Starting phenix.real_space_refine
on Sat Aug 23 15:06:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9utb_64487/08_2025/9utb_64487.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9utb_64487/08_2025/9utb_64487.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9utb_64487/08_2025/9utb_64487.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9utb_64487/08_2025/9utb_64487.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9utb_64487/08_2025/9utb_64487.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9utb_64487/08_2025/9utb_64487.map"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      98      5.16       5
     Cl      3      4.86       5
     C    8035      2.51       5
     N    2101      2.21       5
     O    2234      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12471
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 781, 6235
          Classifications: {'peptide': 781}
          Link IDs: {'PTRANS': 40, 'TRANS': 740}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 803, 6213
          Classifications: {'peptide': 803}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 44, 'TRANS': 758}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'RRJ': 1, 'RRY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.91, per 1000 atoms: 0.23
  Number of scatterers: 12471
  At special positions: 0
  Unit cell: (90.272, 99.008, 183.456, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      3     17.00
     S      98     16.00
     O    2234      8.00
     N    2101      7.00
     C    8035      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=19, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 513 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 495 " - pdb=" SG  CYS A 514 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 499 " - pdb=" SG  CYS A 517 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 535 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 630 " - pdb=" SG  CYS A 720 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B 351 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 517 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 373 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 499 " - pdb=" SG  CYS B 518 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 503 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 524 " - pdb=" SG  CYS B 538 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 541 " - pdb=" SG  CYS B 554 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 633 " - pdb=" SG  CYS B 722 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ?1-2
      " RRY C   1 " - " RRJ C   2 "
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 454.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2986

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 16 sheets defined
      53.0% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 85
      removed outlier: 3.743A  pdb=" N   TYR A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 114
      removed outlier: 3.751A  pdb=" N   VAL A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.002A  pdb=" N   PHE A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 186 through 201
    Processing helix  chain 'A' and resid 213 through 228
    Processing helix  chain 'A' and resid 250 through 267
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 4.201A  pdb=" N   HIS A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 4.215A  pdb=" N   ILE A 306 " --> pdb=" O   GLU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 316 through 320
      removed outlier: 3.882A  pdb=" N   GLY A 320 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 341
    Processing helix  chain 'A' and resid 365 through 373
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 383 through 403
    Processing helix  chain 'A' and resid 416 through 425
    Processing helix  chain 'A' and resid 563 through 590
    Processing helix  chain 'A' and resid 593 through 599
      removed outlier: 3.507A  pdb=" N   ALA A 599 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 622
      removed outlier: 3.706A  pdb=" N   PHE A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A 606 " --> pdb=" O   PRO A 602 " (cutoff:3.500A)
      Proline residue:  A 619  - end of helix
      removed outlier: 3.832A  pdb=" N   VAL A 622 " --> pdb=" O   VAL A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 660
      removed outlier: 4.285A  pdb=" N   PHE A 637 " --> pdb=" O   ARG A 633 " (cutoff:3.500A)
      Proline residue:  A 638  - end of helix
      removed outlier: 3.740A  pdb=" N   ILE A 648 " --> pdb=" O   CYS A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 675
      removed outlier: 4.149A  pdb=" N   TYR A 675 " --> pdb=" O   TYR A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 700
    Processing helix  chain 'A' and resid 723 through 749
      removed outlier: 4.633A  pdb=" N   LEU A 734 " --> pdb=" O   PHE A 730 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ASP A 735 " --> pdb=" O   ASN A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 783
      removed outlier: 3.558A  pdb=" N   PHE A 761 " --> pdb=" O   ASN A 757 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   LEU A 764 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 818
      removed outlier: 5.235A  pdb=" N   GLY A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
      Proline residue:  A 810  - end of helix
    Processing helix  chain 'A' and resid 819 through 822
    Processing helix  chain 'A' and resid 823 through 833
    Processing helix  chain 'B' and resid 26 through 30
      removed outlier: 3.907A  pdb=" N   ARG B  30 " --> pdb=" O   GLN B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 3.880A  pdb=" N   LEU B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 4.676A  pdb=" N   LYS B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
      removed outlier: 3.648A  pdb=" N   LEU B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 160
      removed outlier: 4.180A  pdb=" N   PHE B 159 " --> pdb=" O   LYS B 155 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   PHE B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
    Processing helix  chain 'B' and resid 189 through 204
      removed outlier: 3.902A  pdb=" N   GLN B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 234
    Processing helix  chain 'B' and resid 250 through 266
      removed outlier: 3.848A  pdb=" N   GLY B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 290
    Processing helix  chain 'B' and resid 306 through 311
    Processing helix  chain 'B' and resid 314 through 318
    Processing helix  chain 'B' and resid 333 through 347
      removed outlier: 3.820A  pdb=" N   TYR B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 358
    Processing helix  chain 'B' and resid 377 through 381
    Processing helix  chain 'B' and resid 387 through 408
      removed outlier: 4.374A  pdb=" N   PHE B 391 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   SER B 392 " --> pdb=" O   HIS B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 429
      removed outlier: 3.572A  pdb=" N   LEU B 426 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 485
    Processing helix  chain 'B' and resid 566 through 593
    Processing helix  chain 'B' and resid 596 through 602
      removed outlier: 3.621A  pdb=" N   GLN B 600 " --> pdb=" O   SER B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 622
    Processing helix  chain 'B' and resid 629 through 663
      removed outlier: 4.299A  pdb=" N   GLN B 637 " --> pdb=" O   CYS B 633 " (cutoff:3.500A)
      Proline residue:  B 638  - end of helix
      Proline residue:  B 643  - end of helix
    Processing helix  chain 'B' and resid 666 through 678
      removed outlier: 4.459A  pdb=" N   GLY B 678 " --> pdb=" O   GLY B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 703
      removed outlier: 3.793A  pdb=" N   TRP B 682 " --> pdb=" O   GLY B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 726 through 750
      removed outlier: 3.882A  pdb=" N   PHE B 730 " --> pdb=" O   SER B 726 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ASN B 737 " --> pdb=" O   ALA B 733 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LEU B 750 " --> pdb=" O   LEU B 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 759 through 785
      removed outlier: 3.932A  pdb=" N   GLY B 763 " --> pdb=" O   ASN B 759 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B 764 " --> pdb=" O   ARG B 760 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER B 777 " --> pdb=" O   ILE B 773 " (cutoff:3.500A)
      Proline residue:  B 780  - end of helix
    Processing helix  chain 'B' and resid 788 through 809
      removed outlier: 3.972A  pdb=" N   ALA B 792 " --> pdb=" O   VAL B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 810 through 824
      Proline residue:  B 821  - end of helix
      removed outlier: 3.820A  pdb=" N   ASN B 824 " --> pdb=" O   GLN B 820 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.558A  pdb=" N   TYR A  96 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   LEU A  34 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL A 138 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY A  36 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   ILE A 162 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   VAL A 138 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43
    Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 240
      removed outlier: 7.387A  pdb=" N   ILE A 206 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   GLN A 237 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL A 208 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   THR A 239 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   VAL A 210 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   TRP A 205 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   VAL A 273 " --> pdb=" O   TRP A 205 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE A 207 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   PHE A 275 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A 209 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 325 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   PHE A 322 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR A 468 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA A 466 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   GLN A 452 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   SER A 464 " --> pdb=" O   GLN A 452 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 428 through 430
    Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 507
    Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 525
    Processing sheet with id=AA8, first strand: chain 'A' and resid 555 through 557
      removed outlier: 6.349A  pdb=" N   GLN A 555 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL A 718 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 41
      removed outlier: 5.860A  pdb=" N   GLY B  39 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 143
      removed outlier: 6.508A  pdb=" N   VAL B 141 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 240
      removed outlier: 7.574A  pdb=" N   VAL B 209 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   GLU B 240 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   ALA B 211 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   VAL B 270 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   PHE B 324 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   GLY B 472 " --> pdb=" O   LEU B 456 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LEU B 458 " --> pdb=" O   ASP B 470 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ASP B 470 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 434 through 437
    Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 511
    Processing sheet with id=AB5, first strand: chain 'B' and resid 528 through 529
    Processing sheet with id=AB6, first strand: chain 'B' and resid 545 through 546
    Processing sheet with id=AB7, first strand: chain 'B' and resid 558 through 560

    639 hydrogen bonds defined for protein.
