Starting phenix.real_space_refine
on Sat Aug 23 12:41:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hke_34850/08_2025/8hke_34850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hke_34850/08_2025/8hke_34850.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2025/8hke_34850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2025/8hke_34850.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2025/8hke_34850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2025/8hke_34850.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.059
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      74      5.49       5
     S      66      5.16       5
     C    7400      2.51       5
     N    1983      2.21       5
     O    2329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11854
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 5089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 647, 5089
          Classifications: {'peptide': 647}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 629}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 51
    Chain: "A"
      Number of atoms: 5189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 659, 5189
          Classifications: {'peptide': 659}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 640}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 2, 'ASP:plan': 8, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "C"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 790
          Classifications: {'RNA': 37}
          Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17}
          Link IDs: {'rna3p': 36}
    Chain: "D"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 784
          Classifications: {'RNA': 37}
          Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 20}
          Link IDs: {'rna3p': 36}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.25, per 1000 atoms: 0.27
  Number of scatterers: 11854
  At special positions: 0
  Unit cell: (116.48, 112.32, 132.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      66     16.00
     P      74     15.00
     O    2329      8.00
     N    1983      7.00
     C    7400      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 225 " - pdb=" SG  CYS B 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 464 " - pdb=" SG  CYS B 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 225 " - pdb=" SG  CYS A 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 464 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 731 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 455.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" NE2 HIS A 540 "
        pdb="ZN    ZN A 801 " - pdb=" NE2 HIS A 740 "
        pdb="ZN    ZN A 801 " - pdb=" NE2 HIS A 744 "
      pdb="  ZN B 801 "
        pdb="ZN    ZN B 801 " - pdb=" NE2 HIS B 540 "
        pdb="ZN    ZN B 801 " - pdb=" NE2 HIS B 744 "
        pdb="ZN    ZN B 801 " - pdb=" NE2 HIS B 740 "


  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2508

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 11 sheets defined
      46.1% alpha, 10.5% beta
      24 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 127 through 131
    Processing helix  chain 'B' and resid 205 through 210
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'B' and resid 264 through 272
      removed outlier: 4.084A  pdb=" N   MET B 270 " --> pdb=" O   THR B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 323
    Processing helix  chain 'B' and resid 327 through 332
      removed outlier: 4.118A  pdb=" N   LEU B 331 " --> pdb=" O   PRO B 328 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE B 332 " --> pdb=" O   CYS B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 344
      removed outlier: 3.658A  pdb=" N   ILE B 340 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LYS B 341 " --> pdb=" O   ILE B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 433
      removed outlier: 3.603A  pdb=" N   MET B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   LEU B 431 " --> pdb=" O   HIS B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 444 through 454
      removed outlier: 3.755A  pdb=" N   HIS B 450 " --> pdb=" O   ALA B 446 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP B 452 " --> pdb=" O   GLU B 448 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR B 454 " --> pdb=" O   HIS B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 464
      removed outlier: 3.714A  pdb=" N   CYS B 464 " --> pdb=" O   ARG B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 485
