Starting phenix.real_space_refine
on Wed Mar  4 21:19:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jkq_22367/03_2026/7jkq_22367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jkq_22367/03_2026/7jkq_22367.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jkq_22367/03_2026/7jkq_22367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jkq_22367/03_2026/7jkq_22367.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jkq_22367/03_2026/7jkq_22367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jkq_22367/03_2026/7jkq_22367.map"
  }
  resolution = 3.3
  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=   0.000 sd=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C   10577      2.51       5
     N    2776      2.21       5
     O    3019      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 123 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16437
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 827, 6650
          Classifications: {'peptide': 827}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 54, 'TRANS': 772}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2153
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 19, 'TRANS': 252}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 1023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1023
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 12, 'TRANS': 114}
    Chain: "D"
      Number of atoms: 6611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 822, 6611
          Classifications: {'peptide': 822}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 53, 'TRANS': 768}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 3.35, per 1000 atoms: 0.20
  Number of scatterers: 16437
  At special positions: 0
  Unit cell: (112.2, 117.15, 149.325, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      65     16.00
     O    3019      8.00
     N    2776      7.00
     C   10577      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 673.5 milliseconds
  

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3834

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 30 sheets defined
      18.9% alpha, 28.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 23
      removed outlier: 4.106A  pdb=" N   ALA A  22 " --> pdb=" O   ASP A  19 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG A  23 " --> pdb=" O   PRO A  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 19 through 23'
    Processing helix  chain 'A' and resid 30 through 42
    Processing helix  chain 'A' and resid 44 through 49
      removed outlier: 3.617A  pdb=" N   VAL A  49 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 250
    Processing helix  chain 'A' and resid 341 through 346
    Processing helix  chain 'A' and resid 382 through 384
      No H-bonds generated for 'chain 'A' and resid 382 through 384'
    Processing helix  chain 'A' and resid 392 through 403
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 583 through 587
      removed outlier: 3.526A  pdb=" N   HIS A 586 " --> pdb=" O   ASP A 583 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 587 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 583 through 587'
    Processing helix  chain 'A' and resid 661 through 671
      removed outlier: 3.728A  pdb=" N   ASN A 665 " --> pdb=" O   TYR A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 691
    Processing helix  chain 'A' and resid 692 through 694
      No H-bonds generated for 'chain 'A' and resid 692 through 694'
    Processing helix  chain 'A' and resid 700 through 716
    Processing helix  chain 'A' and resid 730 through 743
    Processing helix  chain 'A' and resid 763 through 771
      removed outlier: 3.926A  pdb=" N   ARG A 769 " --> pdb=" O   GLY A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 777 through 785
    Processing helix  chain 'A' and resid 786 through 793
      removed outlier: 4.181A  pdb=" N   VAL A 790 " --> pdb=" O   ALA A 787 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   GLU A 791 " --> pdb=" O   LEU A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 827
      removed outlier: 4.141A  pdb=" N   THR A 816 " --> pdb=" O   HIS A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 844 through 863
    Processing helix  chain 'B' and resid 213 through 218
      removed outlier: 3.811A  pdb=" N   HIS B 217 " --> pdb=" O   SER B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 264
      No H-bonds generated for 'chain 'B' and resid 262 through 264'
    Processing helix  chain 'B' and resid 317 through 321
      removed outlier: 3.920A  pdb=" N   LEU B 320 " --> pdb=" O   SER B 317 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ILE B 321 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 317 through 321'
    Processing helix  chain 'B' and resid 348 through 360
    Processing helix  chain 'C' and resid 350 through 359
      removed outlier: 3.926A  pdb=" N   PHE C 354 " --> pdb=" O   GLU C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 362
      No H-bonds generated for 'chain 'C' and resid 360 through 362'
    Processing helix  chain 'D' and resid 19 through 23
      removed outlier: 3.889A  pdb=" N   ARG D  23 " --> pdb=" O   PRO D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 42
    Processing helix  chain 'D' and resid 44 through 49
    Processing helix  chain 'D' and resid 243 through 250
    Processing helix  chain 'D' and resid 341 through 346
    Processing helix  chain 'D' and resid 382 through 384
      No H-bonds generated for 'chain 'D' and resid 382 through 384'
    Processing helix  chain 'D' and resid 392 through 403
    Processing helix  chain 'D' and resid 583 through 587
    Processing helix  chain 'D' and resid 661 through 671
      removed outlier: 3.729A  pdb=" N   ASN D 665 " --> pdb=" O   TYR D 661 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 686 through 691
    Processing helix  chain 'D' and resid 692 through 694
      No H-bonds generated for 'chain 'D' and resid 692 through 694'
    Processing helix  chain 'D' and resid 700 through 716
    Processing helix  chain 'D' and resid 730 through 743
    Processing helix  chain 'D' and resid 763 through 771
      removed outlier: 3.974A  pdb=" N   ARG D 769 " --> pdb=" O   GLY D 765 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   TYR D 770 " --> pdb=" O   TYR D 766 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 777 through 785
    Processing helix  chain 'D' and resid 786 through 793
      removed outlier: 4.081A  pdb=" N   VAL D 790 " --> pdb=" O   ALA D 787 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   GLU D 791 " --> pdb=" O   LEU D 788 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 812 through 827
      removed outlier: 4.295A  pdb=" N   THR D 816 " --> pdb=" O   HIS D 812 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 844 through 863
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60
      removed outlier: 5.975A  pdb=" N   ASP A  55 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   LEU A  75 " --> pdb=" O   ASP A  55 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145
      removed outlier: 4.834A  pdb=" N   LEU A 159 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 193
      removed outlier: 6.629A  pdb=" N   SER A 202 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ILE A 193 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   PHE A 200 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239
    Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 239
      removed outlier: 8.980A  pdb=" N   LEU A 317 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LEU A 338 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   SER A 332 " --> pdb=" O   GLN A 323 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 291
    Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 357
      removed outlier: 6.803A  pdb=" N   MET A 367 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ALA A 355 " --> pdb=" O   TRP A 365 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   TRP A 365 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   TYR A 413 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   VAL A 411 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 445