    1839 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3776
        1.33 -     1.46: 3330
        1.46 -     1.59: 5547
        1.59 -     1.72: 0
        1.72 -     1.85: 140
  Bond restraints: 12793
  Sorted by residual:
  bond pdb=" N   GLU A 302 "
       pdb=" CA  GLU A 302 "
    ideal  model  delta    sigma   weight residual
    1.459  1.417  0.042 1.20e-02 6.94e+03 1.21e+01
  bond pdb=" CA  GLU A 302 "
       pdb=" C   GLU A 302 "
    ideal  model  delta    sigma   weight residual
    1.524  1.479  0.045 1.32e-02 5.74e+03 1.14e+01
  bond pdb=" C   GLU A 302 "
       pdb=" N   SER A 303 "
    ideal  model  delta    sigma   weight residual
    1.332  1.286  0.046 1.40e-02 5.10e+03 1.10e+01
  bond pdb=" C   GLU A 302 "
       pdb=" O   GLU A 302 "
    ideal  model  delta    sigma   weight residual
    1.236  1.206  0.030 1.15e-02 7.56e+03 6.92e+00
  bond pdb=" C   SER A 301 "
       pdb=" N   GLU A 302 "
    ideal  model  delta    sigma   weight residual
    1.335  1.307  0.028 1.25e-02 6.40e+03 4.96e+00
  ... (remaining 12788 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 16827
        1.49 -     2.97: 469
        2.97 -     4.46: 115
        4.46 -     5.95: 19
        5.95 -     7.43: 4
  Bond angle restraints: 17434
  Sorted by residual:
  angle pdb=" CA  PRO A 594 "
        pdb=" C   PRO A 594 "
        pdb=" O   PRO A 594 "
      ideal   model   delta    sigma   weight residual
     118.90  113.49    5.41 1.26e+00 6.30e-01 1.84e+01
  angle pdb=" C   SER A 681 "
        pdb=" N   MET A 682 "
        pdb=" CA  MET A 682 "
      ideal   model   delta    sigma   weight residual
     121.14  115.14    6.00 1.75e+00 3.27e-01 1.18e+01
  angle pdb=" N   PRO A 594 "
        pdb=" CA  PRO A 594 "
        pdb=" C   PRO A 594 "
      ideal   model   delta    sigma   weight residual
     114.27  109.73    4.54 1.35e+00 5.49e-01 1.13e+01
  angle pdb=" N   PHE B 766 "
        pdb=" CA  PHE B 766 "
        pdb=" CB  PHE B 766 "
      ideal   model   delta    sigma   weight residual
     110.12  114.51   -4.39 1.47e+00 4.63e-01 8.93e+00
  angle pdb=" CA  GLN A 255 "
        pdb=" CB  GLN A 255 "
        pdb=" CG  GLN A 255 "
      ideal   model   delta    sigma   weight residual
     114.10  119.87   -5.77 2.00e+00 2.50e-01 8.31e+00
  ... (remaining 17429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6619
       17.99 -    35.98: 764
       35.98 -    53.97: 204
       53.97 -    71.96: 53
       71.96 -    89.95: 10
  Dihedral angle restraints: 7650
    sinusoidal: 3030
      harmonic: 4620
  Sorted by residual:
  dihedral pdb=" CB  CYS B 633 "
           pdb=" SG  CYS B 633 "
           pdb=" SG  CYS B 722 "
           pdb=" CB  CYS B 722 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.55  -86.55     1      1.00e+01 1.00e-02 9.02e+01
  dihedral pdb=" CB  CYS A 630 "
           pdb=" SG  CYS A 630 "
           pdb=" SG  CYS A 720 "
           pdb=" CB  CYS A 720 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.60  -70.60     1      1.00e+01 1.00e-02 6.41e+01
  dihedral pdb=" CB  CYS A 495 "
           pdb=" SG  CYS A 495 "
           pdb=" SG  CYS A 514 "
           pdb=" CB  CYS A 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   23.40   69.60     1      1.00e+01 1.00e-02 6.25e+01
  ... (remaining 7647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1342
       0.032 -    0.065: 424
       0.065 -    0.097: 157
       0.097 -    0.130: 54
       0.130 -    0.162: 8
  Chirality restraints: 1985
  Sorted by residual:
  chirality pdb=" CA  ILE A 139 "
            pdb=" N   ILE A 139 "
            pdb=" C   ILE A 139 "
            pdb=" CB  ILE A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" C2  RRY C   1 "
            pdb=" C1  RRY C   1 "
            pdb=" C3  RRY C   1 "
            pdb=" O5  RRY C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.66    2.50    0.16 2.00e-01 2.50e+01 6.21e-01
  chirality pdb=" CA  ILE A 332 "
            pdb=" N   ILE A 332 "
            pdb=" C   ILE A 332 "
            pdb=" CB  ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.67e-01
  ... (remaining 1982 not shown)

  Planarity restraints: 2214
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  90 "    0.060 5.00e-02 4.00e+02   8.96e-02 1.28e+01
        pdb=" N   PRO B  91 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO B  91 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B  91 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 766 "    0.023 2.00e-02 2.50e+03   1.91e-02 6.38e+00
        pdb=" CG  PHE B 766 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 766 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 766 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 766 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 766 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 766 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 506 "    0.038 5.00e-02 4.00e+02   5.86e-02 5.49e+00
        pdb=" N   PRO A 507 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 507 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 507 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2211 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 313
        2.64 -     3.20: 13224
        3.20 -     3.77: 20827
        3.77 -     4.33: 28163
        4.33 -     4.90: 44519
  Nonbonded interactions: 107046
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 214 "
            pdb=" OD1 ASP B 216 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" O   GLU A 563 "
            pdb=" OG1 THR A 566 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" O   ILE B 773 "
            pdb=" OG  SER B 777 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   PRO B 181 "
            pdb=" OH  TYR B 431 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" OG1 THR B 186 "
            pdb=" OG  SER B 392 "
     model   vdw
     2.114 3.040
  ... (remaining 107041 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.720
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12813  Z= 0.168
  Angle     :  0.645  10.154  17475  Z= 0.340
  Chirality :  0.040   0.162   1985
  Planarity :  0.005   0.090   2214
  Dihedral  : 16.651  89.952   4607
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.61 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 24.98 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.21), residues: 1576
  helix:  0.25 (0.19), residues: 751
  sheet: -1.96 (0.38), residues: 186
  loop : -1.46 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 509 
 TYR   0.024   0.001   TYR A 389 
 PHE   0.044   0.002   PHE B 766 
 TRP   0.034   0.001   TRP B 303 
 HIS   0.005   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12793)
  covalent geometry    : angle       0.63703 (17434)