      No H-bonds generated for 'chain 'B' and resid 483 through 485'
    Processing helix  chain 'B' and resid 486 through 502
      removed outlier: 4.143A  pdb=" N   THR B 490 " --> pdb=" O   ASN B 486 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA B 494 " --> pdb=" O   THR B 490 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE B 495 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   PHE B 496 " --> pdb=" O   TYR B 492 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL B 498 " --> pdb=" O   ALA B 494 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 500 " --> pdb=" O   PHE B 496 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE B 501 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 531
      removed outlier: 3.727A  pdb=" N   THR B 524 " --> pdb=" O   LEU B 520 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY B 526 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 540
      removed outlier: 4.411A  pdb=" N   ALA B 537 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 569
      removed outlier: 4.236A  pdb=" N   MET B 563 " --> pdb=" O   CYS B 559 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN B 566 " --> pdb=" O   LEU B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 577
      No H-bonds generated for 'chain 'B' and resid 575 through 577'
    Processing helix  chain 'B' and resid 578 through 596
      removed outlier: 3.956A  pdb=" N   VAL B 584 " --> pdb=" O   ASN B 580 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B 585 " --> pdb=" O   ILE B 581 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 596 " --> pdb=" O   LEU B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 626
      removed outlier: 3.644A  pdb=" N   ILE B 605 " --> pdb=" O   TYR B 601 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA B 607 " --> pdb=" O   ARG B 603 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   HIS B 610 " --> pdb=" O   ILE B 606 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS B 621 " --> pdb=" O   ILE B 617 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU B 622 " --> pdb=" O   CYS B 618 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   SER B 624 " --> pdb=" O   ALA B 620 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 626 " --> pdb=" O   GLU B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 652
      removed outlier: 3.783A  pdb=" N   PHE B 639 " --> pdb=" O   PHE B 635 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE B 644 " --> pdb=" O   SER B 640 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET B 649 " --> pdb=" O   ALA B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 659 through 684
      removed outlier: 4.458A  pdb=" N   THR B 663 " --> pdb=" O   ASN B 659 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TYR B 677 " --> pdb=" O   TYR B 673 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   VAL B 682 " --> pdb=" O   GLY B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 709
      removed outlier: 3.778A  pdb=" N   LEU B 701 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 713
    Processing helix  chain 'B' and resid 722 through 727
      removed outlier: 3.622A  pdb=" N   LEU B 727 " --> pdb=" O   ALA B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 761
      removed outlier: 3.581A  pdb=" N   TRP B 743 " --> pdb=" O   SER B 739 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   HIS B 744 " --> pdb=" O   HIS B 740 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 745 " --> pdb=" O   ASP B 741 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ALA B 748 " --> pdb=" O   HIS B 744 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   PHE B 755 " --> pdb=" O   GLY B 751 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   VAL B 758 " --> pdb=" O   THR B 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 762 through 768
      removed outlier: 3.860A  pdb=" N   ASN B 767 " --> pdb=" O   ASP B 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
      removed outlier: 3.713A  pdb=" N   ILE A  68 " --> pdb=" O   GLN A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 128 through 132
      removed outlier: 3.982A  pdb=" N   PHE A 131 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 210
      removed outlier: 3.731A  pdb=" N   ASN A 210 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 210'
    Processing helix  chain 'A' and resid 264 through 272
    Processing helix  chain 'A' and resid 314 through 325
      removed outlier: 3.696A  pdb=" N   THR A 318 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 320 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   MET A 321 " --> pdb=" O   PRO A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 332
