Starting phenix.real_space_refine
on Mon Jun  9 00:33:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w9a_37362/06_2025/8w9a_37362_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w9a_37362/06_2025/8w9a_37362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w9a_37362/06_2025/8w9a_37362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w9a_37362/06_2025/8w9a_37362.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w9a_37362/06_2025/8w9a_37362_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w9a_37362/06_2025/8w9a_37362_trim.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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      72      5.16       5
     Cl      1      4.86       5
     C    6548      2.51       5
     N    1778      2.21       5
     O    1890      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10289
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 969, 7922
          Classifications: {'peptide': 969}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 923}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2330
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 271}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 37
          Unusual residues: {'UEX': 1}
          Classifications: {'undetermined': 1, 'water': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 6.49, per 1000 atoms: 0.63
  Number of scatterers: 10289
  At special positions: 0
  Unit cell: (88.06, 125.06, 117.66, 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      1     17.00
     S      72     16.00
     O    1890      8.00
     N    1778      7.00
     C    6548      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2386

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 9 sheets defined
      48.5% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 53
      removed outlier: 3.626A  pdb=" N   PHE A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LYS A  51 " --> pdb=" O   HIS A  47 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A  52 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 122
      removed outlier: 3.672A  pdb=" N   LEU A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG A 115 " --> pdb=" O   LYS A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 4.017A  pdb=" N   ASP A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET A 130 " --> pdb=" O   CYS A 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 125 through 130'
    Processing helix  chain 'A' and resid 133 through 143
      removed outlier: 3.711A  pdb=" N   ARG A 141 " --> pdb=" O   GLN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 152
      removed outlier: 3.541A  pdb=" N   VAL A 151 " --> pdb=" O   CYS A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 3.540A  pdb=" N   ALA A 222 " --> pdb=" O   GLU A 218 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU A 223 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ARG A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 4.003A  pdb=" N   MET A 278 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 295
    Processing helix  chain 'A' and resid 305 through 310
      removed outlier: 3.994A  pdb=" N   ARG A 309 " --> pdb=" O   PRO A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 497
      removed outlier: 3.578A  pdb=" N   ASN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 536
      removed outlier: 3.943A  pdb=" N   LEU A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 557 through 563
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 3.835A  pdb=" N   LEU A 570 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 588
      removed outlier: 3.541A  pdb=" N   GLN A 582 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   CYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 600 through 603
      removed outlier: 3.534A  pdb=" N   ASP A 603 " --> pdb=" O   GLU A 600 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 600 through 603'
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.583A  pdb=" N   PHE A 614 " --> pdb=" O   MET A 610 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 621 " --> pdb=" O   ARG A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 639 through 641
      No H-bonds generated for 'chain 'A' and resid 639 through 641'
    Processing helix  chain 'A' and resid 647 through 658
    Processing helix  chain 'A' and resid 660 through 673
      removed outlier: 3.775A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 693
    Processing helix  chain 'A' and resid 697 through 722
      removed outlier: 4.340A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE A 718 " --> pdb=" O   ASN A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 741
      removed outlier: 3.633A  pdb=" N   VAL A 736 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG A 741 " --> pdb=" O   GLU A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 748
    Processing helix  chain 'A' and resid 807 through 826
      removed outlier: 3.578A  pdb=" N   ARG A 818 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASN A 822 " --> pdb=" O   ARG A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 864
    Processing helix  chain 'A' and resid 875 through 884
    Processing helix  chain 'A' and resid 886 through 888
      No H-bonds generated for 'chain 'A' and resid 886 through 888'
    Processing helix  chain 'A' and resid 889 through 911
      removed outlier: 3.600A  pdb=" N   ALA A 893 " --> pdb=" O   ILE A 889 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 897 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLY A 903 " --> pdb=" O   ARG A 899 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE A 909 " --> pdb=" O   CYS A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 956 through 965