  SS BOND              : bond        0.00508 (   19)
  SS BOND              : angle       1.45370 (   38)
  hydrogen bonds       : bond        0.16828 (  639)
  hydrogen bonds       : angle       6.47500 ( 1839)
  glycosidic custom    : bond        0.03195 (    1)
  glycosidic custom    : angle       6.00521 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 333
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  682 MET cc_start: 0.7245 (ppp) cc_final: 0.6380 (pmm)
REVERT: A  761 PHE cc_start: 0.7346 (m-10) cc_final: 0.6991 (m-10)
REVERT: A  776 LEU cc_start: 0.8466 (tp) cc_final: 0.8213 (tp)
REVERT: B  223 LEU cc_start: 0.8226 (tp) cc_final: 0.7882 (tp)
REVERT: B  736 THR cc_start: 0.8497 (m) cc_final: 0.8176 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 334
  average time/residue: 0.1003
  time to fit residues: 47.3975
Evaluate side-chains
  195 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0980
   chunk 149 optimal weight:    9.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN
A 266 GLN
A 286 ASN
A 454 GLN
A 488 ASN
A 755 ASN
B 207 ASN
B 387 HIS
B 532 ASN
** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.108165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.085369 restraints weight = 46306.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.086923 restraints weight = 23731.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.087671 restraints weight = 18142.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.087947 restraints weight = 16405.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.088359 restraints weight = 14735.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
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      :  0.005   0.043  12813  Z= 0.212
  Angle     :  0.814  11.127  17475  Z= 0.401
  Chirality :  0.047   0.236   1985
  Planarity :  0.006   0.056   2214
  Dihedral  :  5.082  37.555   1759
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.28 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 24.11 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.21), residues: 1576
  helix:  0.26 (0.18), residues: 772
  sheet: -1.86 (0.38), residues: 188
  loop : -1.11 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 191 
 TYR   0.030   0.002   TYR A 615 
 PHE   0.045   0.002   PHE B 766 
 TRP   0.030   0.002   TRP B 303 
 HIS   0.008   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (12793)
  covalent geometry    : angle       0.81340 (17434)
  SS BOND              : bond        0.00356 (   19)
  SS BOND              : angle       1.12063 (   38)
  hydrogen bonds       : bond        0.05179 (  639)
  hydrogen bonds       : angle       5.14680 ( 1839)
  glycosidic custom    : bond        0.00540 (    1)
  glycosidic custom    : angle       1.84859 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 221
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 GLN cc_start: 0.8606 (mp10) cc_final: 0.8266 (mp10)
REVERT: A  237 GLN cc_start: 0.8137 (tt0) cc_final: 0.7805 (tm-30)
REVERT: A  249 MET cc_start: 0.8184 (mmm) cc_final: 0.7703 (mmm)
REVERT: A  256 ARG cc_start: 0.9127 (tpt-90) cc_final: 0.8534 (ttt90)
REVERT: A  273 VAL cc_start: 0.9325 (t) cc_final: 0.9074 (m)
REVERT: A  397 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8674 (m170)
REVERT: A  455 TRP cc_start: 0.7234 (m100) cc_final: 0.7011 (m100)
REVERT: A  553 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8191 (mmmt)
REVERT: A  572 LEU cc_start: 0.8697 (mt) cc_final: 0.8404 (pp)
REVERT: A  661 MET cc_start: 0.5731 (mpp) cc_final: 0.5485 (mpp)
REVERT: A  807 TYR cc_start: 0.7915 (t80) cc_final: 0.7212 (t80)
REVERT: A  808 PHE cc_start: 0.8484 (m-80) cc_final: 0.8254 (m-10)
REVERT: A  830 MET cc_start: 0.4384 (tmm) cc_final: 0.3732 (ttt)
REVERT: B  115 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8042 (tmm)
REVERT: B  310 MET cc_start: 0.7799 (mmm) cc_final: 0.7495 (mmt)
REVERT: B  398 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8106 (m-10)
REVERT: B  529 TYR cc_start: 0.9075 (p90) cc_final: 0.8715 (p90)
REVERT: B  532 ASN cc_start: 0.9213 (t0) cc_final: 0.8923 (t0)
REVERT: B  692 GLU cc_start: 0.8337 (tp30) cc_final: 0.7961 (tp30)
REVERT: B  696 CYS cc_start: 0.8014 (m) cc_final: 0.6775 (m)
REVERT: B  768 MET cc_start: 0.6376 (mpp) cc_final: 0.6056 (mpp)
  outliers start: 79
  outliers final: 27
  residues processed: 275
  average time/residue: 0.0814
  time to fit residues: 34.0034
Evaluate side-chains
  210 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  779 PHE
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  499 CYS
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 120 optimal weight:    1.9990
   chunk 154 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0870
   chunk 27 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 759 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.108774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.083842 restraints weight = 46575.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.086691 restraints weight = 25832.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.088583 restraints weight = 17725.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.089811 restraints weight = 13754.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.090673 restraints weight = 11536.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12813  Z= 0.159
  Angle     :  0.744  12.947  17475  Z= 0.362
  Chirality :  0.044   0.250   1985
  Planarity :  0.005   0.044   2214
  Dihedral  :  4.962  54.783   1759
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.08 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 25.20 %
    Favored  : 69.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.21), residues: 1576
  helix:  0.56 (0.18), residues: 760
  sheet: -1.74 (0.38), residues: 187
  loop : -1.07 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 509 
 TYR   0.042   0.002   TYR A 615 
 PHE   0.037   0.002   PHE B 772 
 TRP   0.018   0.001   TRP B 303 
 HIS   0.007   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (12793)
  covalent geometry    : angle       0.74298 (17434)
  SS BOND              : bond        0.00333 (   19)
  SS BOND              : angle       0.98530 (   38)
  hydrogen bonds       : bond        0.04526 (  639)
  hydrogen bonds       : angle       4.80557 ( 1839)
  glycosidic custom    : bond        0.00224 (    1)
  glycosidic custom    : angle       1.27438 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 200
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 PHE cc_start: 0.7667 (m-80) cc_final: 0.7459 (m-10)
REVERT: A  237 GLN cc_start: 0.8045 (tt0) cc_final: 0.7704 (tm-30)
REVERT: A  249 MET cc_start: 0.8133 (mmm) cc_final: 0.7776 (mmm)
REVERT: A  256 ARG cc_start: 0.9037 (tpt-90) cc_final: 0.8765 (ttt90)