    Processing helix  chain 'A' and resid 335 through 340
    Processing helix  chain 'A' and resid 341 through 344
    Processing helix  chain 'A' and resid 426 through 433
    Processing helix  chain 'A' and resid 438 through 454
    Processing helix  chain 'A' and resid 458 through 464
    Processing helix  chain 'A' and resid 480 through 485
    Processing helix  chain 'A' and resid 486 through 493
      removed outlier: 3.683A  pdb=" N   THR A 490 " --> pdb=" O   ASN A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 503
      removed outlier: 4.193A  pdb=" N   ILE A 501 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 540
      removed outlier: 3.692A  pdb=" N   SER A 533 " --> pdb=" O   MET A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 569
      removed outlier: 4.158A  pdb=" N   MET A 563 " --> pdb=" O   CYS A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 596
      removed outlier: 4.199A  pdb=" N   ILE A 581 " --> pdb=" O   ALA A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 626
      removed outlier: 3.547A  pdb=" N   SER A 624 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU A 625 " --> pdb=" O   LYS A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 652
      removed outlier: 4.032A  pdb=" N   MET A 637 " --> pdb=" O   ARG A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 684
      removed outlier: 3.619A  pdb=" N   ILE A 661 " --> pdb=" O   HIS A 657 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   ALA A 662 " --> pdb=" O   LEU A 658 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   THR A 663 " --> pdb=" O   ASN A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 711
    Processing helix  chain 'A' and resid 720 through 726
    Processing helix  chain 'A' and resid 739 through 759
      removed outlier: 3.609A  pdb=" N   ALA A 748 " --> pdb=" O   HIS A 744 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 39
      removed outlier: 3.531A  pdb=" N   VAL B 151 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR B 152 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN B 154 " --> pdb=" O   GLU B  93 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLU B  93 " --> pdb=" O   GLN B 154 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 4.255A  pdb=" N   ARG B 164 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLU B  77 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 193
      removed outlier: 5.693A  pdb=" N   THR B 188 " --> pdb=" O   PHE B 306 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   PHE B 306 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   SER B 190 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   PHE B 304 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 200 through 204
      removed outlier: 3.544A  pdb=" N   ILE B 200 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASN B 227 " --> pdb=" O   PHE B 279 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   THR B 230 " --> pdb=" O   ARG B 251 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 36 through 39
      removed outlier: 3.796A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR A 152 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 51
      removed outlier: 3.656A  pdb=" N   LYS A  49 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 121
      removed outlier: 3.606A  pdb=" N   LYS A  73 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 109 through 110
    Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 187
      removed outlier: 3.805A  pdb=" N   GLN A 213 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 201
    Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 201
      removed outlier: 3.572A  pdb=" N   ASN A 227 " --> pdb=" O   PHE A 279 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   PHE A 255 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      58 hydrogen bonds
      108 hydrogen bond angles
      0 basepair planarities
      24 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3281
        1.33 -     1.45: 2716
        1.45 -     1.57: 6027
        1.57 -     1.69: 146
        1.69 -     1.81: 98
  Bond restraints: 12268
  Sorted by residual:
  bond pdb=" CA  TYR B 492 "
       pdb=" C   TYR B 492 "
    ideal  model  delta    sigma   weight residual
    1.523  1.458  0.065 1.80e-02 3.09e+03 1.31e+01
  bond pdb=" C   PRO A 574 "
       pdb=" N   SER A 575 "
    ideal  model  delta    sigma   weight residual