      removed outlier: 3.591A  pdb=" N   ILE A 962 " --> pdb=" O   GLN A 958 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 973
      removed outlier: 3.849A  pdb=" N   LYS A 973 " --> pdb=" O   GLU A 970 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 970 through 973'
    Processing helix  chain 'A' and resid 974 through 992
      removed outlier: 3.531A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1004
      removed outlier: 3.776A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A1002 " --> pdb=" O   PHE A 998 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1026
      removed outlier: 3.961A  pdb=" N   ARG A1023 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1045
      removed outlier: 3.640A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASP A1045 " --> pdb=" O   LYS A1041 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 344
    Processing helix  chain 'B' and resid 400 through 409
      removed outlier: 3.549A  pdb=" N   TYR B 408 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 416
    Processing helix  chain 'B' and resid 417 through 421
      removed outlier: 3.852A  pdb=" N   ASP B 421 " --> pdb=" O   PRO B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 437
      removed outlier: 3.682A  pdb=" N   VAL B 437 " --> pdb=" O   ASP B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 504
      removed outlier: 3.805A  pdb=" N   VAL B 445 " --> pdb=" O   ASN B 441 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY B 446 " --> pdb=" O   ILE B 442 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LYS B 447 " --> pdb=" O   GLU B 443 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR B 452 " --> pdb=" O   LYS B 448 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN B 457 " --> pdb=" O   ASN B 453 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ARG B 465 " --> pdb=" O   ARG B 461 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU B 466 " --> pdb=" O   GLU B 462 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR B 471 " --> pdb=" O   TYR B 467 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE B 493 " --> pdb=" O   GLU B 489 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLU B 496 " --> pdb=" O   LYS B 492 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR B 500 " --> pdb=" O   GLU B 496 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU B 502 " --> pdb=" O   CYS B 498 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG B 503 " --> pdb=" O   GLN B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 524
      removed outlier: 4.248A  pdb=" N   GLN B 522 " --> pdb=" O   GLU B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 553
      removed outlier: 3.525A  pdb=" N   GLU B 537 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE B 538 " --> pdb=" O   ARG B 534 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE B 539 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER B 541 " --> pdb=" O   GLU B 537 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG B 544 " --> pdb=" O   ASP B 540 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP B 548 " --> pdb=" O   ARG B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 582
      removed outlier: 3.642A  pdb=" N   ASP B 560 " --> pdb=" O   TYR B 556 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   MET B 563 " --> pdb=" O   ILE B 559 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN B 564 " --> pdb=" O   ASP B 560 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
      removed outlier: 3.543A  pdb=" N   ILE B 571 " --> pdb=" O   LYS B 567 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN B 572 " --> pdb=" O   PRO B 568 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU B 573 " --> pdb=" O   ASP B 569 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG B 574 " --> pdb=" O   LEU B 570 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   TYR B 580 " --> pdb=" O   THR B 576 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU B 581 " --> pdb=" O   ARG B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 593 through 598
      removed outlier: 3.711A  pdb=" N   LEU B 598 " --> pdb=" O   LEU B 594 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36
      removed outlier: 7.815A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLU A  23 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   VAL A 101 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   LEU A  25 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 212
      removed outlier: 5.832A  pdb=" N   ILE A 197 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA A 289 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 326
      removed outlier: 6.558A  pdb=" N   LYS A 325 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392
      removed outlier: 7.000A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 476 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   GLU A 476 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   CYS A 340 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.910A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372
      removed outlier: 6.601A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 770 through 771
      removed outlier: 6.819A  pdb=" N   VAL A 845 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AA9, first strand: chain 'B' and resid 377 through 381
      removed outlier: 4.132A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.56

  Time building geometry restraints manager: 2.99 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1725
        1.30 -     1.43: 2679
        1.43 -     1.56: 5984
        1.56 -     1.69: 1
        1.69 -     1.82: 113