REVERT: A  260 ILE cc_start: 0.9115 (mt) cc_final: 0.8861 (mt)
REVERT: A  397 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.8633 (m170)
REVERT: A  451 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8574 (p)
REVERT: A  604 CYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8421 (p)
REVERT: A  661 MET cc_start: 0.5112 (mpp) cc_final: 0.4866 (mpp)
REVERT: A  807 TYR cc_start: 0.7691 (t80) cc_final: 0.7245 (t80)
REVERT: A  830 MET cc_start: 0.4185 (tmm) cc_final: 0.3979 (ttt)
REVERT: B  101 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7880 (t0)
REVERT: B  171 MET cc_start: 0.7285 (mtp) cc_final: 0.4845 (mtp)
REVERT: B  174 LEU cc_start: 0.9122 (mm) cc_final: 0.8890 (mm)
REVERT: B  215 ASP cc_start: 0.8778 (t70) cc_final: 0.8510 (t0)
REVERT: B  310 MET cc_start: 0.7728 (mmm) cc_final: 0.7339 (mmm)
REVERT: B  398 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.7621 (m-10)
REVERT: B  529 TYR cc_start: 0.9107 (p90) cc_final: 0.8650 (p90)
REVERT: B  532 ASN cc_start: 0.9194 (t0) cc_final: 0.8901 (t0)
REVERT: B  634 LEU cc_start: 0.8400 (mt) cc_final: 0.8103 (pp)
REVERT: B  692 GLU cc_start: 0.8301 (tp30) cc_final: 0.7831 (tp30)
REVERT: B  696 CYS cc_start: 0.7976 (m) cc_final: 0.6820 (m)
REVERT: B  699 TYR cc_start: 0.8493 (p90) cc_final: 0.8128 (p90)
REVERT: B  713 MET cc_start: 0.8482 (ppp) cc_final: 0.7665 (ppp)
  outliers start: 66
  outliers final: 40
  residues processed: 245
  average time/residue: 0.0888
  time to fit residues: 33.0397
Evaluate side-chains
  211 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 166
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  779 PHE
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  621 VAL
Chi-restraints excluded: chain B residue  627 GLN
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 149 optimal weight:    0.9990
   chunk 152 optimal weight:    5.9990
   chunk 91 optimal weight:    0.6980
   chunk 133 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 144 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0770
   chunk 42 optimal weight:    0.4980
   chunk 107 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.109581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.087309 restraints weight = 45699.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.089008 restraints weight = 23183.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.089993 restraints weight = 17099.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.090229 restraints weight = 15393.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.090492 restraints weight = 13705.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12813  Z= 0.144
  Angle     :  0.715  13.474  17475  Z= 0.345
  Chirality :  0.043   0.257   1985
  Planarity :  0.005   0.047   2214
  Dihedral  :  4.857  53.430   1759
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.89 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 24.91 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.21), residues: 1576
  helix:  0.65 (0.18), residues: 760
  sheet: -1.63 (0.38), residues: 187
  loop : -1.03 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 509 
 TYR   0.041   0.002   TYR A 615 
 PHE   0.036   0.002   PHE B 772 
 TRP   0.018   0.001   TRP A 455 
 HIS   0.007   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12793)
  covalent geometry    : angle       0.71490 (17434)
  SS BOND              : bond        0.00325 (   19)
  SS BOND              : angle       0.89296 (   38)
  hydrogen bonds       : bond        0.04332 (  639)
  hydrogen bonds       : angle       4.68545 ( 1839)
  glycosidic custom    : bond        0.00180 (    1)
  glycosidic custom    : angle       1.03282 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 195
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 GLN cc_start: 0.8005 (tt0) cc_final: 0.7626 (tm-30)
REVERT: A  249 MET cc_start: 0.8312 (mmm) cc_final: 0.7875 (mmm)
REVERT: A  397 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.8640 (m170)
REVERT: A  451 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8583 (p)
REVERT: A  587 PHE cc_start: 0.7887 (m-80) cc_final: 0.7365 (m-80)
REVERT: A  604 CYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8548 (p)
REVERT: A  661 MET cc_start: 0.4992 (mpp) cc_final: 0.4613 (mpp)
REVERT: A  715 ILE cc_start: 0.9575 (mm) cc_final: 0.9323 (tp)
REVERT: A  794 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8847 (mm)
REVERT: A  830 MET cc_start: 0.4609 (tmm) cc_final: 0.4125 (ttt)
REVERT: B  101 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7915 (t0)
REVERT: B  117 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7751 (mt)
REVERT: B  272 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9346 (mt)
REVERT: B  310 MET cc_start: 0.7839 (mmm) cc_final: 0.7244 (mmm)
REVERT: B  398 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7452 (m-10)
REVERT: B  529 TYR cc_start: 0.9027 (p90) cc_final: 0.8611 (p90)
REVERT: B  532 ASN cc_start: 0.9251 (t0) cc_final: 0.8930 (t0)
REVERT: B  692 GLU cc_start: 0.8427 (tp30) cc_final: 0.7953 (tp30)
REVERT: B  696 CYS cc_start: 0.7862 (m) cc_final: 0.7216 (m)
REVERT: B  699 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7996 (p90)
  outliers start: 66
  outliers final: 39
  residues processed: 236
  average time/residue: 0.0933
  time to fit residues: 33.9041
Evaluate side-chains
  219 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 171
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  604 CYS
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  779 PHE
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  262 GLN
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  627 GLN
Chi-restraints excluded: chain B residue  658 ILE
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 118 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 134 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 34 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 153 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 402 GLN
** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 636 GLN
** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.106628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.084388 restraints weight = 46555.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.085974 restraints weight = 23250.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.086533 restraints weight = 17773.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.086783 restraints weight = 16100.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.087394 restraints weight = 14545.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12813  Z= 0.207
  Angle     :  0.743  10.340  17475  Z= 0.366
  Chirality :  0.044   0.200   1985
  Planarity :  0.005   0.049   2214
  Dihedral  :  4.866  44.955   1759