    1.331  1.256  0.075 2.07e-02 2.33e+03 1.30e+01
  bond pdb=" C   GLU A  93 "
       pdb=" N   VAL A  94 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.031 1.48e-02 4.57e+03 4.28e+00
  bond pdb=" CA  VAL A 278 "
       pdb=" C   VAL A 278 "
    ideal  model  delta    sigma   weight residual
    1.527  1.509  0.018 8.50e-03 1.38e+04 4.25e+00
  bond pdb=" CA  SER B 269 "
       pdb=" C   SER B 269 "
    ideal  model  delta    sigma   weight residual
    1.523  1.490  0.033 1.80e-02 3.09e+03 3.41e+00
  ... (remaining 12263 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.96: 16946
        4.96 -     9.92: 34
        9.92 -    14.88: 4
       14.88 -    19.84: 0
       19.84 -    24.80: 2
  Bond angle restraints: 16986
  Sorted by residual:
  angle pdb=" C   ASN A 234 "
        pdb=" CA  ASN A 234 "
        pdb=" CB  ASN A 234 "
      ideal   model   delta    sigma   weight residual
     110.81  135.61  -24.80 1.60e+00 3.91e-01 2.40e+02
  angle pdb=" N   ALA A 469 "
        pdb=" CA  ALA A 469 "
        pdb=" C   ALA A 469 "
      ideal   model   delta    sigma   weight residual
     110.80   90.59   20.21 2.13e+00 2.20e-01 9.01e+01
  angle pdb=" C   PRO B 553 "
        pdb=" CA  PRO B 553 "
        pdb=" CB  PRO B 553 "
      ideal   model   delta    sigma   weight residual
     111.56  125.99  -14.43 1.65e+00 3.67e-01 7.64e+01
  angle pdb=" N   SER A  66 "
        pdb=" CA  SER A  66 "
        pdb=" C   SER A  66 "
      ideal   model   delta    sigma   weight residual
     113.01  122.68   -9.67 1.20e+00 6.94e-01 6.50e+01
  angle pdb=" C   HIS A 468 "
        pdb=" CA  HIS A 468 "
        pdb=" CB  HIS A 468 "
      ideal   model   delta    sigma   weight residual
     111.83  100.42   11.41 1.60e+00 3.91e-01 5.09e+01
  ... (remaining 16981 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6465
       17.99 -    35.98: 637
       35.98 -    53.97: 136
       53.97 -    71.95: 105
       71.95 -    89.94: 27
  Dihedral angle restraints: 7370
    sinusoidal: 3523
      harmonic: 3847
  Sorted by residual:
  dihedral pdb=" C   ASN A 234 "
           pdb=" N   ASN A 234 "
           pdb=" CA  ASN A 234 "
           pdb=" CB  ASN A 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -153.92   31.32     0      2.50e+00 1.60e-01 1.57e+02
  dihedral pdb=" CB  CYS A 470 "
           pdb=" SG  CYS A 470 "
           pdb=" SG  CYS A 731 "
           pdb=" CB  CYS A 731 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.25   77.25     1      1.00e+01 1.00e-02 7.48e+01
  dihedral pdb=" N   ASN A 234 "
           pdb=" C   ASN A 234 "
           pdb=" CA  ASN A 234 "
           pdb=" CB  ASN A 234 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  144.03  -21.23     0      2.50e+00 1.60e-01 7.21e+01
  ... (remaining 7367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.234: 2047
       0.234 -    0.467: 2
       0.467 -    0.701: 2
       0.701 -    0.934: 0
       0.934 -    1.168: 1
  Chirality restraints: 2052
  Sorted by residual:
  chirality pdb=" CA  ASN A 234 "
            pdb=" N   ASN A 234 "
            pdb=" C   ASN A 234 "
            pdb=" CB  ASN A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.34    1.17 2.00e-01 2.50e+01 3.41e+01
  chirality pdb=" CA  PRO B 553 "
            pdb=" N   PRO B 553 "
            pdb=" C   PRO B 553 "
            pdb=" CB  PRO B 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.15    0.57 2.00e-01 2.50e+01 8.01e+00
  chirality pdb=" CA  HIS A 468 "
            pdb=" N   HIS A 468 "
            pdb=" C   HIS A 468 "
            pdb=" CB  HIS A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.06   -0.55 2.00e-01 2.50e+01 7.62e+00
  ... (remaining 2049 not shown)

  Planarity restraints: 1837
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G D  12 "    0.032 2.00e-02 2.50e+03   1.39e-02 5.80e+00
        pdb=" N9    G D  12 "   -0.031 2.00e-02 2.50e+03
        pdb=" C8    G D  12 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    G D  12 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    G D  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    G D  12 "    0.004 2.00e-02 2.50e+03
        pdb=" O6    G D  12 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    G D  12 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G D  12 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2    G D  12 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G D  12 "   -0.012 2.00e-02 2.50e+03
        pdb=" C4    G D  12 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 542 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO A 543 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  13 "    0.024 2.00e-02 2.50e+03   1.35e-02 4.09e+00