      removed outlier: 3.616A  pdb=" N   HIS A 453 " --> pdb=" O   ASN A 445 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 496 through 497
      removed outlier: 4.817A  pdb=" N   GLN A 516 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 496 through 497
      removed outlier: 4.817A  pdb=" N   GLN A 516 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 547 through 552
      removed outlier: 6.622A  pdb=" N   VAL A 572 " --> pdb=" O   MET A 595 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   LYS A 576 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 5.388A  pdb=" N   PHE A 591 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER A 578 " --> pdb=" O   PRO A 589 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 609 through 614
      removed outlier: 4.107A  pdb=" N   TYR A 622 " --> pdb=" O   ASP A 678 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ILE A 677 " --> pdb=" O   PHE A 642 " (cutoff:3.500A)
      removed outlier: 10.190A  pdb=" N   HIS A 637 " --> pdb=" O   LEU A 721 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ARG A 723 " --> pdb=" O   HIS A 637 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   TRP A 729 " --> pdb=" O   VAL A 643 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL A 749 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL A 724 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   ILE A 751 " --> pdb=" O   VAL A 724 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE A 726 " --> pdb=" O   ILE A 751 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   GLY A 753 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   GLY A 728 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ALA A 750 " --> pdb=" O   LEU A 801 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   LEU A 803 " --> pdb=" O   ALA A 750 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ALA A 752 " --> pdb=" O   LEU A 803 " (cutoff:3.500A)
      removed outlier: 8.551A  pdb=" N   GLY A 805 " --> pdb=" O   ALA A 752 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 171 through 174
      removed outlier: 7.039A  pdb=" N   ARG B 179 " --> pdb=" O   ILE B 173 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP B 236 " --> pdb=" O   ALA B 210 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU B 234 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 191 through 192
    Processing sheet with id=AB7, first strand: chain 'B' and resid 326 through 334
      removed outlier: 3.834A  pdb=" N   LYS B 345 " --> pdb=" O   HIS B 326 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 396 through 398
    Processing sheet with id=AB9, first strand: chain 'C' and resid 326 through 332
    Processing sheet with id=AC1, first strand: chain 'C' and resid 396 through 399
      removed outlier: 4.165A  pdb=" N   ALA C 380 " --> pdb=" O   ILE C 399 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ARG C 422 " --> pdb=" O   LEU C 439 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   LEU C 439 " --> pdb=" O   ARG C 422 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLY C 424 " --> pdb=" O   LEU C 437 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   LEU C 437 " --> pdb=" O   GLY C 424 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU C 426 " --> pdb=" O   VAL C 435 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 57 through 60
      removed outlier: 3.612A  pdb=" N   HIS D  70 " --> pdb=" O   ILE D  91 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR D  74 " --> pdb=" O   LEU D  87 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 140 through 145
      removed outlier: 6.337A  pdb=" N   SER D 141 " --> pdb=" O   GLN D 154 " (cutoff:3.500A)
      removed outlier: 5.880A  pdb=" N   GLN D 154 " --> pdb=" O   SER D 141 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   SER D 158 " --> pdb=" O   ALA D 155 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 188 through 193
      removed outlier: 6.597A  pdb=" N   SER D 202 " --> pdb=" O   PRO D 191 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   ILE D 193 " --> pdb=" O   PHE D 200 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   PHE D 200 " --> pdb=" O   ILE D 193 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 237 through 239
    Processing sheet with id=AC6, first strand: chain 'D' and resid 237 through 239
      removed outlier: 3.520A  pdb=" N   PHE D 322 " --> pdb=" O   LEU D 273 " (cutoff:3.500A)
      removed outlier: 9.448A  pdb=" N   LEU D 317 " --> pdb=" O   LEU D 338 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   LEU D 338 " --> pdb=" O   LEU D 317 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   SER D 332 " --> pdb=" O   GLN D 323 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 287 through 291
    Processing sheet with id=AC8, first strand: chain 'D' and resid 351 through 355
      removed outlier: 5.482A  pdb=" N   ILE D 352 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU D 369 " --> pdb=" O   ILE D 352 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG D 354 " --> pdb=" O   MET D 367 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TYR D 413 " --> pdb=" O   LEU D 378 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   LEU D 380 " --> pdb=" O   VAL D 411 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   VAL D 411 " --> pdb=" O   LEU D 380 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 427 through 429
      removed outlier: 3.735A  pdb=" N   HIS D 453 " --> pdb=" O   ASN D 445 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU D 454 " --> pdb=" O   ALA D 488 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   ALA D 488 " --> pdb=" O   LEU D 454 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   LYS D 456 " --> pdb=" O   GLU D 486 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLU D 486 " --> pdb=" O   LYS D 456 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   THR D 458 " --> pdb=" O   LYS D 484 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 505 through 507
    Processing sheet with id=AD2, first strand: chain 'D' and resid 547 through 552
      removed outlier: 6.767A  pdb=" N   VAL D 572 " --> pdb=" O   MET D 595 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   LYS D 576 " --> pdb=" O   PHE D 591 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   PHE D 591 " --> pdb=" O   LYS D 576 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   SER D 578 " --> pdb=" O   PRO D 589 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'D' and resid 609 through 614
      removed outlier: 4.213A  pdb=" N   TYR D 622 " --> pdb=" O   ASP D 678 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ILE D 677 " --> pdb=" O   PHE D 642 " (cutoff:3.500A)
      removed outlier: 10.311A  pdb=" N   HIS D 637 " --> pdb=" O   LEU D 721 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ARG D 723 " --> pdb=" O   HIS D 637 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   TRP D 729 " --> pdb=" O   VAL D 643 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   VAL D 749 " --> pdb=" O   SER D 722 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL D 724 " --> pdb=" O   VAL D 749 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   ILE D 751 " --> pdb=" O   VAL D 724 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ILE D 726 " --> pdb=" O   ILE D 751 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   GLY D 753 " --> pdb=" O   ILE D 726 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   GLY D 728 " --> pdb=" O   GLY D 753 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ALA D 750 " --> pdb=" O   LEU D 801 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   LEU D 803 " --> pdb=" O   ALA D 750 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ALA D 752 " --> pdb=" O   LEU D 803 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   GLY D 805 " --> pdb=" O   ALA D 752 " (cutoff:3.500A)

    553 hydrogen bonds defined for protein.
    1488 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: 3.11

  Time building geometry restraints manager: 1.71 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: 4975
        1.34 -     1.46: 3760
        1.46 -     1.58: 8097
        1.58 -     1.70: 0
        1.70 -     1.82: 102