  Bond restraints: 10502
  Sorted by residual:
  bond pdb=" C25 UEX A1101 "
       pdb=" N35 UEX A1101 "
    ideal  model  delta    sigma   weight residual
    1.291  1.455 -0.164 2.00e-02 2.50e+03 6.74e+01
  bond pdb=" C15 UEX A1101 "
       pdb=" N35 UEX A1101 "
    ideal  model  delta    sigma   weight residual
    1.364  1.479 -0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" C04 UEX A1101 "
       pdb=" N03 UEX A1101 "
    ideal  model  delta    sigma   weight residual
    1.359  1.456 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" C25 UEX A1101 "
       pdb=" N26 UEX A1101 "
    ideal  model  delta    sigma   weight residual
    1.367  1.449 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" C25 UEX A1101 "
       pdb=" N23 UEX A1101 "
    ideal  model  delta    sigma   weight residual
    1.379  1.452 -0.073 2.00e-02 2.50e+03 1.33e+01
  ... (remaining 10497 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 13772
        2.05 -     4.11: 348
        4.11 -     6.16: 33
        6.16 -     8.22: 10
        8.22 -    10.27: 4
  Bond angle restraints: 14167
  Sorted by residual:
  angle pdb=" N   ILE B 509 "
        pdb=" CA  ILE B 509 "
        pdb=" C   ILE B 509 "
      ideal   model   delta    sigma   weight residual
     113.71  108.94    4.77 9.50e-01 1.11e+00 2.52e+01
  angle pdb=" C25 UEX A1101 "
        pdb=" N26 UEX A1101 "
        pdb=" C27 UEX A1101 "
      ideal   model   delta    sigma   weight residual
     121.93  132.20  -10.27 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" C   ARG B 386 "
        pdb=" N   ASP B 387 "
        pdb=" CA  ASP B 387 "
      ideal   model   delta    sigma   weight residual
     121.54  127.95   -6.41 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" N23 UEX A1101 "
        pdb=" C25 UEX A1101 "
        pdb=" N26 UEX A1101 "
      ideal   model   delta    sigma   weight residual
     118.03  127.92   -9.89 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" CA  TYR A 392 "
        pdb=" CB  TYR A 392 "
        pdb=" CG  TYR A 392 "
      ideal   model   delta    sigma   weight residual
     113.90  119.11   -5.21 1.80e+00 3.09e-01 8.37e+00
  ... (remaining 14162 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.59: 6090
       15.59 -    31.18: 271
       31.18 -    46.77: 55
       46.77 -    62.35: 3
       62.35 -    77.94: 10
  Dihedral angle restraints: 6429
    sinusoidal: 2754
      harmonic: 3675
  Sorted by residual:
  dihedral pdb=" CA  ARG A1047 "
           pdb=" C   ARG A1047 "
           pdb=" N   HIS A1048 "
           pdb=" CA  HIS A1048 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.04  -26.96     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  LYS B 506 "
           pdb=" C   LYS B 506 "
           pdb=" N   GLU B 507 "
           pdb=" CA  GLU B 507 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.74   23.26     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  TRP B 597 "
           pdb=" C   TRP B 597 "
           pdb=" N   LEU B 598 "
           pdb=" CA  LEU B 598 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.04  -20.96     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 6426 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1174
       0.062 -    0.123: 327
       0.123 -    0.185: 28
       0.185 -    0.246: 1
       0.246 -    0.308: 1
  Chirality restraints: 1531
  Sorted by residual:
  chirality pdb=" CG  LEU A 456 "
            pdb=" CB  LEU A 456 "
            pdb=" CD1 LEU A 456 "
            pdb=" CD2 LEU A 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CA  ASP A 258 "
            pdb=" N   ASP A 258 "
            pdb=" C   ASP A 258 "
            pdb=" CB  ASP A 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CB  ILE A 391 "
            pdb=" CA  ILE A 391 "
            pdb=" CG1 ILE A 391 "
            pdb=" CG2 ILE A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.79e-01
  ... (remaining 1528 not shown)

  Planarity restraints: 1818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 759 "   -0.014 2.00e-02 2.50e+03   1.86e-02 5.20e+00
        pdb=" CG  HIS A 759 "    0.039 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 759 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 759 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 759 "    0.006 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 759 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 780 "   -0.007 2.00e-02 2.50e+03   1.35e-02 4.58e+00
        pdb=" CG  TRP A 780 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 780 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 780 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 780 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 780 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 780 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 780 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 780 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 780 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 174 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO A 175 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 175 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 175 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1815 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 302
        2.70 -     3.25: 9967
        3.25 -     3.80: 14712
        3.80 -     4.35: 21567
        4.35 -     4.90: 34523
  Nonbonded interactions: 81071
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 358 "
            pdb=" OH  TYR A 389 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" N   ARG A  19 "
            pdb=" O   CYS A  36 "
     model   vdw
     2.170 3.120