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 16.84
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.15 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 25.78 %
    Favored  : 68.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.21), residues: 1576
  helix:  0.64 (0.18), residues: 769
  sheet: -1.47 (0.39), residues: 193
  loop : -1.12 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 137 
 TYR   0.045   0.002   TYR A 615 
 PHE   0.036   0.002   PHE B 772 
 TRP   0.019   0.001   TRP A 455 
 HIS   0.007   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (12793)
  covalent geometry    : angle       0.74280 (17434)
  SS BOND              : bond        0.00376 (   19)
  SS BOND              : angle       0.89219 (   38)
  hydrogen bonds       : bond        0.04458 (  639)
  hydrogen bonds       : angle       4.79698 ( 1839)
  glycosidic custom    : bond        0.00421 (    1)
  glycosidic custom    : angle       1.30276 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 169
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 GLN cc_start: 0.8345 (tt0) cc_final: 0.7885 (tm-30)
REVERT: A  249 MET cc_start: 0.8351 (mmm) cc_final: 0.7915 (mmm)
REVERT: A  256 ARG cc_start: 0.9042 (ttt90) cc_final: 0.8722 (tpt-90)
REVERT: A  397 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.8584 (m170)
REVERT: A  562 HIS cc_start: 0.8053 (t70) cc_final: 0.7837 (p-80)
REVERT: A  584 LEU cc_start: 0.8797 (mt) cc_final: 0.8585 (mt)
REVERT: A  587 PHE cc_start: 0.7829 (m-80) cc_final: 0.7489 (m-80)
REVERT: A  607 MET cc_start: 0.8016 (ttt) cc_final: 0.7049 (tpp)
REVERT: A  616 MET cc_start: 0.8510 (ppp) cc_final: 0.8051 (ppp)
REVERT: A  661 MET cc_start: 0.5111 (mpp) cc_final: 0.4682 (mpp)
REVERT: A  715 ILE cc_start: 0.9568 (mm) cc_final: 0.9328 (tp)
REVERT: A  830 MET cc_start: 0.4162 (tmm) cc_final: 0.3708 (ttp)
REVERT: B   31 MET cc_start: 0.8540 (ttm) cc_final: 0.8183 (mtp)
REVERT: B  101 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7749 (t0)
REVERT: B  115 MET cc_start: 0.8792 (tmm) cc_final: 0.8455 (tmm)
REVERT: B  117 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7664 (mt)
REVERT: B  162 MET cc_start: 0.8508 (ttp) cc_final: 0.8200 (ttp)
REVERT: B  310 MET cc_start: 0.7849 (mmm) cc_final: 0.7355 (mmm)
REVERT: B  398 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8048 (m-10)
REVERT: B  529 TYR cc_start: 0.9122 (p90) cc_final: 0.8654 (p90)
REVERT: B  532 ASN cc_start: 0.9259 (t0) cc_final: 0.8924 (t0)
REVERT: B  543 GLN cc_start: 0.9212 (pm20) cc_final: 0.8697 (pp30)
REVERT: B  590 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5397 (t80)
REVERT: B  699 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7942 (p90)
REVERT: B  768 MET cc_start: 0.6679 (mpp) cc_final: 0.6450 (mpp)
  outliers start: 85
  outliers final: 60
  residues processed: 230
  average time/residue: 0.0916
  time to fit residues: 32.6248
Evaluate side-chains
  224 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 158
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  546 GLN
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  684 PHE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  779 PHE
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  285 ASN
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  590 PHE
Chi-restraints excluded: chain B residue  627 GLN
Chi-restraints excluded: chain B residue  658 ILE
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  750 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 131 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 122 optimal weight:    0.2980
   chunk 77 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0970
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.107468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.084779 restraints weight = 46779.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.086283 restraints weight = 23972.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.087317 restraints weight = 17562.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.087534 restraints weight = 16256.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.087750 restraints weight = 14434.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12813  Z= 0.143
  Angle     :  0.744  12.955  17475  Z= 0.354
  Chirality :  0.044   0.327   1985
  Planarity :  0.005   0.049   2214
  Dihedral  :  4.803  41.405   1759
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.08 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 26.80 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.22), residues: 1576
  helix:  0.75 (0.18), residues: 774
  sheet: -1.51 (0.38), residues: 197
  loop : -1.05 (0.27), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 509 
 TYR   0.046   0.002   TYR A 615 
 PHE   0.041   0.002   PHE B 772 
 TRP   0.022   0.001   TRP A 455 
 HIS   0.007   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12793)
  covalent geometry    : angle       0.74227 (17434)
  SS BOND              : bond        0.00412 (   19)
  SS BOND              : angle       1.28926 (   38)
  hydrogen bonds       : bond        0.04238 (  639)
  hydrogen bonds       : angle       4.67327 ( 1839)
  glycosidic custom    : bond        0.00198 (    1)
  glycosidic custom    : angle       0.88240 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 176
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 GLN cc_start: 0.8222 (tt0) cc_final: 0.7719 (tm-30)
REVERT: A  249 MET cc_start: 0.8341 (mmm) cc_final: 0.7902 (mmm)
REVERT: A  256 ARG cc_start: 0.9137 (ttt90) cc_final: 0.8538 (tpt-90)
REVERT: A  338 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6591 (t80)
REVERT: A  397 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.8544 (m170)
REVERT: A  455 TRP cc_start: 0.7214 (m100) cc_final: 0.6933 (m100)
REVERT: A  587 PHE cc_start: 0.7839 (m-80) cc_final: 0.7524 (m-80)
REVERT: A  607 MET cc_start: 0.7952 (ttt) cc_final: 0.7112 (tpp)
REVERT: A  616 MET cc_start: 0.8417 (ppp) cc_final: 0.7949 (ppp)
REVERT: A  661 MET cc_start: 0.4979 (mpp) cc_final: 0.4576 (mpp)
REVERT: A  667 ARG cc_start: 0.8758 (mmp-170) cc_final: 0.8455 (ppt170)
REVERT: A  715 ILE cc_start: 0.9562 (mm) cc_final: 0.9322 (tp)
REVERT: A  830 MET cc_start: 0.4609 (tmm) cc_final: 0.3823 (ttp)
REVERT: B   31 MET cc_start: 0.8563 (ttm) cc_final: 0.8148 (mtp)
REVERT: B  101 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7634 (t0)
REVERT: B  115 MET cc_start: 0.8841 (tmm) cc_final: 0.8569 (tmm)
REVERT: B  117 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7678 (mt)
REVERT: B  162 MET cc_start: 0.8500 (ttp) cc_final: 0.8193 (ttp)
REVERT: B  190 ASP cc_start: 0.8647 (p0) cc_final: 0.7940 (p0)
REVERT: B  310 MET cc_start: 0.7849 (mmm) cc_final: 0.7361 (mmm)