  Bond restraints: 16934
  Sorted by residual:
  bond pdb=" CB  MET D 558 "
       pdb=" CG  MET D 558 "
    ideal  model  delta    sigma   weight residual
    1.520  1.453  0.067 3.00e-02 1.11e+03 4.99e+00
  bond pdb=" N   PRO B 363 "
       pdb=" CA  PRO B 363 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.40e-02 5.10e+03 4.85e+00
  bond pdb=" CG  LEU D 369 "
       pdb=" CD2 LEU D 369 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.43e+00
  bond pdb=" CB  VAL A 786 "
       pdb=" CG2 VAL A 786 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 4.01e+00
  bond pdb=" CB  VAL A 786 "
       pdb=" CG1 VAL A 786 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.94e+00
  ... (remaining 16929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.19: 22343
        3.19 -     6.38: 581
        6.38 -     9.58: 77
        9.58 -    12.77: 14
       12.77 -    15.96: 4
  Bond angle restraints: 23019
  Sorted by residual:
  angle pdb=" N   LYS D 336 "
        pdb=" CA  LYS D 336 "
        pdb=" CB  LYS D 336 "
      ideal   model   delta    sigma   weight residual
     111.37   99.77   11.60 1.82e+00 3.02e-01 4.06e+01
  angle pdb=" CA  LYS D 336 "
        pdb=" CB  LYS D 336 "
        pdb=" CG  LYS D 336 "
      ideal   model   delta    sigma   weight residual
     114.10  126.26  -12.16 2.00e+00 2.50e-01 3.69e+01
  angle pdb=" CB  ARG A 354 "
        pdb=" CG  ARG A 354 "
        pdb=" CD  ARG A 354 "
      ideal   model   delta    sigma   weight residual
     111.30  124.00  -12.70 2.30e+00 1.89e-01 3.05e+01
  angle pdb=" C   MET D 189 "
        pdb=" N   ASP D 190 "
        pdb=" CA  ASP D 190 "
      ideal   model   delta    sigma   weight residual
     122.83  128.25   -5.42 1.08e+00 8.57e-01 2.52e+01
  angle pdb=" CB  MET A 558 "
        pdb=" CG  MET A 558 "
        pdb=" SD  MET A 558 "
      ideal   model   delta    sigma   weight residual
     112.70   98.61   14.09 3.00e+00 1.11e-01 2.20e+01
  ... (remaining 23014 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 8992
       17.99 -    35.97: 814
       35.97 -    53.96: 150
       53.96 -    71.94: 35
       71.94 -    89.93: 16
  Dihedral angle restraints: 10007
    sinusoidal: 4041
      harmonic: 5966
  Sorted by residual:
  dihedral pdb=" CA  TRP D 729 "
           pdb=" C   TRP D 729 "
           pdb=" N   SER D 730 "
           pdb=" CA  SER D 730 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -123.85  -56.15     0      5.00e+00 4.00e-02 1.26e+02
  dihedral pdb=" CA  TRP A 729 "
           pdb=" C   TRP A 729 "
           pdb=" N   SER A 730 "
           pdb=" CA  SER A 730 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -124.38  -55.62     0      5.00e+00 4.00e-02 1.24e+02
  dihedral pdb=" CA  ALA A 599 "
           pdb=" C   ALA A 599 "
           pdb=" N   SER A 600 "
           pdb=" CA  SER A 600 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.61  -33.39     0      5.00e+00 4.00e-02 4.46e+01
  ... (remaining 10004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 2295
       0.139 -    0.278: 128
       0.278 -    0.416: 5
       0.416 -    0.555: 0
       0.555 -    0.694: 2
  Chirality restraints: 2430
  Sorted by residual:
  chirality pdb=" CG  LEU A 803 "
            pdb=" CB  LEU A 803 "
            pdb=" CD1 LEU A 803 "
            pdb=" CD2 LEU A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.90   -0.69 2.00e-01 2.50e+01 1.20e+01
  chirality pdb=" CG  LEU D 664 "
            pdb=" CB  LEU D 664 "
            pdb=" CD1 LEU D 664 "
            pdb=" CD2 LEU D 664 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.02   -0.57 2.00e-01 2.50e+01 8.18e+00
  chirality pdb=" CB  ILE B 418 "
            pdb=" CA  ILE B 418 "
            pdb=" CG1 ILE B 418 "
            pdb=" CG2 ILE B 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.91e+00
  ... (remaining 2427 not shown)

  Planarity restraints: 2987
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 197 "    0.100 5.00e-02 4.00e+02   1.49e-01 3.54e+01
        pdb=" N   PRO D 198 "   -0.257 5.00e-02 4.00e+02
        pdb=" CA  PRO D 198 "    0.082 5.00e-02 4.00e+02
        pdb=" CD  PRO D 198 "    0.076 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D 393 "    0.022 2.00e-02 2.50e+03   4.32e-02 1.87e+01
        pdb=" C   GLU D 393 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   GLU D 393 "    0.028 2.00e-02 2.50e+03
        pdb=" N   GLU D 394 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 543 "   -0.061 5.00e-02 4.00e+02   9.32e-02 1.39e+01
        pdb=" N   PRO D 544 "    0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO D 544 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO D 544 "   -0.050 5.00e-02 4.00e+02
  ... (remaining 2984 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2690
        2.77 -     3.30: 14942
        3.30 -     3.84: 28462
        3.84 -     4.37: 33023
        4.37 -     4.90: 56837
  Nonbonded interactions: 135954
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 259 "
            pdb=" OH  TYR B 322 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OH  TYR A 466 "
            pdb=" OE1 GLU A 478 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OD2 ASP B 262 "
            pdb=" OG  SER B 264 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG  SER D 207 "
            pdb=" OG  SER D 238 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER A 158 "
            pdb=" OE2 GLU A 179 "
     model   vdw
     2.284 3.040
  ... (remaining 135949 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 18 through 114 or (resid 139 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 140 through 863))
  selection = chain 'D'
}

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=0.45 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.580
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.860
  Find NCS groups from input model:        0.220
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
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      :  0.007   0.077  16934  Z= 0.288
  Angle     :  1.219  15.962  23019  Z= 0.659
  Chirality :  0.071   0.694   2430
  Planarity :  0.009   0.149   2987
  Dihedral  : 14.736  89.926   6173
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.19 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.72 %
    Twisted General : 0.21 %

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: -3.03 (0.16), residues: 2034
  helix: -1.57 (0.25), residues: 304
  sheet: -2.17 (0.18), residues: 618
  loop : -2.02 (0.16), residues: 1112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 359 
 TYR   0.050   0.003   TYR D 563 
 PHE   0.044   0.004   PHE B 332 
 TRP   0.047   0.003   TRP D 258 
 HIS   0.018   0.002   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 (16934)
  covalent geometry    : angle       1.21918 (23019)
  hydrogen bonds       : bond        0.12128 (  548)
  hydrogen bonds       : angle       7.97826 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 422
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8125 (mmm) cc_final: 0.7783 (mtp)
REVERT: A  350 GLU cc_start: 0.6878 (tp30) cc_final: 0.6575 (tp30)
REVERT: A  401 ARG cc_start: 0.7685 (mmt90) cc_final: 0.7317 (mmm-85)
REVERT: A  772 ASP cc_start: 0.6596 (m-30) cc_final: 0.6372 (m-30)
REVERT: A  773 VAL cc_start: 0.7259 (t) cc_final: 0.6946 (t)
REVERT: B  189 TRP cc_start: 0.7262 (t-100) cc_final: 0.7028 (t-100)
REVERT: B  372 SER cc_start: 0.7779 (m) cc_final: 0.7313 (p)
REVERT: C  427 VAL cc_start: 0.6952 (t) cc_final: 0.6638 (m)
REVERT: D   42 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6982 (mtt90)
REVERT: D   91 ILE cc_start: 0.8175 (mm) cc_final: 0.7943 (pt)
REVERT: D  108 MET cc_start: 0.6762 (tpt) cc_final: 0.5813 (tmm)
REVERT: D  468 TRP cc_start: 0.7567 (m100) cc_final: 0.7337 (m100)
REVERT: D  809 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6860 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 422
  average time/residue: 0.1272
  time to fit residues: 79.0331
Evaluate side-chains
  281 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 98 optimal weight:    0.0020
   chunk 194 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    9.9990
   chunk 200 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.6980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