        pdb=" N1    C D  13 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2    C D  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2    C D  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    C D  13 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    C D  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" N4    C D  13 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    C D  13 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C D  13 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1834 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 212
        2.62 -     3.19: 11379
        3.19 -     3.76: 18463
        3.76 -     4.33: 25886
        4.33 -     4.90: 40241
  Nonbonded interactions: 96181
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  45 "
            pdb=" OP1   U D  25 "
     model   vdw
     2.049 3.120
  nonbonded pdb=" OD2 ASP B 551 "
            pdb="ZN    ZN B 801 "
     model   vdw
     2.077 2.230
  nonbonded pdb=" NZ  LYS A 299 "
            pdb=" OP2   C C  19 "
     model   vdw
     2.141 3.120
  nonbonded pdb=" O   ILE B 606 "
            pdb=" OH  TYR B 650 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OG1 THR A 515 "
            pdb=" O   VAL A 569 "
     model   vdw
     2.158 3.040
  ... (remaining 96176 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 34 through 131 or resid 144 through 170 or (resid 171 thro \ 
ugh 173 and (name N or name CA or name C or name O or name CB )) or resid 174 th \ 
rough 292 or (resid 293 through 294 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 295 through 296 or (resid 297 through 299 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 300 through 801))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.520
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
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   0.188  12279  Z= 0.341
  Angle     :  0.826  24.798  16996  Z= 0.450
  Chirality :  0.057   1.168   2052
  Planarity :  0.004   0.056   1837
  Dihedral  : 17.029  89.943   4847
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  9.10 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.32 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.00 (0.19), residues: 1292
  helix: -3.04 (0.17), residues: 513
  sheet: -3.93 (0.28), residues: 230
  loop : -3.12 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 135 
 TYR   0.020   0.002   TYR A 650 
 PHE   0.033   0.002   PHE A 639 
 TRP   0.020   0.002   TRP A 452 
 HIS   0.008   0.002   HIS A 744 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 (12268)
  covalent geometry    : angle       0.82335 (16986)
  SS BOND              : bond        0.00466 (    5)
  SS BOND              : angle       2.84565 (   10)
  hydrogen bonds       : bond        0.23477 (  487)
  hydrogen bonds       : angle       9.42759 ( 1287)
  metal coordination   : bond        0.13506 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7679 (mt-10)
REVERT: B  484 ILE cc_start: 0.9276 (tp) cc_final: 0.8861 (tp)
REVERT: B  591 PHE cc_start: 0.8249 (t80) cc_final: 0.8016 (t80)
REVERT: A  106 LYS cc_start: 0.8704 (mttt) cc_final: 0.8172 (mtmt)
REVERT: A  219 TYR cc_start: 0.8276 (m-80) cc_final: 0.7847 (m-80)
REVERT: A  314 TYR cc_start: 0.8733 (m-80) cc_final: 0.8473 (m-80)
REVERT: A  637 MET cc_start: 0.7661 (ttp) cc_final: 0.6338 (tmm)
REVERT: A  641 MET cc_start: 0.5650 (ptt) cc_final: 0.5204 (ptt)
REVERT: A  681 LYS cc_start: 0.9091 (tttp) cc_final: 0.8851 (tttt)
REVERT: A  728 ASN cc_start: 0.8183 (p0) cc_final: 0.7608 (p0)
REVERT: A  741 ASP cc_start: 0.7995 (m-30) cc_final: 0.7717 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 201
  average time/residue: 0.1155
  time to fit residues: 33.3369
Evaluate side-chains
  151 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
B 113 ASN
B 566 GLN
** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 GLN
A 432 GLN
A 444 HIS
A 566 GLN
A 590 ASN
A 643 ASN
A 657 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.141179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.099573 restraints weight = 21091.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102237 restraints weight = 12373.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.103989 restraints weight = 9172.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.105059 restraints weight = 7736.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.105534 restraints weight = 7003.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12279  Z= 0.148