  nonbonded pdb=" OE1 GLU A 768 "
            pdb=" ND2 ASN A 782 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   SER A  66 "
            pdb=" OG  SER A  67 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NZ  LYS A 733 "
            pdb=" OE2 GLU A 737 "
     model   vdw
     2.229 3.120
  ... (remaining 81066 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.930
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
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      :  0.008   0.164  10502  Z= 0.342
  Angle     :  0.803  10.272  14167  Z= 0.429
  Chirality :  0.053   0.308   1531
  Planarity :  0.006   0.051   1818
  Dihedral  : 10.206  77.942   4043
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.31 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.40 (0.20), residues: 1231
  helix: -3.79 (0.14), residues: 563
  sheet: -1.75 (0.35), residues: 166
  loop : -1.98 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP A 780 
 HIS   0.023   0.003   HIS A 759 
 PHE   0.023   0.004   PHE A 937 
 TYR   0.032   0.004   TYR B 426 
 ARG   0.012   0.001   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.32266 (  413)
  hydrogen bonds       : angle       9.46925 ( 1182)
  covalent geometry    : bond        0.00790 (10502)
  covalent geometry    : angle       0.80266 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 240
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 ASP cc_start: 0.7485 (m-30) cc_final: 0.7239 (m-30)
REVERT: B  364 MET cc_start: 0.5882 (tmm) cc_final: 0.3614 (mtp)
REVERT: B  367 ASP cc_start: 0.5420 (m-30) cc_final: 0.4975 (m-30)
REVERT: B  420 LEU cc_start: 0.8383 (tp) cc_final: 0.8122 (tp)
REVERT: B  465 ARG cc_start: 0.6916 (ttp80) cc_final: 0.6703 (ttm-80)
REVERT: B  478 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7435 (tp-100)
REVERT: B  528 TYR cc_start: 0.8020 (t80) cc_final: 0.7747 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 242
  average time/residue: 1.4404
  time to fit residues: 370.4692
Evaluate side-chains
  169 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 96 optimal weight:    8.9990
   chunk 37 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 157 ASN
A 213 HIS
A 370 ASN
A 380 ASN
A 384 ASN
A 419 HIS
A 630 GLN
A 738 GLN
A 795 GLN
A 917 HIS
** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 HIS
B 499 GLN
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 552 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.178668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.144596 restraints weight = 10980.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.92
r_work: 0.3303 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10502  Z= 0.151
  Angle     :  0.650   9.743  14167  Z= 0.337
  Chirality :  0.045   0.182   1531
  Planarity :  0.005   0.050   1818
  Dihedral  :  5.287  21.992   1381
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.41 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.22), residues: 1231
  helix: -1.60 (0.20), residues: 555
  sheet: -1.00 (0.38), residues: 160
  loop : -1.41 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 780 
 HIS   0.008   0.001   HIS A 759 
 PHE   0.020   0.002   PHE A 744 
 TYR   0.026   0.002   TYR A 392 
 ARG   0.005   0.001   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07015 (  413)
  hydrogen bonds       : angle       4.78910 ( 1182)
  covalent geometry    : bond        0.00333 (10502)
  covalent geometry    : angle       0.64962 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 176
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8398 (m-30)
REVERT: A  227 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7104 (tttt)
REVERT: A  454 ASP cc_start: 0.8077 (m-30) cc_final: 0.7694 (m-30)
REVERT: A  528 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7205 (mtmt)
REVERT: A  529 GLU cc_start: 0.7555 (mp0) cc_final: 0.7137 (mp0)
REVERT: A  717 ASP cc_start: 0.7743 (m-30) cc_final: 0.7397 (m-30)
REVERT: A  883 ASP cc_start: 0.6747 (m-30) cc_final: 0.6359 (m-30)
REVERT: A 1044 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7990 (t0)
REVERT: B  326 MET cc_start: 0.6788 (mpp) cc_final: 0.5895 (ptp)
REVERT: B  342 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7027 (tm-30)
REVERT: B  364 MET cc_start: 0.5261 (tmm) cc_final: 0.3208 (mtp)
REVERT: B  367 ASP cc_start: 0.6031 (m-30) cc_final: 0.5425 (m-30)
REVERT: B  420 LEU cc_start: 0.8558 (tp) cc_final: 0.8148 (tp)
REVERT: B  468 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6543 (mm-30)
REVERT: B  537 GLU cc_start: 0.6835 (tt0) cc_final: 0.6560 (tt0)
REVERT: B  551 LYS cc_start: 0.8328 (tttt) cc_final: 0.7961 (tmmt)
REVERT: B  582 MET cc_start: 0.5781 (tmm) cc_final: 0.5535 (mtp)
  outliers start: 14
  outliers final: 2
  residues processed: 185
  average time/residue: 1.4093
  time to fit residues: 278.9072
Evaluate side-chains
  153 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  528 LYS
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0270
   chunk 71 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 213 HIS
A1048 HIS
B 417 ASN
B 527 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.177957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.143836 restraints weight = 11254.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.38
r_work: 0.3237 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10502  Z= 0.153
  Angle     :  0.607   9.819  14167  Z= 0.312
  Chirality :  0.045   0.171   1531
  Planarity :  0.004   0.047   1818
  Dihedral  :  4.940  19.867   1381
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  9.37 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.23), residues: 1231
  helix: -0.49 (0.22), residues: 558