A 629 HIS
** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 798 ASN
A 860 GLN
** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
D 516 GLN
D 525 HIS
D 699 GLN
D 840 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.184943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135975 restraints weight = 22010.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 3.13
r_work: 0.3320 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16934  Z= 0.144
  Angle     :  0.663   9.345  23019  Z= 0.346
  Chirality :  0.046   0.219   2430
  Planarity :  0.006   0.087   2987
  Dihedral  :  6.105  51.558   2218
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.19 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.17), residues: 2034
  helix: -0.08 (0.28), residues: 316
  sheet: -1.60 (0.19), residues: 632
  loop : -1.77 (0.17), residues: 1086

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 499 
 TYR   0.025   0.002   TYR B 322 
 PHE   0.015   0.001   PHE B 253 
 TRP   0.034   0.002   TRP A 375 
 HIS   0.006   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (16934)
  covalent geometry    : angle       0.66284 (23019)
  hydrogen bonds       : bond        0.03842 (  548)
  hydrogen bonds       : angle       6.34446 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 316
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7629 (mmtt)
REVERT: A  154 GLN cc_start: 0.8289 (tt0) cc_final: 0.7979 (tt0)
REVERT: A  189 MET cc_start: 0.8340 (mmm) cc_final: 0.7980 (mtm)
REVERT: A  190 ASP cc_start: 0.8401 (t70) cc_final: 0.8087 (t70)
REVERT: A  350 GLU cc_start: 0.7774 (tp30) cc_final: 0.7311 (tp30)
REVERT: A  464 GLN cc_start: 0.7320 (tm-30) cc_final: 0.6820 (tm-30)
REVERT: A  524 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8220 (mt-10)
REVERT: A  604 ASP cc_start: 0.7307 (t0) cc_final: 0.6997 (t0)
REVERT: A  772 ASP cc_start: 0.7352 (m-30) cc_final: 0.7079 (m-30)
REVERT: A  782 GLU cc_start: 0.7922 (pp20) cc_final: 0.7713 (pp20)
REVERT: B  220 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7993 (tt)
REVERT: B  272 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7654 (mmtt)
REVERT: B  345 LYS cc_start: 0.6006 (mmmt) cc_final: 0.5484 (mmmt)
REVERT: B  372 SER cc_start: 0.7967 (m) cc_final: 0.7667 (p)
REVERT: C  427 VAL cc_start: 0.7119 (t) cc_final: 0.6655 (m)
REVERT: D   42 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6772 (mtt90)
REVERT: D   74 TYR cc_start: 0.8164 (p90) cc_final: 0.7605 (p90)
REVERT: D  108 MET cc_start: 0.6625 (tpt) cc_final: 0.5822 (tmm)
REVERT: D  218 GLU cc_start: 0.7679 (tt0) cc_final: 0.7478 (tt0)
REVERT: D  249 GLU cc_start: 0.7303 (mp0) cc_final: 0.6805 (mp0)
REVERT: D  314 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7685 (mtpp)
REVERT: D  375 TRP cc_start: 0.8455 (t60) cc_final: 0.7599 (t60)
REVERT: D  468 TRP cc_start: 0.7730 (m100) cc_final: 0.7263 (m100)
REVERT: D  661 TYR cc_start: 0.8931 (m-80) cc_final: 0.8278 (m-80)
REVERT: D  688 ARG cc_start: 0.8367 (tpp80) cc_final: 0.8092 (mmm-85)
REVERT: D  809 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: D  817 ASN cc_start: 0.8929 (m-40) cc_final: 0.8699 (m-40)
  outliers start: 23
  outliers final: 17
  residues processed: 326
  average time/residue: 0.1291
  time to fit residues: 62.6303
Evaluate side-chains
  294 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 275
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  355 HIS
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain D residue  314 LYS
Chi-restraints excluded: chain D residue  407 VAL
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  721 LEU
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  786 VAL
Chi-restraints excluded: chain D residue  811 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 193 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 131 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 173 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 109 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 156 optimal weight:    6.9990
   chunk 90 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS
A 573 HIS
** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 840 HIS
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 377 GLN
D 464 GLN
D 573 HIS
D 840 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.177437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.128168 restraints weight = 22453.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.35
r_work: 0.3207 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  16934  Z= 0.291
  Angle     :  0.721  10.751  23019  Z= 0.373
  Chirality :  0.049   0.308   2430
  Planarity :  0.006   0.075   2987
  Dihedral  :  5.967  43.821   2218
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.16 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.17), residues: 2034
  helix: -0.05 (0.28), residues: 317
  sheet: -1.45 (0.19), residues: 643
  loop : -1.55 (0.18), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 499 
 TYR   0.024   0.003   TYR B 322 
 PHE   0.021   0.002   PHE B 253 
 TRP   0.043   0.003   TRP A 375 
 HIS   0.012   0.002   HIS A 804 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 (16934)
  covalent geometry    : angle       0.72084 (23019)
  hydrogen bonds       : bond        0.04137 (  548)
  hydrogen bonds       : angle       6.12842 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 285
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8089 (mmtt)
REVERT: A  151 PHE cc_start: 0.8969 (m-80) cc_final: 0.8633 (m-80)
REVERT: A  154 GLN cc_start: 0.8462 (tt0) cc_final: 0.8221 (tt0)
REVERT: A  189 MET cc_start: 0.8413 (mmm) cc_final: 0.8033 (mtm)
REVERT: A  190 ASP cc_start: 0.8488 (t70) cc_final: 0.8196 (t0)
REVERT: A  350 GLU cc_start: 0.8146 (tp30) cc_final: 0.7875 (tp30)
REVERT: A  378 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8730 (tt)
REVERT: A  464 GLN cc_start: 0.7529 (tm-30) cc_final: 0.6923 (tm-30)
REVERT: A  604 ASP cc_start: 0.7804 (t0) cc_final: 0.7469 (t0)
REVERT: A  616 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7980 (mtt-85)
REVERT: A  772 ASP cc_start: 0.7400 (m-30) cc_final: 0.7135 (m-30)
REVERT: A  844 CYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8262 (t)
REVERT: B  190 TYR cc_start: 0.6277 (m-10) cc_final: 0.5969 (m-10)
REVERT: B  223 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7589 (mp10)
REVERT: B  272 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7843 (mmtt)
REVERT: B  352 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7536 (m-30)
REVERT: B  372 SER cc_start: 0.8074 (m) cc_final: 0.7695 (p)
REVERT: B  438 GLN cc_start: 0.2417 (OUTLIER) cc_final: 0.1990 (mp10)
REVERT: D   42 ARG cc_start: 0.7216 (mtm-85) cc_final: 0.6828 (mtt90)
REVERT: D  108 MET cc_start: 0.6592 (tpt) cc_final: 0.5817 (tmm)
REVERT: D  192 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8627 (mtmt)
REVERT: D  375 TRP cc_start: 0.8619 (t60) cc_final: 0.8295 (t60)
REVERT: D  468 TRP cc_start: 0.7867 (m100) cc_final: 0.7260 (m100)
REVERT: D  660 LYS cc_start: 0.8533 (pptt) cc_final: 0.8292 (pttt)
REVERT: D  772 ASP cc_start: 0.7502 (p0) cc_final: 0.7275 (p0)
REVERT: D  846 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7820 (mt-10)
  outliers start: 55
  outliers final: 28
  residues processed: 323
  average time/residue: 0.1282
  time to fit residues: 61.4877
Evaluate side-chains
  298 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 265
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  791 GLU
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  223 GLN
Chi-restraints excluded: chain B residue  262 ASP
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  407 VAL
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain D residue  834 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 126 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 197 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 193 optimal weight:    0.8980
   chunk 144 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 665 ASN
A 840 HIS
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 815 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.179930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.131712 restraints weight = 22105.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 3.16