REVERT: B  398 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7425 (m-10)
REVERT: B  532 ASN cc_start: 0.9253 (t0) cc_final: 0.8907 (t0)
REVERT: B  543 GLN cc_start: 0.9203 (pm20) cc_final: 0.8754 (pp30)
REVERT: B  634 LEU cc_start: 0.8605 (mm) cc_final: 0.7953 (pp)
REVERT: B  699 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7920 (p90)
  outliers start: 79
  outliers final: 55
  residues processed: 232
  average time/residue: 0.0994
  time to fit residues: 34.8627
Evaluate side-chains
  223 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 162
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  684 PHE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  262 GLN
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  627 GLN
Chi-restraints excluded: chain B residue  658 ILE
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 91 optimal weight:    0.3980
   chunk 64 optimal weight:    5.9990
   chunk 150 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    9.9990
   chunk 153 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 144 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 154 optimal weight:    0.3980
   chunk 111 optimal weight:    8.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.107921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.085277 restraints weight = 46321.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.087237 restraints weight = 23970.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.088030 restraints weight = 17038.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.088261 restraints weight = 16088.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.089097 restraints weight = 14147.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12813  Z= 0.144
  Angle     :  0.742  13.064  17475  Z= 0.354
  Chirality :  0.044   0.267   1985
  Planarity :  0.005   0.050   2214
  Dihedral  :  4.783  40.178   1759
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.14 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 27.17 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.22), residues: 1576
  helix:  0.79 (0.18), residues: 775
  sheet: -1.52 (0.38), residues: 195
  loop : -0.99 (0.27), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 357 
 TYR   0.041   0.002   TYR A 615 
 PHE   0.040   0.002   PHE B 772 
 TRP   0.015   0.001   TRP A 455 
 HIS   0.007   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12793)
  covalent geometry    : angle       0.74084 (17434)
  SS BOND              : bond        0.00294 (   19)
  SS BOND              : angle       1.04469 (   38)
  hydrogen bonds       : bond        0.04235 (  639)
  hydrogen bonds       : angle       4.65062 ( 1839)
  glycosidic custom    : bond        0.00202 (    1)
  glycosidic custom    : angle       0.83368 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 169
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 GLN cc_start: 0.8217 (tt0) cc_final: 0.7685 (tm-30)
REVERT: A  249 MET cc_start: 0.8319 (mmm) cc_final: 0.7890 (mmm)
REVERT: A  256 ARG cc_start: 0.9127 (ttt90) cc_final: 0.8790 (ttt90)
REVERT: A  397 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8507 (m170)
REVERT: A  584 LEU cc_start: 0.8485 (mt) cc_final: 0.8234 (mt)
REVERT: A  587 PHE cc_start: 0.7803 (m-80) cc_final: 0.7485 (m-80)
REVERT: A  607 MET cc_start: 0.8162 (ttt) cc_final: 0.7318 (tpp)
REVERT: A  616 MET cc_start: 0.8420 (ppp) cc_final: 0.7910 (ppp)
REVERT: A  647 CYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5965 (t)
REVERT: A  715 ILE cc_start: 0.9557 (mm) cc_final: 0.9326 (tp)
REVERT: A  830 MET cc_start: 0.4213 (tmm) cc_final: 0.3816 (ttp)
REVERT: B   31 MET cc_start: 0.8536 (ttm) cc_final: 0.8112 (mtp)
REVERT: B  101 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7466 (t0)
REVERT: B  115 MET cc_start: 0.8841 (tmm) cc_final: 0.8566 (tmm)
REVERT: B  117 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7713 (mt)
REVERT: B  310 MET cc_start: 0.7914 (mmm) cc_final: 0.7437 (mmm)
REVERT: B  398 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.7670 (m-10)
REVERT: B  529 TYR cc_start: 0.9218 (p90) cc_final: 0.8753 (p90)
REVERT: B  532 ASN cc_start: 0.9253 (t0) cc_final: 0.8919 (t0)
REVERT: B  543 GLN cc_start: 0.9178 (pm20) cc_final: 0.8715 (pp30)
REVERT: B  634 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7928 (pp)
REVERT: B  636 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.5380 (tt0)
REVERT: B  699 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7856 (p90)
  outliers start: 76
  outliers final: 52
  residues processed: 225
  average time/residue: 0.0863
  time to fit residues: 30.3340
Evaluate side-chains
  217 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 157
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  684 PHE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  262 GLN
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  561 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  627 GLN
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  636 GLN
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 116 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 129 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 154 optimal weight:   10.0000
   chunk 14 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0970
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 546 GLN
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.106694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.084026 restraints weight = 46422.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.085661 restraints weight = 24030.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.087534 restraints weight = 17440.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.087669 restraints weight = 15444.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.087908 restraints weight = 12940.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12813  Z= 0.161
  Angle     :  0.752  16.186  17475  Z= 0.361
  Chirality :  0.045   0.311   1985
  Planarity :  0.005   0.050   2214
  Dihedral  :  4.770  37.711   1759
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.46 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 27.53 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.22), residues: 1576
  helix:  0.79 (0.18), residues: 777
  sheet: -1.52 (0.38), residues: 200
  loop : -0.95 (0.27), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 357 
 TYR   0.040   0.002   TYR A 615 
 PHE   0.043   0.002   PHE B 772 
 TRP   0.029   0.001   TRP A 455 
 HIS   0.006   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (12793)
  covalent geometry    : angle       0.75131 (17434)
  SS BOND              : bond        0.00322 (   19)
  SS BOND              : angle       0.89375 (   38)
  hydrogen bonds       : bond        0.04287 (  639)