  sheet: -0.68 (0.38), residues: 160
  loop : -1.24 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 597 
 HIS   0.008   0.001   HIS A 759 
 PHE   0.020   0.002   PHE A 667 
 TYR   0.022   0.002   TYR A 392 
 ARG   0.005   0.001   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06353 (  413)
  hydrogen bonds       : angle       4.38576 ( 1182)
  covalent geometry    : bond        0.00353 (10502)
  covalent geometry    : angle       0.60735 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8533 (m-30)
REVERT: A  162 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7541 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8104 (p0) cc_final: 0.7655 (p0)
REVERT: A  227 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7263 (tttt)
REVERT: B  326 MET cc_start: 0.6737 (mpp) cc_final: 0.6430 (mmt)
REVERT: B  342 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7146 (tm-30)
REVERT: B  364 MET cc_start: 0.4937 (tmm) cc_final: 0.3024 (mtp)
REVERT: B  367 ASP cc_start: 0.6265 (m-30) cc_final: 0.5602 (m-30)
REVERT: B  465 ARG cc_start: 0.7141 (ttp80) cc_final: 0.6759 (ptm-80)
REVERT: B  469 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7210 (tt0)
REVERT: B  495 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7023 (mm-30)
REVERT: B  525 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6226 (mpp)
REVERT: B  537 GLU cc_start: 0.6816 (tt0) cc_final: 0.6567 (tt0)
REVERT: B  551 LYS cc_start: 0.8297 (tttt) cc_final: 0.7935 (tmmt)
  outliers start: 28
  outliers final: 8
  residues processed: 177
  average time/residue: 1.3288
  time to fit residues: 251.8445
Evaluate side-chains
  164 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  525 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 40 optimal weight:    0.0470
   chunk 112 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 93 optimal weight:    9.9990
   chunk 77 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 96 optimal weight:   20.0000
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 384 ASN
A 796 ASN
A 936 HIS
A1048 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.180855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145493 restraints weight = 11113.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.13
r_work: 0.3297 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10502  Z= 0.103
  Angle     :  0.527  10.060  14167  Z= 0.269
  Chirality :  0.041   0.163   1531
  Planarity :  0.004   0.046   1818
  Dihedral  :  4.513  22.163   1381
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.03 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.24), residues: 1231
  helix:  0.26 (0.23), residues: 556
  sheet: -0.52 (0.37), residues: 170
  loop : -1.04 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 669 
 HIS   0.007   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 667 
 TYR   0.018   0.001   TYR A 392 
 ARG   0.003   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04773 (  413)
  hydrogen bonds       : angle       3.96119 ( 1182)
  covalent geometry    : bond        0.00212 (10502)
  covalent geometry    : angle       0.52723 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 1.178 
Fit side-chains
REVERT: A   93 ARG cc_start: 0.7246 (mtm180) cc_final: 0.7002 (mtp180)
REVERT: A  162 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7567 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8018 (p0) cc_final: 0.7597 (p0)
REVERT: A  227 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7337 (tttt)
REVERT: A  529 GLU cc_start: 0.7533 (mp0) cc_final: 0.7051 (mp0)
REVERT: A  766 LEU cc_start: 0.8908 (mm) cc_final: 0.8575 (mm)
REVERT: A  787 ASP cc_start: 0.7964 (t0) cc_final: 0.7755 (t0)
REVERT: A 1044 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (t0)
REVERT: B  326 MET cc_start: 0.6625 (mpp) cc_final: 0.6303 (mmt)
REVERT: B  341 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7279 (mp0)
REVERT: B  342 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7076 (tm-30)
REVERT: B  364 MET cc_start: 0.4924 (tmm) cc_final: 0.2905 (mtm)
REVERT: B  367 ASP cc_start: 0.6227 (m-30) cc_final: 0.5591 (m-30)
REVERT: B  495 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6969 (mm-30)
REVERT: B  525 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6228 (mpp)
REVERT: B  551 LYS cc_start: 0.8176 (tttt) cc_final: 0.7839 (tmmt)
REVERT: B  582 MET cc_start: 0.5514 (tmm) cc_final: 0.4828 (ptt)
  outliers start: 21
  outliers final: 4
  residues processed: 178
  average time/residue: 1.4270
  time to fit residues: 271.6615
Evaluate side-chains
  159 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  525 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 79 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 3 optimal weight:    0.1980
   chunk 58 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 738 GLN
A 936 HIS
A1048 HIS
B 415 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.178490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.143838 restraints weight = 11034.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.48
r_work: 0.3179 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10502  Z= 0.143
  Angle     :  0.577   9.975  14167  Z= 0.295
  Chirality :  0.044   0.164   1531
  Planarity :  0.004   0.039   1818
  Dihedral  :  4.568  19.776   1381
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.56 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.24), residues: 1231
  helix:  0.34 (0.23), residues: 558
  sheet: -0.22 (0.38), residues: 161
  loop : -0.95 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 479 
 HIS   0.007   0.001   HIS A 213 
 PHE   0.018   0.002   PHE A 667 
 TYR   0.018   0.002   TYR A 392 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05599 (  413)