r_work: 0.3233 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16934  Z= 0.167
  Angle     :  0.623   8.808  23019  Z= 0.322
  Chirality :  0.046   0.282   2430
  Planarity :  0.005   0.071   2987
  Dihedral  :  5.684  41.885   2218
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.56 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.18), residues: 2034
  helix:  0.30 (0.30), residues: 316
  sheet: -1.12 (0.20), residues: 625
  loop : -1.48 (0.18), residues: 1093

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 499 
 TYR   0.023   0.002   TYR B 322 
 PHE   0.015   0.001   PHE B 253 
 TRP   0.036   0.002   TRP A 375 
 HIS   0.005   0.001   HIS A 804 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (16934)
  covalent geometry    : angle       0.62266 (23019)
  hydrogen bonds       : bond        0.03503 (  548)
  hydrogen bonds       : angle       5.82659 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 297
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7226 (t-90)
REVERT: A   43 LYS cc_start: 0.8304 (mmmt) cc_final: 0.8090 (mmtp)
REVERT: A  151 PHE cc_start: 0.8941 (m-80) cc_final: 0.8657 (m-80)
REVERT: A  154 GLN cc_start: 0.8460 (tt0) cc_final: 0.8231 (tt0)
REVERT: A  189 MET cc_start: 0.8327 (mmm) cc_final: 0.7948 (mtm)
REVERT: A  190 ASP cc_start: 0.8445 (t70) cc_final: 0.8150 (t0)
REVERT: A  210 TRP cc_start: 0.8227 (m100) cc_final: 0.8011 (m100)
REVERT: A  277 TYR cc_start: 0.9055 (p90) cc_final: 0.8852 (p90)
REVERT: A  464 GLN cc_start: 0.7574 (tm-30) cc_final: 0.6964 (tm-30)
REVERT: A  604 ASP cc_start: 0.7768 (t0) cc_final: 0.7445 (t0)
REVERT: A  703 GLU cc_start: 0.8309 (tp30) cc_final: 0.8057 (mm-30)
REVERT: A  772 ASP cc_start: 0.7352 (m-30) cc_final: 0.7078 (m-30)
REVERT: A  809 GLU cc_start: 0.8304 (pm20) cc_final: 0.7974 (pm20)
REVERT: A  844 CYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8180 (t)
REVERT: B  190 TYR cc_start: 0.6446 (m-10) cc_final: 0.6115 (m-10)
REVERT: B  272 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7815 (mmtt)
REVERT: B  352 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7513 (m-30)
REVERT: B  372 SER cc_start: 0.8004 (m) cc_final: 0.7602 (p)
REVERT: B  438 GLN cc_start: 0.2418 (OUTLIER) cc_final: 0.2127 (mp10)
REVERT: D   42 ARG cc_start: 0.7134 (mtm-85) cc_final: 0.6828 (mtt90)
REVERT: D  108 MET cc_start: 0.6642 (tpt) cc_final: 0.5822 (tmm)
REVERT: D  375 TRP cc_start: 0.8534 (t60) cc_final: 0.7616 (t60)
REVERT: D  468 TRP cc_start: 0.7845 (m100) cc_final: 0.7395 (m100)
REVERT: D  556 PHE cc_start: 0.9076 (m-80) cc_final: 0.8803 (m-80)
REVERT: D  609 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8277 (mt-10)
REVERT: D  660 LYS cc_start: 0.8447 (pptt) cc_final: 0.8129 (pttt)
REVERT: D  771 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.6840 (mmm)
REVERT: D  772 ASP cc_start: 0.7443 (p0) cc_final: 0.7219 (p0)
REVERT: D  846 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7779 (mt-10)
REVERT: D  861 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7703 (mm-30)
  outliers start: 57
  outliers final: 33
  residues processed: 330
  average time/residue: 0.1246
  time to fit residues: 61.5402
Evaluate side-chains
  312 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 274
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 ASP
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  337 GLU
Chi-restraints excluded: chain D residue  378 LEU
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  697 MET
Chi-restraints excluded: chain D residue  721 LEU
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  811 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 127 optimal weight:    0.0970
   chunk 58 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 92 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 141 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 742 HIS
A 798 ASN
A 840 HIS
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 665 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.181811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.124994 restraints weight = 21975.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.91
r_work: 0.3266 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16934  Z= 0.129
  Angle     :  0.603   8.363  23019  Z= 0.310
  Chirality :  0.045   0.184   2430
  Planarity :  0.005   0.072   2987
  Dihedral  :  5.440  40.537   2218
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.45 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.18), residues: 2034
  helix:  0.51 (0.30), residues: 316
  sheet: -0.85 (0.21), residues: 599
  loop : -1.46 (0.18), residues: 1119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 499 
 TYR   0.022   0.002   TYR B 322 
 PHE   0.014   0.001   PHE B 253 
 TRP   0.055   0.002   TRP A 375 
 HIS   0.004   0.001   HIS D 815 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (16934)
  covalent geometry    : angle       0.60281 (23019)
  hydrogen bonds       : bond        0.03235 (  548)
  hydrogen bonds       : angle       5.60281 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 297
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7182 (t-90)
REVERT: A   43 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8127 (mmtp)
REVERT: A   68 HIS cc_start: 0.8124 (m-70) cc_final: 0.7844 (m-70)
REVERT: A  151 PHE cc_start: 0.8897 (m-80) cc_final: 0.8629 (m-80)
REVERT: A  154 GLN cc_start: 0.8413 (tt0) cc_final: 0.8198 (tt0)
REVERT: A  189 MET cc_start: 0.8308 (mmm) cc_final: 0.7938 (mtm)
REVERT: A  190 ASP cc_start: 0.8422 (t70) cc_final: 0.8112 (t0)
REVERT: A  350 GLU cc_start: 0.8289 (tp30) cc_final: 0.7986 (tp30)
REVERT: A  378 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8700 (tt)
REVERT: A  464 GLN cc_start: 0.7553 (tm-30) cc_final: 0.6945 (tm-30)
REVERT: A  604 ASP cc_start: 0.7750 (t0) cc_final: 0.7233 (t0)
REVERT: A  703 GLU cc_start: 0.8277 (tp30) cc_final: 0.8038 (mm-30)
REVERT: A  772 ASP cc_start: 0.7268 (m-30) cc_final: 0.7007 (m-30)
REVERT: A  809 GLU cc_start: 0.8253 (pm20) cc_final: 0.7872 (pm20)
REVERT: A  844 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8140 (t)
REVERT: B  190 TYR cc_start: 0.6614 (m-10) cc_final: 0.6216 (m-10)
REVERT: B  272 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7909 (mmtt)
REVERT: B  274 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7198 (mm-30)
REVERT: B  352 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7485 (m-30)
REVERT: B  372 SER cc_start: 0.7968 (m) cc_final: 0.7540 (p)
REVERT: B  438 GLN cc_start: 0.2642 (OUTLIER) cc_final: 0.2349 (mp10)
REVERT: D   42 ARG cc_start: 0.7080 (mtm-85) cc_final: 0.6756 (mtt90)
REVERT: D  108 MET cc_start: 0.6732 (tpt) cc_final: 0.5826 (tmm)
REVERT: D  192 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8593 (mttt)
REVERT: D  336 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7619 (mmmm)
REVERT: D  375 TRP cc_start: 0.8494 (t60) cc_final: 0.8197 (t60)
REVERT: D  468 TRP cc_start: 0.7788 (m100) cc_final: 0.7418 (m100)
REVERT: D  609 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8276 (mt-10)
REVERT: D  660 LYS cc_start: 0.8444 (pttt) cc_final: 0.8177 (pttt)
REVERT: D  771 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.6856 (mmm)
REVERT: D  846 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7800 (mt-10)
REVERT: D  861 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7645 (mm-30)
  outliers start: 55
  outliers final: 38
  residues processed: 326
  average time/residue: 0.1212
  time to fit residues: 59.4252
Evaluate side-chains
  319 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 274
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  791 GLU
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  336 LYS
Chi-restraints excluded: chain D residue  337 GLU
Chi-restraints excluded: chain D residue  378 LEU
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  560 VAL
Chi-restraints excluded: chain D residue  624 MET
Chi-restraints excluded: chain D residue  697 MET
Chi-restraints excluded: chain D residue  709 LEU
Chi-restraints excluded: chain D residue  721 LEU