  hydrogen bonds       : angle       4.71051 ( 1839)
  glycosidic custom    : bond        0.00284 (    1)
  glycosidic custom    : angle       0.83582 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 165
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8837 (mt) cc_final: 0.8548 (tp)
REVERT: A  237 GLN cc_start: 0.8317 (tt0) cc_final: 0.7798 (tm-30)
REVERT: A  249 MET cc_start: 0.8303 (mmm) cc_final: 0.8017 (mmm)
REVERT: A  256 ARG cc_start: 0.9170 (ttt90) cc_final: 0.8870 (ttt90)
REVERT: A  338 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6723 (t80)
REVERT: A  397 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8483 (m170)
REVERT: A  455 TRP cc_start: 0.7279 (m100) cc_final: 0.7008 (m100)
REVERT: A  584 LEU cc_start: 0.8499 (mt) cc_final: 0.8200 (mt)
REVERT: A  587 PHE cc_start: 0.7854 (m-80) cc_final: 0.7617 (m-80)
REVERT: A  607 MET cc_start: 0.8145 (ttt) cc_final: 0.7413 (tpp)
REVERT: A  690 MET cc_start: 0.8556 (tmm) cc_final: 0.8318 (tmm)
REVERT: A  715 ILE cc_start: 0.9559 (mm) cc_final: 0.9333 (tp)
REVERT: A  766 MET cc_start: 0.8354 (ptt) cc_final: 0.7856 (ttp)
REVERT: A  830 MET cc_start: 0.4227 (tmm) cc_final: 0.3837 (ttp)
REVERT: B   31 MET cc_start: 0.8485 (ttm) cc_final: 0.7402 (mtp)
REVERT: B  101 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7556 (t0)
REVERT: B  115 MET cc_start: 0.8843 (tmm) cc_final: 0.8570 (tmm)
REVERT: B  223 LEU cc_start: 0.8915 (tp) cc_final: 0.8599 (tp)
REVERT: B  310 MET cc_start: 0.7909 (mmm) cc_final: 0.7421 (mmm)
REVERT: B  398 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.7792 (m-10)
REVERT: B  532 ASN cc_start: 0.9260 (t0) cc_final: 0.8922 (t0)
REVERT: B  543 GLN cc_start: 0.9211 (pm20) cc_final: 0.8770 (pp30)
REVERT: B  634 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7987 (pp)
REVERT: B  636 GLN cc_start: 0.5803 (OUTLIER) cc_final: 0.5301 (tt0)
REVERT: B  699 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7853 (p90)
REVERT: B  795 MET cc_start: 0.7907 (mmt) cc_final: 0.7553 (mmm)
  outliers start: 75
  outliers final: 59
  residues processed: 218
  average time/residue: 0.0813
  time to fit residues: 27.2107
Evaluate side-chains
  216 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 150
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  546 GLN
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  684 PHE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  262 GLN
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  561 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  627 GLN
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  636 GLN
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 57 optimal weight:    0.0570
   chunk 122 optimal weight:    0.5980
   chunk 125 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 129 optimal weight:    8.9990
   chunk 100 optimal weight:    0.3980
   chunk 53 optimal weight:    3.9990
   chunk 144 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 389 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.109838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.087553 restraints weight = 48083.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.090116 restraints weight = 24465.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.093318 restraints weight = 15387.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.093246 restraints weight = 11426.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.093295 restraints weight = 10239.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.5143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12813  Z= 0.143
  Angle     :  0.755  13.358  17475  Z= 0.362
  Chirality :  0.045   0.254   1985
  Planarity :  0.005   0.050   2214
  Dihedral  :  4.759  35.910   1759
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.33 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 28.04 %
    Favored  : 66.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.22), residues: 1576
  helix:  0.79 (0.18), residues: 776
  sheet: -1.48 (0.38), residues: 198
  loop : -0.98 (0.27), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 339 
 TYR   0.044   0.002   TYR A 783 
 PHE   0.044   0.002   PHE A 373 
 TRP   0.020   0.001   TRP A 455 
 HIS   0.008   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (12793)
  covalent geometry    : angle       0.75424 (17434)
  SS BOND              : bond        0.00300 (   19)
  SS BOND              : angle       0.89055 (   38)
  hydrogen bonds       : bond        0.04185 (  639)
  hydrogen bonds       : angle       4.59336 ( 1839)
  glycosidic custom    : bond        0.00171 (    1)
  glycosidic custom    : angle       0.67780 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 155
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8909 (mt) cc_final: 0.8568 (tp)
REVERT: A  237 GLN cc_start: 0.8250 (tt0) cc_final: 0.7702 (tm-30)
REVERT: A  249 MET cc_start: 0.8191 (mmm) cc_final: 0.7954 (mmm)
REVERT: A  256 ARG cc_start: 0.9032 (ttt90) cc_final: 0.8744 (ttt90)
REVERT: A  397 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8522 (m170)
REVERT: A  455 TRP cc_start: 0.7194 (m100) cc_final: 0.6944 (m100)
REVERT: A  553 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8399 (mmmt)
REVERT: A  584 LEU cc_start: 0.8399 (mt) cc_final: 0.8197 (mt)
REVERT: A  587 PHE cc_start: 0.7869 (m-80) cc_final: 0.7620 (m-80)
REVERT: A  607 MET cc_start: 0.8222 (ttt) cc_final: 0.8015 (tpp)
REVERT: A  661 MET cc_start: 0.5808 (mpp) cc_final: 0.5200 (mpp)
REVERT: A  715 ILE cc_start: 0.9560 (mm) cc_final: 0.9337 (tp)
REVERT: A  766 MET cc_start: 0.8276 (ptt) cc_final: 0.7828 (ttp)
REVERT: A  794 LEU cc_start: 0.9000 (mm) cc_final: 0.8752 (mm)
REVERT: A  830 MET cc_start: 0.4025 (tmm) cc_final: 0.3633 (ttp)
REVERT: B   31 MET cc_start: 0.8311 (ttm) cc_final: 0.7840 (mtp)
REVERT: B  101 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7512 (t0)
REVERT: B  115 MET cc_start: 0.8770 (tmm) cc_final: 0.8494 (tmm)
REVERT: B  310 MET cc_start: 0.7855 (mmm) cc_final: 0.7392 (mmm)
REVERT: B  398 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7253 (m-10)
REVERT: B  529 TYR cc_start: 0.9179 (p90) cc_final: 0.8654 (p90)
REVERT: B  532 ASN cc_start: 0.9244 (t0) cc_final: 0.8908 (t0)
REVERT: B  543 GLN cc_start: 0.9142 (pm20) cc_final: 0.8695 (pp30)
REVERT: B  634 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8013 (pp)
REVERT: B  636 GLN cc_start: 0.5734 (OUTLIER) cc_final: 0.5219 (tt0)
  outliers start: 70
  outliers final: 52
  residues processed: 206
  average time/residue: 0.0806
  time to fit residues: 26.2005
Evaluate side-chains
  208 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 150
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  684 PHE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  262 GLN