  hydrogen bonds       : angle       4.04206 ( 1182)
  covalent geometry    : bond        0.00329 (10502)
  covalent geometry    : angle       0.57687 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 1.296 
Fit side-chains
REVERT: A   85 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7921 (mp0)
REVERT: A   93 ARG cc_start: 0.7324 (mtm180) cc_final: 0.7026 (mtp180)
REVERT: A  115 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8249 (tmm160)
REVERT: A  155 ASP cc_start: 0.7863 (t0) cc_final: 0.7653 (m-30)
REVERT: A  162 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7549 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8072 (p0) cc_final: 0.7599 (p0)
REVERT: A  227 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7261 (tttm)
REVERT: A  766 LEU cc_start: 0.8957 (mm) cc_final: 0.8635 (mm)
REVERT: A  768 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7422 (mt-10)
REVERT: B  326 MET cc_start: 0.6695 (mpp) cc_final: 0.6416 (mmt)
REVERT: B  342 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7154 (tm-30)
REVERT: B  364 MET cc_start: 0.4807 (tmm) cc_final: 0.2814 (mtm)
REVERT: B  367 ASP cc_start: 0.6233 (m-30) cc_final: 0.5596 (m-30)
REVERT: B  525 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6055 (mpp)
REVERT: B  551 LYS cc_start: 0.8253 (tttt) cc_final: 0.7890 (tmmt)
REVERT: B  581 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5385 (mp)
  outliers start: 30
  outliers final: 11
  residues processed: 176
  average time/residue: 1.3226
  time to fit residues: 249.3113
Evaluate side-chains
  166 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  502 GLU
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 117 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 122 optimal weight:    0.0570
   chunk 18 optimal weight:    0.5980
   chunk 121 optimal weight:    7.9990
   chunk 119 optimal weight:    5.9990
   overall best weight:    1.2900

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 384 ASN
A 738 GLN
A 936 HIS
A1048 HIS
B 415 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.180549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.146290 restraints weight = 11131.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.36
r_work: 0.3272 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10502  Z= 0.109
  Angle     :  0.530  10.043  14167  Z= 0.270
  Chirality :  0.042   0.161   1531
  Planarity :  0.003   0.039   1818
  Dihedral  :  4.380  20.725   1381
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.87 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.24), residues: 1231
  helix:  0.61 (0.23), residues: 563
  sheet: -0.18 (0.37), residues: 170
  loop : -0.87 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.007   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 667 
 TYR   0.016   0.001   TYR A 392 
 ARG   0.002   0.000   ARG A1047 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04765 (  413)
  hydrogen bonds       : angle       3.81883 ( 1182)
  covalent geometry    : bond        0.00240 (10502)
  covalent geometry    : angle       0.52965 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7933 (mp0)
REVERT: A   93 ARG cc_start: 0.7223 (mtm180) cc_final: 0.6974 (mtp180)
REVERT: A  162 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7389 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8046 (p0) cc_final: 0.7581 (p0)
REVERT: A  227 LYS cc_start: 0.7778 (ttmt) cc_final: 0.7321 (tttm)
REVERT: A  529 GLU cc_start: 0.7504 (mp0) cc_final: 0.7063 (mp0)
REVERT: A  738 GLN cc_start: 0.7884 (mm110) cc_final: 0.7649 (mm-40)
REVERT: A  766 LEU cc_start: 0.8933 (mm) cc_final: 0.8608 (mm)
REVERT: A  787 ASP cc_start: 0.7941 (t0) cc_final: 0.7739 (t0)
REVERT: B  326 MET cc_start: 0.6669 (mpp) cc_final: 0.6397 (mmt)
REVERT: B  342 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7160 (tm-30)
REVERT: B  364 MET cc_start: 0.4821 (tmm) cc_final: 0.2806 (mtm)
REVERT: B  367 ASP cc_start: 0.6069 (m-30) cc_final: 0.5415 (m-30)
REVERT: B  525 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6098 (mpp)
REVERT: B  551 LYS cc_start: 0.8152 (tttt) cc_final: 0.7820 (tmmt)
REVERT: B  581 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.5442 (mp)
  outliers start: 22
  outliers final: 9
  residues processed: 172
  average time/residue: 1.5343
  time to fit residues: 283.0822
Evaluate side-chains
  162 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 22 optimal weight:    8.9990
   chunk 119 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 122 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 117 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 384 ASN
A 936 HIS
A1048 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.176003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.135140 restraints weight = 11127.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.51
r_work: 0.3260 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10502  Z= 0.212
  Angle     :  0.658   9.807  14167  Z= 0.337
  Chirality :  0.048   0.165   1531
  Planarity :  0.005   0.033   1818
  Dihedral  :  4.796  21.926   1381
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.78 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.24), residues: 1231
  helix:  0.21 (0.22), residues: 568
  sheet:  0.03 (0.39), residues: 161
  loop : -0.99 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 479 
 HIS   0.009   0.002   HIS A 759 
 PHE   0.018   0.002   PHE A 667 
 TYR   0.018   0.002   TYR A  56 
 ARG   0.006   0.001   ARG A 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06605 (  413)
  hydrogen bonds       : angle       4.15454 ( 1182)
  covalent geometry    : bond        0.00511 (10502)