  Angle     :  0.618   8.173  16996  Z= 0.316
  Chirality :  0.042   0.166   2052
  Planarity :  0.004   0.049   1837
  Dihedral  : 17.377  93.492   2543
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.01 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.19 (0.22), residues: 1292
  helix: -1.13 (0.21), residues: 528
  sheet: -3.35 (0.29), residues: 240
  loop : -2.37 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 769 
 TYR   0.025   0.001   TYR A 650 
 PHE   0.026   0.001   PHE B 324 
 TRP   0.010   0.001   TRP A 452 
 HIS   0.007   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12268)
  covalent geometry    : angle       0.61718 (16986)
  SS BOND              : bond        0.00301 (    5)
  SS BOND              : angle       1.57262 (   10)
  hydrogen bonds       : bond        0.05658 (  487)
  hydrogen bonds       : angle       5.15405 ( 1287)
  metal coordination   : bond        0.00567 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7502 (pm20)
REVERT: B  322 MET cc_start: 0.8141 (mmt) cc_final: 0.7925 (mmt)
REVERT: B  484 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8902 (tp)
REVERT: B  563 MET cc_start: 0.7276 (mtt) cc_final: 0.6844 (mmm)
REVERT: B  676 TYR cc_start: 0.7824 (t80) cc_final: 0.7611 (t80)
REVERT: A  164 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7426 (mtm-85)
REVERT: A  193 LYS cc_start: 0.9188 (tptt) cc_final: 0.8934 (tttp)
REVERT: A  219 TYR cc_start: 0.8070 (m-80) cc_final: 0.7593 (m-10)
REVERT: A  261 ILE cc_start: 0.9175 (mt) cc_final: 0.8941 (mm)
REVERT: A  637 MET cc_start: 0.7310 (ttp) cc_final: 0.6111 (tmm)
REVERT: A  641 MET cc_start: 0.5260 (ptt) cc_final: 0.4839 (ptt)
REVERT: A  672 MET cc_start: 0.8956 (mtm) cc_final: 0.8071 (tpt)
REVERT: A  681 LYS cc_start: 0.9023 (tttp) cc_final: 0.8313 (tttm)
REVERT: A  728 ASN cc_start: 0.8058 (p0) cc_final: 0.7492 (p0)
  outliers start: 20
  outliers final: 12
  residues processed: 195
  average time/residue: 0.0964
  time to fit residues: 28.6386
Evaluate side-chains
  157 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  701 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  733 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 134 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 106 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 103 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 GLN
A 148 ASN
A 466 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.134238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.093233 restraints weight = 21757.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.095705 restraints weight = 12779.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.097288 restraints weight = 9516.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.098286 restraints weight = 8027.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.098684 restraints weight = 7282.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063  12279  Z= 0.359
  Angle     :  0.759  11.121  16996  Z= 0.386
  Chirality :  0.047   0.177   2052
  Planarity :  0.005   0.048   1837
  Dihedral  : 17.519  98.793   2543
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.68 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.03 (0.23), residues: 1292
  helix: -0.95 (0.22), residues: 547
  sheet: -3.28 (0.29), residues: 241
  loop : -2.38 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 504 
 TYR   0.023   0.002   TYR A 650 
 PHE   0.031   0.002   PHE A 131 
 TRP   0.024   0.002   TRP A 452 
 HIS   0.006   0.002   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00824 (12268)
  covalent geometry    : angle       0.75684 (16986)
  SS BOND              : bond        0.00523 (    5)
  SS BOND              : angle       2.43782 (   10)
  hydrogen bonds       : bond        0.05874 (  487)
  hydrogen bonds       : angle       5.17485 ( 1287)
  metal coordination   : bond        0.00997 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 151
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  484 ILE cc_start: 0.9143 (tp) cc_final: 0.8711 (tp)
REVERT: B  563 MET cc_start: 0.7647 (mtt) cc_final: 0.6316 (tmm)
REVERT: A  106 LYS cc_start: 0.8705 (mttt) cc_final: 0.8427 (mttm)
REVERT: A  164 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7443 (mtm-85)
REVERT: A  219 TYR cc_start: 0.8351 (m-80) cc_final: 0.8028 (m-10)
REVERT: A  314 TYR cc_start: 0.8589 (m-80) cc_final: 0.8263 (m-80)
REVERT: A  637 MET cc_start: 0.7467 (ttp) cc_final: 0.6253 (tmm)
REVERT: A  641 MET cc_start: 0.5260 (ptt) cc_final: 0.4841 (ptt)
