36 (16670)
  SS BOND              : bond        0.00235 /  0.16 (   22)
  SS BOND              : angle       1.15583 /  0.68 (   44)
  hydrogen bonds       : bond        0.03340 /  2.32 (  399)
  hydrogen bonds       : angle       6.19754 /  4.45 ( 1117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1867.28 seconds
wall clock time: 33 minutes 11.54 seconds (1991.54 seconds total)