  covalent geometry    : angle       0.65772 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 2.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7867 (mp0)
REVERT: A  115 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8238 (tmm160)
REVERT: A  162 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7494 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8078 (p0) cc_final: 0.7632 (p0)
REVERT: A  227 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7341 (tttt)
REVERT: A  766 LEU cc_start: 0.9007 (mm) cc_final: 0.8695 (mm)
REVERT: A  883 ASP cc_start: 0.6831 (m-30) cc_final: 0.6525 (m-30)
REVERT: B  341 GLU cc_start: 0.7724 (pt0) cc_final: 0.7224 (mp0)
REVERT: B  342 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7240 (tm-30)
REVERT: B  364 MET cc_start: 0.5027 (tmm) cc_final: 0.2898 (mtm)
REVERT: B  367 ASP cc_start: 0.6143 (m-30) cc_final: 0.5463 (m-30)
REVERT: B  476 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7645 (mt-10)
REVERT: B  525 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6147 (mpp)
REVERT: B  551 LYS cc_start: 0.8202 (tttt) cc_final: 0.7881 (tmmt)
REVERT: B  581 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5539 (mp)
  outliers start: 28
  outliers final: 14
  residues processed: 169
  average time/residue: 1.6256
  time to fit residues: 294.8147
Evaluate side-chains
  160 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 110 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 119 optimal weight:    7.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 384 ASN
A 738 GLN
A 936 HIS
A1048 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.176126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.137531 restraints weight = 10831.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.45
r_work: 0.3237 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10502  Z= 0.103
  Angle     :  0.526  10.152  14167  Z= 0.267
  Chirality :  0.042   0.161   1531
  Planarity :  0.003   0.038   1818
  Dihedral  :  4.443  20.631   1381
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 14.45 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.24), residues: 1231
  helix:  0.79 (0.23), residues: 561
  sheet:  0.17 (0.40), residues: 155
  loop : -0.85 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 597 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.013   0.001   PHE A 667 
 TYR   0.015   0.001   TYR A 392 
 ARG   0.002   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04509 (  413)
  hydrogen bonds       : angle       3.75365 ( 1182)
  covalent geometry    : bond        0.00217 (10502)
  covalent geometry    : angle       0.52646 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 153
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7916 (mp0)
REVERT: A   93 ARG cc_start: 0.7332 (mtm180) cc_final: 0.7052 (mtp180)
REVERT: A  115 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8262 (tmm160)
REVERT: A  162 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7376 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8051 (p0) cc_final: 0.7572 (p0)
REVERT: A  227 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7317 (tttt)
REVERT: A  263 GLU cc_start: 0.7930 (tt0) cc_final: 0.7722 (mt-10)
REVERT: A  529 GLU cc_start: 0.7471 (mp0) cc_final: 0.7035 (mp0)
REVERT: A  765 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7299 (mmm160)
REVERT: A  787 ASP cc_start: 0.7928 (t0) cc_final: 0.7653 (t0)
REVERT: B  326 MET cc_start: 0.6798 (mmt) cc_final: 0.5748 (ptp)
REVERT: B  341 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7197 (mp0)
REVERT: B  342 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7214 (tm-30)
REVERT: B  364 MET cc_start: 0.4871 (tmm) cc_final: 0.2833 (mtm)
REVERT: B  367 ASP cc_start: 0.6060 (m-30) cc_final: 0.5419 (m-30)
REVERT: B  476 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7800 (mt-10)
REVERT: B  522 GLN cc_start: 0.5903 (tm130) cc_final: 0.5636 (tp-100)
REVERT: B  525 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6074 (mpp)
REVERT: B  551 LYS cc_start: 0.8171 (tttt) cc_final: 0.7810 (tmmt)
  outliers start: 15
  outliers final: 6
  residues processed: 162
  average time/residue: 2.0576
  time to fit residues: 356.9091
Evaluate side-chains
  155 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  525 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 113 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 213 HIS
A 826 ASN
A 936 HIS
A1048 HIS
B 407 HIS
** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.172473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.135166 restraints weight = 10834.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.26
r_work: 0.3172 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10502  Z= 0.171
  Angle     :  0.611   9.904  14167  Z= 0.312
  Chirality :  0.046   0.163   1531
  Planarity :  0.004   0.034   1818
  Dihedral  :  4.623  21.298   1381
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.62 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.24), residues: 1231
  helix:  0.57 (0.22), residues: 564
  sheet:  0.28 (0.40), residues: 156
  loop : -0.97 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 479 
 HIS   0.008   0.002   HIS A 213 
 PHE   0.018   0.002   PHE A 667 
 TYR   0.018   0.002   TYR A 392 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05921 (  413)
  hydrogen bonds       : angle       3.97320 ( 1182)
  covalent geometry    : bond        0.00408 (10502)
  covalent geometry    : angle       0.61090 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7958 (mp0)
REVERT: A   93 ARG cc_start: 0.7369 (mtm180) cc_final: 0.7118 (mtp180)
REVERT: A  115 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8333 (tmm160)