REVERT: A  681 LYS cc_start: 0.8959 (tttp) cc_final: 0.8691 (tttt)
REVERT: A  728 ASN cc_start: 0.8172 (p0) cc_final: 0.7551 (p0)
  outliers start: 46
  outliers final: 30
  residues processed: 186
  average time/residue: 0.0849
  time to fit residues: 24.5908
Evaluate side-chains
  169 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  555 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  609 ILE
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  679 CYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  579 THR
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  674 LEU
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 89 optimal weight:    0.2980
   chunk 57 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 109 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0980
   chunk 131 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 482 ASN
** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 GLN
A 166 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.141687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.100859 restraints weight = 21307.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.103470 restraints weight = 12661.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.105192 restraints weight = 9432.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.106225 restraints weight = 7943.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.106737 restraints weight = 7186.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12279  Z= 0.113
  Angle     :  0.562   9.510  16996  Z= 0.286
  Chirality :  0.040   0.155   2052
  Planarity :  0.003   0.044   1837
  Dihedral  : 16.917  95.770   2543
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.87 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.19 (0.23), residues: 1292
  helix: -0.26 (0.23), residues: 542
  sheet: -2.81 (0.30), residues: 242
  loop : -1.92 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 478 
 TYR   0.025   0.001   TYR A 650 
 PHE   0.032   0.001   PHE B 324 
 TRP   0.011   0.001   TRP A 567 
 HIS   0.005   0.001   HIS B 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12268)
  covalent geometry    : angle       0.56148 (16986)
  SS BOND              : bond        0.00285 (    5)
  SS BOND              : angle       1.20330 (   10)
  hydrogen bonds       : bond        0.04479 (  487)
  hydrogen bonds       : angle       4.55879 ( 1287)
  metal coordination   : bond        0.00251 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7083 (ppp) cc_final: 0.6598 (ppp)
REVERT: A   88 ASP cc_start: 0.7599 (p0) cc_final: 0.7049 (p0)
REVERT: A  193 LYS cc_start: 0.9174 (tptt) cc_final: 0.8854 (tttt)
REVERT: A  219 TYR cc_start: 0.8030 (m-80) cc_final: 0.7558 (m-10)
REVERT: A  484 ILE cc_start: 0.8871 (tp) cc_final: 0.8500 (tp)
REVERT: A  637 MET cc_start: 0.7218 (ttp) cc_final: 0.6580 (ptt)
REVERT: A  672 MET cc_start: 0.8776 (mtp) cc_final: 0.7934 (tpt)
REVERT: A  675 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7189 (mmp)
REVERT: A  728 ASN cc_start: 0.8052 (p0) cc_final: 0.7494 (p0)
REVERT: A  741 ASP cc_start: 0.7998 (m-30) cc_final: 0.7673 (m-30)
  outliers start: 23
  outliers final: 9
  residues processed: 189
  average time/residue: 0.0706
  time to fit residues: 20.7837
Evaluate side-chains
  162 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 129 optimal weight:   20.0000
   chunk 98 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 ASN
A 148 ASN
A 466 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.137658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.096534 restraints weight = 21330.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.099178 restraints weight = 12438.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.100884 restraints weight = 9189.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.101955 restraints weight = 7714.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102501 restraints weight = 6968.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12279  Z= 0.202
  Angle     :  0.608   9.423  16996  Z= 0.309
  Chirality :  0.042   0.163   2052
  Planarity :  0.003   0.040   1837
  Dihedral  : 16.814  93.453   2543
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.98 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.24), residues: 1292
  helix: -0.16 (0.23), residues: 544
  sheet: -2.70 (0.31), residues: 244
  loop : -1.90 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 164 
 TYR   0.023   0.002   TYR A 650 
 PHE   0.033   0.002   PHE A 755 
 TRP   0.017   0.002   TRP A 452 