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  561 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  636 GLN
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 66 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.109299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.086981 restraints weight = 48068.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.089421 restraints weight = 24455.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.091701 restraints weight = 15637.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.091698 restraints weight = 12691.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.091861 restraints weight = 11654.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.5257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12813  Z= 0.158
  Angle     :  0.760  14.048  17475  Z= 0.367
  Chirality :  0.045   0.270   1985
  Planarity :  0.005   0.050   2214
  Dihedral  :  4.807  35.070   1759
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.39 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 28.55 %
    Favored  : 67.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.22), residues: 1576
  helix:  0.77 (0.18), residues: 780
  sheet: -1.41 (0.38), residues: 198
  loop : -0.98 (0.27), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.042   0.002   TYR A 615 
 PHE   0.044   0.002   PHE B 772 
 TRP   0.018   0.001   TRP A 455 
 HIS   0.007   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12793)
  covalent geometry    : angle       0.75960 (17434)
  SS BOND              : bond        0.00308 (   19)
  SS BOND              : angle       0.87513 (   38)
  hydrogen bonds       : bond        0.04228 (  639)
  hydrogen bonds       : angle       4.65081 ( 1839)
  glycosidic custom    : bond        0.00246 (    1)
  glycosidic custom    : angle       0.72646 (    3)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 154
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 GLU cc_start: 0.7888 (mp0) cc_final: 0.7548 (mp0)
REVERT: A  154 LEU cc_start: 0.8961 (mt) cc_final: 0.8708 (tp)
REVERT: A  237 GLN cc_start: 0.8327 (tt0) cc_final: 0.7854 (tm-30)
REVERT: A  256 ARG cc_start: 0.9068 (ttt90) cc_final: 0.8755 (ttt90)
REVERT: A  260 ILE cc_start: 0.9155 (mt) cc_final: 0.8947 (mt)
REVERT: A  397 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8482 (m170)
REVERT: A  587 PHE cc_start: 0.7911 (m-80) cc_final: 0.7650 (m-80)
REVERT: A  616 MET cc_start: 0.8367 (ppp) cc_final: 0.7897 (ppp)
REVERT: A  661 MET cc_start: 0.5642 (mpp) cc_final: 0.4974 (mpp)
REVERT: A  690 MET cc_start: 0.8567 (tmm) cc_final: 0.8304 (tmm)
REVERT: A  715 ILE cc_start: 0.9562 (mm) cc_final: 0.9346 (tp)
REVERT: A  766 MET cc_start: 0.8359 (ptt) cc_final: 0.7772 (ttp)
REVERT: A  830 MET cc_start: 0.4024 (tmm) cc_final: 0.3636 (ttp)
REVERT: B   31 MET cc_start: 0.8338 (ttm) cc_final: 0.7907 (mtp)
REVERT: B  115 MET cc_start: 0.8763 (tmm) cc_final: 0.8503 (tmm)
REVERT: B  310 MET cc_start: 0.7858 (mmm) cc_final: 0.7390 (mmm)
REVERT: B  398 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.7675 (m-10)
REVERT: B  529 TYR cc_start: 0.9173 (p90) cc_final: 0.8657 (p90)
REVERT: B  532 ASN cc_start: 0.9245 (t0) cc_final: 0.8911 (t0)
REVERT: B  543 GLN cc_start: 0.9161 (pm20) cc_final: 0.8716 (pp30)
REVERT: B  634 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7922 (pp)
REVERT: B  636 GLN cc_start: 0.5679 (OUTLIER) cc_final: 0.5094 (tt0)
REVERT: B  795 MET cc_start: 0.7829 (mmt) cc_final: 0.7514 (mmt)
  outliers start: 58
  outliers final: 50
  residues processed: 199
  average time/residue: 0.0798
  time to fit residues: 24.8849
Evaluate side-chains
  203 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 149
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  318 HIS
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  672 TRP
Chi-restraints excluded: chain A residue  684 PHE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  730 PHE
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue   97 TYR
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  262 GLN
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  370 CYS
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  388 HIS
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  430 MET
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  519 TYR
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  561 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  634 LEU
Chi-restraints excluded: chain B residue  636 GLN
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  730 PHE
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  801 CYS
Chi-restraints excluded: chain B residue  806 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 148 optimal weight:    8.9990
   chunk 97 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   chunk 132 optimal weight:    0.0770
   chunk 1 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 154 optimal weight:    0.9980
   chunk 122 optimal weight:    0.0570
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 317 GLN
B 449 ASN
B 637 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.108664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.085223 restraints weight = 46356.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.088073 restraints weight = 24925.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.089881 restraints weight = 16776.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.091107 restraints weight = 12866.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.091963 restraints weight = 10673.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12813  Z= 0.133
  Angle     :  0.769  14.522  17475  Z= 0.366
  Chirality :  0.045   0.311   1985
  Planarity :  0.005   0.050   2214
  Dihedral  :  4.775  35.681   1759
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.08 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 28.26 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.22), residues: 1576
  helix:  0.91 (0.18), residues: 764
  sheet: -1.39 (0.38), residues: 199
  loop : -1.03 (0.27), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 247 
 TYR   0.044   0.002   TYR A 615 
 PHE   0.046   0.002   PHE B 772 
 TRP   0.035   0.001   TRP A 455 
 HIS   0.006   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12793)
  covalent geometry    : angle       0.76912 (17434)
  SS BOND              : bond        0.00319 (   19)
  SS BOND              : angle       0.92020 (   38)
  hydrogen bonds       : bond        0.04021 (  639)
  hydrogen bonds       : angle       4.56375 ( 1839)
  glycosidic custom    : bond        0.00110 (    1)
  glycosidic custom    : angle       0.59253 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1977.71 seconds
wall clock time: 35 minutes 1.26 seconds (2101.26 seconds total)