Chi-restraints excluded: chain D residue  771 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 169 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 193 optimal weight:    0.1980
   chunk 67 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 159 optimal weight:    0.9980
   chunk 165 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 131 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS
A 798 ASN
A 840 HIS
A 860 GLN
** B 324 HIS ** 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 = 0.4057 r_free = 0.4057 target = 0.179743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.128714 restraints weight = 22043.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 3.24
r_work: 0.3228 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16934  Z= 0.171
  Angle     :  0.609   9.014  23019  Z= 0.313
  Chirality :  0.045   0.194   2430
  Planarity :  0.005   0.071   2987
  Dihedral  :  5.382  40.071   2218
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 15.12 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.18), residues: 2034
  helix:  0.48 (0.30), residues: 322
  sheet: -0.82 (0.21), residues: 606
  loop : -1.42 (0.18), residues: 1106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 499 
 TYR   0.027   0.002   TYR A 277 
 PHE   0.016   0.001   PHE B 253 
 TRP   0.062   0.002   TRP A 375 
 HIS   0.006   0.001   HIS A 804 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (16934)
  covalent geometry    : angle       0.60884 (23019)
  hydrogen bonds       : bond        0.03315 (  548)
  hydrogen bonds       : angle       5.52418 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 276
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7485 (t-90)
REVERT: A  103 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8810 (mm)
REVERT: A  151 PHE cc_start: 0.8922 (m-80) cc_final: 0.8639 (m-80)
REVERT: A  154 GLN cc_start: 0.8428 (tt0) cc_final: 0.8227 (tt0)
REVERT: A  175 MET cc_start: 0.8381 (pmm) cc_final: 0.7727 (ptp)
REVERT: A  189 MET cc_start: 0.8334 (mmm) cc_final: 0.7963 (mtm)
REVERT: A  190 ASP cc_start: 0.8487 (t70) cc_final: 0.8146 (t0)
REVERT: A  327 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7908 (tm-30)
REVERT: A  350 GLU cc_start: 0.8383 (tp30) cc_final: 0.8083 (tp30)
REVERT: A  378 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8677 (tt)
REVERT: A  464 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7045 (tm-30)
REVERT: A  604 ASP cc_start: 0.7816 (t0) cc_final: 0.7403 (t0)
REVERT: A  703 GLU cc_start: 0.8309 (tp30) cc_final: 0.8061 (mm-30)
REVERT: A  809 GLU cc_start: 0.8287 (pm20) cc_final: 0.7883 (pm20)
REVERT: A  844 CYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8206 (t)
REVERT: B  190 TYR cc_start: 0.6642 (m-10) cc_final: 0.6193 (m-10)
REVERT: B  261 VAL cc_start: 0.4082 (OUTLIER) cc_final: 0.3755 (t)
REVERT: B  272 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7884 (mmtt)
REVERT: B  352 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (m-30)
REVERT: B  372 SER cc_start: 0.7973 (m) cc_final: 0.7551 (p)
REVERT: B  438 GLN cc_start: 0.2688 (OUTLIER) cc_final: 0.2391 (mp10)
REVERT: D  108 MET cc_start: 0.6743 (tpt) cc_final: 0.5795 (tmm)
REVERT: D  192 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8650 (mttt)
REVERT: D  249 GLU cc_start: 0.7296 (mp0) cc_final: 0.6850 (mp0)
REVERT: D  314 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7662 (mtpp)
REVERT: D  336 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7654 (mmmm)
REVERT: D  375 TRP cc_start: 0.8564 (t60) cc_final: 0.7944 (t60)
REVERT: D  468 TRP cc_start: 0.7791 (m100) cc_final: 0.7318 (m100)
REVERT: D  609 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8310 (mt-10)
REVERT: D  771 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.6968 (mmm)
REVERT: D  852 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: D  861 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7706 (mm-30)
  outliers start: 68
  outliers final: 45
  residues processed: 317
  average time/residue: 0.1264
  time to fit residues: 59.9321
Evaluate side-chains
  317 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 262
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  816 THR
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  314 LYS
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  336 LYS
Chi-restraints excluded: chain D residue  337 GLU
Chi-restraints excluded: chain D residue  378 LEU
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  560 VAL
Chi-restraints excluded: chain D residue  624 MET
Chi-restraints excluded: chain D residue  697 MET
Chi-restraints excluded: chain D residue  709 LEU
Chi-restraints excluded: chain D residue  721 LEU
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain D residue  834 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 157 optimal weight:    0.5980
   chunk 176 optimal weight:    7.9990
   chunk 191 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0070
   chunk 178 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 119 optimal weight:    9.9990
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 555 ASN
A 798 ASN
A 840 HIS
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 555 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.181541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.130610 restraints weight = 21912.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 3.37
r_work: 0.3238 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16934  Z= 0.127
  Angle     :  0.586   8.262  23019  Z= 0.301
  Chirality :  0.044   0.158   2430
  Planarity :  0.005   0.063   2987
  Dihedral  :  5.203  39.821   2218
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.35 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.18), residues: 2034
  helix:  0.72 (0.30), residues: 316
  sheet: -0.73 (0.21), residues: 597
  loop : -1.38 (0.18), residues: 1121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 499 
 TYR   0.022   0.001   TYR A 277 
 PHE   0.014   0.001   PHE B 253 
 TRP   0.062   0.002   TRP A 375 
 HIS   0.004   0.001   HIS D 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (16934)
  covalent geometry    : angle       0.58631 (23019)
  hydrogen bonds       : bond        0.03112 (  548)
  hydrogen bonds       : angle       5.40678 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 287
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A   39 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7424 (t-90)
REVERT: A  175 MET cc_start: 0.8356 (pmm) cc_final: 0.7761 (ptp)
REVERT: A  189 MET cc_start: 0.8345 (mmm) cc_final: 0.7967 (mtm)
REVERT: A  190 ASP cc_start: 0.8481 (t70) cc_final: 0.8140 (t0)
REVERT: A  327 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: A  464 GLN cc_start: 0.7592 (tm-30) cc_final: 0.6934 (tm-30)
REVERT: A  604 ASP cc_start: 0.7766 (t0) cc_final: 0.7317 (t0)
REVERT: A  703 GLU cc_start: 0.8290 (tp30) cc_final: 0.8044 (mm-30)
REVERT: A  844 CYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7780 (t)
REVERT: A  846 GLU cc_start: 0.8245 (pm20) cc_final: 0.7869 (pm20)
REVERT: B  190 TYR cc_start: 0.6737 (m-10) cc_final: 0.6271 (m-10)
REVERT: B  261 VAL cc_start: 0.4022 (OUTLIER) cc_final: 0.3706 (t)
REVERT: B  372 SER cc_start: 0.8001 (m) cc_final: 0.7535 (p)
REVERT: B  438 GLN cc_start: 0.2660 (OUTLIER) cc_final: 0.1485 (mt0)
REVERT: D  108 MET cc_start: 0.6778 (tpt) cc_final: 0.6154 (tmm)
REVERT: D  181 LYS cc_start: 0.8231 (tptp) cc_final: 0.7585 (mmmt)
REVERT: D  249 GLU cc_start: 0.7280 (mp0) cc_final: 0.6732 (mp0)
REVERT: D  314 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7681 (mtpp)
REVERT: D  336 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7621 (mmmm)
REVERT: D  375 TRP cc_start: 0.8494 (t60) cc_final: 0.8225 (t60)
REVERT: D  468 TRP cc_start: 0.7703 (m100) cc_final: 0.7315 (m100)
REVERT: D  609 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8338 (mt-10)
REVERT: D  771 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.6897 (mmm)
REVERT: D  852 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7983 (mt-10)
REVERT: D  861 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7646 (mm-30)
  outliers start: 63
  outliers final: 45
  residues processed: 327
  average time/residue: 0.1226
  time to fit residues: 60.3298
Evaluate side-chains