REVERT: A  162 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7458 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8112 (p0) cc_final: 0.7676 (p0)
REVERT: A  227 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7364 (tttt)
REVERT: A  820 MET cc_start: 0.9247 (mtt) cc_final: 0.9020 (mtt)
REVERT: A  883 ASP cc_start: 0.6984 (m-30) cc_final: 0.6656 (m-30)
REVERT: B  326 MET cc_start: 0.6819 (mmt) cc_final: 0.5727 (ptp)
REVERT: B  341 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: B  342 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7403 (tm-30)
REVERT: B  364 MET cc_start: 0.4928 (tmm) cc_final: 0.2883 (mtm)
REVERT: B  367 ASP cc_start: 0.6168 (m-30) cc_final: 0.5526 (m-30)
REVERT: B  420 LEU cc_start: 0.8525 (tp) cc_final: 0.8274 (tt)
REVERT: B  476 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7978 (mt-10)
REVERT: B  525 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6160 (mpp)
REVERT: B  551 LYS cc_start: 0.8284 (tttt) cc_final: 0.7949 (tmmt)
  outliers start: 16
  outliers final: 8
  residues processed: 157
  average time/residue: 1.4069
  time to fit residues: 236.5716
Evaluate side-chains
  155 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  525 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 75 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 99 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0030
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.0194

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 213 HIS
A 219 GLN
A 936 HIS
A1048 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.176179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.138283 restraints weight = 10735.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.25
r_work: 0.3228 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10502  Z= 0.106
  Angle     :  0.530  10.153  14167  Z= 0.270
  Chirality :  0.042   0.161   1531
  Planarity :  0.003   0.037   1818
  Dihedral  :  4.352  20.366   1381
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 15.15 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.24), residues: 1231
  helix:  0.93 (0.22), residues: 567
  sheet:  0.35 (0.40), residues: 155
  loop : -0.84 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 479 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 667 
 TYR   0.014   0.001   TYR A 392 
 ARG   0.002   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04565 (  413)
  hydrogen bonds       : angle       3.70469 ( 1182)
  covalent geometry    : bond        0.00232 (10502)
  covalent geometry    : angle       0.52973 (14167)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7875 (mp0)
REVERT: A   93 ARG cc_start: 0.7390 (mtm180) cc_final: 0.7123 (mtp180)
REVERT: A  162 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7528 (mtm-85)
REVERT: A  186 ASP cc_start: 0.8105 (p0) cc_final: 0.7659 (p0)
REVERT: A  227 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7379 (tttt)
REVERT: A  529 GLU cc_start: 0.7581 (mp0) cc_final: 0.7175 (mp0)
REVERT: A  738 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7487 (mm-40)
REVERT: A  765 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7405 (mmm160)
REVERT: A  787 ASP cc_start: 0.7896 (t0) cc_final: 0.7609 (t0)
REVERT: B  326 MET cc_start: 0.6811 (mmt) cc_final: 0.5662 (ptp)
REVERT: B  341 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7277 (mp0)
REVERT: B  342 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7336 (tm-30)
REVERT: B  364 MET cc_start: 0.4905 (tmm) cc_final: 0.2875 (mtm)
REVERT: B  367 ASP cc_start: 0.6165 (m-30) cc_final: 0.5714 (m-30)
REVERT: B  420 LEU cc_start: 0.8503 (tp) cc_final: 0.8254 (tt)
REVERT: B  476 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7967 (mt-10)
REVERT: B  522 GLN cc_start: 0.5940 (tm130) cc_final: 0.5682 (tp-100)
REVERT: B  525 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6081 (mpp)
REVERT: B  551 LYS cc_start: 0.8201 (tttt) cc_final: 0.7892 (tmmt)
  outliers start: 12
  outliers final: 7
  residues processed: 158
  average time/residue: 1.3316
  time to fit residues: 225.1380
Evaluate side-chains
  154 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  525 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0970
   chunk 65 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0970
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.1980

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 213 HIS
A 219 GLN
A 826 ASN
A 936 HIS
A1048 HIS
B 453 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.175892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.137885 restraints weight = 10745.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.28
r_work: 0.3228 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10502  Z= 0.109
  Angle     :  0.531  10.118  14167  Z= 0.271
  Chirality :  0.042   0.161   1531
  Planarity :  0.003   0.036   1818
  Dihedral  :  4.266  20.078   1381
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.41 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.24), residues: 1231
  helix:  1.04 (0.22), residues: 567
  sheet:  0.45 (0.40), residues: 155
  loop : -0.78 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 479 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.014   0.001   PHE A 667 
 TYR   0.016   0.001   TYR A 392 
 ARG   0.002   0.000   ARG A1047 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04649 (  413)
  hydrogen bonds       : angle       3.67053 ( 1182)
  covalent geometry    : bond        0.00241 (10502)
  covalent geometry    : angle       0.53111 (14167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9761.01 seconds
wall clock time: 170 minutes 24.81 seconds (10224.81 seconds total)