  321 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 269
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  329 LYS
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  816 THR
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  267 SER
Chi-restraints excluded: chain D residue  314 LYS
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  336 LYS
Chi-restraints excluded: chain D residue  337 GLU
Chi-restraints excluded: chain D residue  378 LEU
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  560 VAL
Chi-restraints excluded: chain D residue  624 MET
Chi-restraints excluded: chain D residue  697 MET
Chi-restraints excluded: chain D residue  721 LEU
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain D residue  841 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 155 optimal weight:    0.7980
   chunk 91 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   chunk 124 optimal weight:    5.9990
   chunk 158 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A  68 HIS
A 555 ASN
A 798 ASN
A 840 HIS
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 213 ASN
D 555 ASN
D 815 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.180276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.123805 restraints weight = 22040.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.89
r_work: 0.3253 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16934  Z= 0.164
  Angle     :  0.612   9.860  23019  Z= 0.312
  Chirality :  0.045   0.174   2430
  Planarity :  0.005   0.067   2987
  Dihedral  :  5.216  39.685   2218
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 16.97 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.18), residues: 2034
  helix:  0.72 (0.30), residues: 316
  sheet: -0.73 (0.21), residues: 597
  loop : -1.33 (0.18), residues: 1121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 499 
 TYR   0.022   0.002   TYR D 514 
 PHE   0.016   0.001   PHE B 253 
 TRP   0.072   0.002   TRP A 375 
 HIS   0.005   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (16934)
  covalent geometry    : angle       0.61189 (23019)
  hydrogen bonds       : bond        0.03216 (  548)
  hydrogen bonds       : angle       5.41454 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 276
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7456 (t-90)
REVERT: A  151 PHE cc_start: 0.8905 (m-80) cc_final: 0.8618 (m-80)
REVERT: A  154 GLN cc_start: 0.8386 (tt0) cc_final: 0.8146 (tt0)
REVERT: A  175 MET cc_start: 0.8357 (pmm) cc_final: 0.7774 (ptp)
REVERT: A  189 MET cc_start: 0.8363 (mmm) cc_final: 0.7985 (mtm)
REVERT: A  190 ASP cc_start: 0.8521 (t70) cc_final: 0.8173 (t0)
REVERT: A  327 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: A  464 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7019 (tm-30)
REVERT: A  604 ASP cc_start: 0.7787 (t0) cc_final: 0.7353 (t0)
REVERT: A  620 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7170 (ttp-170)
REVERT: A  703 GLU cc_start: 0.8302 (tp30) cc_final: 0.8061 (mm-30)
REVERT: A  844 CYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8235 (t)
REVERT: B  190 TYR cc_start: 0.6792 (m-10) cc_final: 0.6341 (m-80)
REVERT: B  261 VAL cc_start: 0.4045 (OUTLIER) cc_final: 0.3721 (t)
REVERT: B  334 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5568 (tt)
REVERT: B  438 GLN cc_start: 0.2606 (OUTLIER) cc_final: 0.1403 (mt0)
REVERT: D  108 MET cc_start: 0.7155 (tpt) cc_final: 0.6171 (tmm)
REVERT: D  181 LYS cc_start: 0.8206 (tptp) cc_final: 0.7562 (mmmt)
REVERT: D  314 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7737 (mtpp)
REVERT: D  336 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7623 (mmmm)
REVERT: D  375 TRP cc_start: 0.8504 (t60) cc_final: 0.8245 (t60)
REVERT: D  413 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7836 (t80)
REVERT: D  468 TRP cc_start: 0.7732 (m100) cc_final: 0.7343 (m100)
REVERT: D  609 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8328 (mt-10)
REVERT: D  771 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.6979 (mmm)
REVERT: D  825 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7963 (mtm-85)
REVERT: D  861 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7677 (mm-30)
  outliers start: 69
  outliers final: 48
  residues processed: 320
  average time/residue: 0.1272
  time to fit residues: 60.8559
Evaluate side-chains
  327 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 269
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  620 ARG
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  267 SER
Chi-restraints excluded: chain D residue  314 LYS
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  336 LYS
Chi-restraints excluded: chain D residue  337 GLU
Chi-restraints excluded: chain D residue  378 LEU
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  560 VAL
Chi-restraints excluded: chain D residue  624 MET
Chi-restraints excluded: chain D residue  682 SER
Chi-restraints excluded: chain D residue  697 MET
Chi-restraints excluded: chain D residue  709 LEU
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  786 VAL
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain D residue  834 ILE
Chi-restraints excluded: chain D residue  841 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 160 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 199 optimal weight:    0.5980
   chunk 154 optimal weight:    0.9980
   chunk 145 optimal weight:    0.0870
   chunk 176 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 144 optimal weight:    0.7980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A  68 HIS
A 161 HIS
A 377 GLN
A 555 ASN
A 798 ASN
A 840 HIS
** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 555 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.180059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.128799 restraints weight = 22239.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 3.34
r_work: 0.3240 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16934  Z= 0.137
  Angle     :  0.605   9.581  23019  Z= 0.307
  Chirality :  0.045   0.155   2430
  Planarity :  0.005   0.076   2987
  Dihedral  :  5.148  39.575   2218
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.69 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.18), residues: 2034
  helix:  0.75 (0.30), residues: 317
  sheet: -0.70 (0.22), residues: 581
  loop : -1.34 (0.18), residues: 1136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D 499 
 TYR   0.020   0.001   TYR A 277 
 PHE   0.015   0.001   PHE B 253 
 TRP   0.069   0.002   TRP A 375 
 HIS   0.006   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (16934)
  covalent geometry    : angle       0.60480 (23019)
  hydrogen bonds       : bond        0.03139 (  548)
  hydrogen bonds       : angle       5.37355 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 283
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7480 (t-90)
REVERT: A  151 PHE cc_start: 0.8900 (m-80) cc_final: 0.8606 (m-80)
REVERT: A  154 GLN cc_start: 0.8411 (tt0) cc_final: 0.8168 (tt0)
REVERT: A  175 MET cc_start: 0.8356 (pmm) cc_final: 0.7777 (ptp)
REVERT: A  189 MET cc_start: 0.8383 (mmm) cc_final: 0.8001 (mtm)
REVERT: A  190 ASP cc_start: 0.8529 (t70) cc_final: 0.8157 (t0)
REVERT: A  350 GLU cc_start: 0.8502 (tp30) cc_final: 0.8204 (tp30)
REVERT: A  464 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7008 (tm-30)
REVERT: A  604 ASP cc_start: 0.7779 (t0) cc_final: 0.7375 (t0)
REVERT: A  620 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7130 (ttp-170)
REVERT: A  703 GLU cc_start: 0.8311 (tp30) cc_final: 0.8070 (mm-30)
REVERT: A  844 CYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7754 (t)
REVERT: B  222 LEU cc_start: 0.8327 (mt) cc_final: 0.7913 (mt)
REVERT: B  261 VAL cc_start: 0.4055 (OUTLIER) cc_final: 0.3726 (t)
REVERT: B  334 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5563 (tt)
REVERT: B  438 GLN cc_start: 0.2767 (OUTLIER) cc_final: 0.1499 (mt0)
REVERT: C  427 VAL cc_start: 0.6752 (t) cc_final: 0.6285 (m)
REVERT: D  181 LYS cc_start: 0.8192 (tptp) cc_final: 0.7556 (mmmt)
REVERT: D  314 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7707 (mtpp)
REVERT: D  336 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7602 (mmmm)
REVERT: D  413 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7810 (t80)
REVERT: D  468 TRP cc_start: 0.7684 (m100) cc_final: 0.7325 (m100)
REVERT: D  609 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8350 (mt-10)
REVERT: D  771 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7861 (mtt)
REVERT: D  825 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7990 (ttm-80)
REVERT: D  846 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7860 (mt-10)
REVERT: D  861 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7675 (mm-30)
  outliers start: 61
  outliers final: 47
  residues processed: 321
  average time/residue: 0.1248
  time to fit residues: 59.8882
Evaluate side-chains
  334 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 277
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  321 GLU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  620 ARG
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  267 SER
Chi-restraints excluded: chain D residue  314 LYS
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  336 LYS
Chi-restraints excluded: chain D residue  337 GLU
Chi-restraints excluded: chain D residue  378 LEU
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  560 VAL
Chi-restraints excluded: chain D residue  624 MET
Chi-restraints excluded: chain D residue  682 SER
Chi-restraints excluded: chain D residue  697 MET
Chi-restraints excluded: chain D residue  721 LEU
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  771 MET
Chi-restraints excluded: chain D residue  811 VAL
Chi-restraints excluded: chain D residue  841 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 139 optimal weight:    3.9990
   chunk 182 optimal weight:    0.7980
   chunk 110 optimal weight:    8.9990
   chunk 150 optimal weight:    2.9990
   chunk 164 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 192 optimal weight:    0.6980
   chunk 156 optimal weight:    4.9990
   chunk 189 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0020
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A  68 HIS
A 555 ASN
A 798 ASN
A 840 HIS
** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.180013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.130670 restraints weight = 22189.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 3.49
r_work: 0.3229 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16934  Z= 0.128
  Angle     :  0.609   8.993  23019  Z= 0.309
  Chirality :  0.045   0.177   2430
  Planarity :  0.005   0.069   2987
  Dihedral  :  5.094  39.275   2218
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.14 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.18), residues: 2034
  helix:  0.82 (0.30), residues: 317
  sheet: -0.74 (0.21), residues: 587
  loop : -1.31 (0.18), residues: 1130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 499 
 TYR   0.032   0.001   TYR A 277 
 PHE   0.015   0.001   PHE B 253 
 TRP   0.085   0.002   TRP A 375 
 HIS   0.006   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (16934)
  covalent geometry    : angle       0.60926 (23019)
  hydrogen bonds       : bond        0.03067 (  548)
  hydrogen bonds       : angle       5.29454 ( 1488)

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

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

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4068 Ramachandran restraints generated.
    2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 290
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7472 (t-90)
REVERT: A  154 GLN cc_start: 0.8419 (tt0) cc_final: 0.8172 (tt0)
REVERT: A  175 MET cc_start: 0.8376 (pmm) cc_final: 0.7783 (ptm)
REVERT: A  189 MET cc_start: 0.8372 (mmm) cc_final: 0.8005 (mtm)
REVERT: A  190 ASP cc_start: 0.8521 (t70) cc_final: 0.8127 (t0)
REVERT: A  464 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7010 (tm-30)
REVERT: A  604 ASP cc_start: 0.7758 (t0) cc_final: 0.7358 (t0)
REVERT: A  620 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7144 (ttp-170)
REVERT: A  703 GLU cc_start: 0.8328 (tp30) cc_final: 0.8087 (mm-30)
REVERT: A  844 CYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7959 (t)
REVERT: B  222 LEU cc_start: 0.8306 (mt) cc_final: 0.7894 (mt)
REVERT: B  261 VAL cc_start: 0.4024 (OUTLIER) cc_final: 0.3710 (t)
REVERT: B  334 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5567 (tt)
REVERT: B  438 GLN cc_start: 0.2748 (OUTLIER) cc_final: 0.1505 (mt0)
REVERT: C  427 VAL cc_start: 0.6770 (t) cc_final: 0.6313 (m)
REVERT: D  108 MET cc_start: 0.7188 (tmm) cc_final: 0.6259 (tmm)
REVERT: D  181 LYS cc_start: 0.8231 (tptp) cc_final: 0.7591 (mmmt)
REVERT: D  314 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7763 (mtpp)
REVERT: D  336 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7698 (mmmm)
REVERT: D  413 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7820 (t80)
REVERT: D  468 TRP cc_start: 0.7647 (m100) cc_final: 0.7307 (m100)
REVERT: D  558 MET cc_start: 0.8441 (mtm) cc_final: 0.7919 (mtm)
REVERT: D  576 LYS cc_start: 0.8688 (tptm) cc_final: 0.8403 (tptp)
REVERT: D  609 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8352 (mt-10)
REVERT: D  825 ARG cc_start: 0.8282 (mtp85) cc_final: 0.8001 (ttm-80)
REVERT: D  846 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7852 (mt-10)
REVERT: D  861 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7672 (mm-30)
  outliers start: 55
  outliers final: 43
  residues processed: 326
  average time/residue: 0.1315
  time to fit residues: 64.0282
Evaluate side-chains
  329 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 277
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 THR
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  620 ARG
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  844 CYS
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  261 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  378 ASN
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain B residue  440 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  417 GLU
Chi-restraints excluded: chain D residue   91 ILE
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  267 SER
Chi-restraints excluded: chain D residue  314 LYS
Chi-restraints excluded: chain D residue  330 ILE
Chi-restraints excluded: chain D residue  336 LYS
Chi-restraints excluded: chain D residue  337 GLU
Chi-restraints excluded: chain D residue  378 LEU
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  483 ILE
Chi-restraints excluded: chain D residue  551 SER
Chi-restraints excluded: chain D residue  554 GLN
Chi-restraints excluded: chain D residue  560 VAL
Chi-restraints excluded: chain D residue  624 MET
Chi-restraints excluded: chain D residue  721 LEU
Chi-restraints excluded: chain D residue  756 VAL
Chi-restraints excluded: chain D residue  811 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 142 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 121 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 170 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 197 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A  68 HIS
A 555 ASN
A 798 ASN
A 840 HIS
** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.178368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.127286 restraints weight = 22160.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 3.15
r_work: 0.3216 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16934  Z= 0.187
  Angle     :  0.633   9.883  23019  Z= 0.322
  Chirality :  0.046   0.191   2430
  Planarity :  0.005   0.061   2987
  Dihedral  :  5.190  39.950   2218
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.97 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.18), residues: 2034
  helix:  0.71 (0.30), residues: 317
  sheet: -0.81 (0.21), residues: 595
  loop : -1.32 (0.18), residues: 1122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 499 
 TYR   0.031   0.002   TYR A 277 
 PHE   0.017   0.001   PHE B 253 
 TRP   0.091   0.002   TRP A 375 
 HIS   0.008   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (16934)
  covalent geometry    : angle       0.63297 (23019)
  hydrogen bonds       : bond        0.03303 (  548)
  hydrogen bonds       : angle       5.39034 ( 1488)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4231.07 seconds
wall clock time: 73 minutes 15.85 seconds (4395.85 seconds total)