 HIS   0.005   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (12268)
  covalent geometry    : angle       0.60643 (16986)
  SS BOND              : bond        0.00408 (    5)
  SS BOND              : angle       1.72894 (   10)
  hydrogen bonds       : bond        0.04514 (  487)
  hydrogen bonds       : angle       4.58180 ( 1287)
  metal coordination   : bond        0.00576 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 149
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  260 ASP cc_start: 0.8769 (m-30) cc_final: 0.8541 (m-30)
REVERT: A   88 ASP cc_start: 0.7638 (p0) cc_final: 0.7088 (p0)
REVERT: A  193 LYS cc_start: 0.9198 (tptt) cc_final: 0.8882 (tttt)
REVERT: A  219 TYR cc_start: 0.8222 (m-80) cc_final: 0.7885 (m-80)
REVERT: A  450 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7301 (t70)
REVERT: A  452 TRP cc_start: 0.9092 (OUTLIER) cc_final: 0.8791 (t-100)
REVERT: A  637 MET cc_start: 0.7319 (ttp) cc_final: 0.6702 (ptt)
REVERT: A  675 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7023 (mmp)
REVERT: A  728 ASN cc_start: 0.8114 (p0) cc_final: 0.7487 (p0)
REVERT: A  741 ASP cc_start: 0.7946 (m-30) cc_final: 0.7695 (m-30)
  outliers start: 49
  outliers final: 35
  residues processed: 184
  average time/residue: 0.0783
  time to fit residues: 22.4434
Evaluate side-chains
  177 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  555 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  609 ILE
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  701 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  452 TRP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  579 THR
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 129 optimal weight:   20.0000
   chunk 112 optimal weight:    5.9990
   chunk 133 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 126 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0970
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.141369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.100654 restraints weight = 21133.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.103392 restraints weight = 12370.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.105177 restraints weight = 9123.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.106322 restraints weight = 7612.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.106867 restraints weight = 6843.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12279  Z= 0.111
  Angle     :  0.539  10.492  16996  Z= 0.273
  Chirality :  0.039   0.177   2052
  Planarity :  0.003   0.042   1837
  Dihedral  : 16.401  84.670   2543
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.21 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.24), residues: 1292
  helix:  0.11 (0.23), residues: 543
  sheet: -2.48 (0.31), residues: 246
  loop : -1.60 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 478 
 TYR   0.024   0.001   TYR A 650 
 PHE   0.032   0.001   PHE A 708 
 TRP   0.010   0.001   TRP A 703 
 HIS   0.005   0.001   HIS B 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12268)
  covalent geometry    : angle       0.53830 (16986)
  SS BOND              : bond        0.00246 (    5)
  SS BOND              : angle       1.07805 (   10)
  hydrogen bonds       : bond        0.04169 (  487)
  hydrogen bonds       : angle       4.35593 ( 1287)
  metal coordination   : bond        0.00184 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   46 MET cc_start: 0.8455 (tpp) cc_final: 0.8233 (tpt)
REVERT: B  563 MET cc_start: 0.7362 (mtm) cc_final: 0.5961 (tmm)
REVERT: B  676 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6635 (t80)
REVERT: B  680 MET cc_start: 0.7955 (mtp) cc_final: 0.7699 (mtp)
REVERT: A   88 ASP cc_start: 0.7493 (p0) cc_final: 0.6915 (p0)
REVERT: A  193 LYS cc_start: 0.9152 (tptt) cc_final: 0.8951 (pttt)
REVERT: A  219 TYR cc_start: 0.8051 (m-80) cc_final: 0.7676 (m-80)
REVERT: A  450 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.7219 (t70)
REVERT: A  484 ILE cc_start: 0.8860 (tp) cc_final: 0.8459 (tp)
REVERT: A  520 LEU cc_start: 0.8149 (mm) cc_final: 0.7792 (mt)
REVERT: A  522 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8018 (t0)
REVERT: A  533 SER cc_start: 0.8765 (t) cc_final: 0.8450 (t)
REVERT: A  637 MET cc_start: 0.7249 (ttp) cc_final: 0.6583 (ptt)
REVERT: A  675 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7157 (mmp)
REVERT: A  728 ASN cc_start: 0.8040 (p0) cc_final: 0.7484 (p0)
  outliers start: 34
  outliers final: 21
  residues processed: 188
  average time/residue: 0.0857
  time to fit residues: 25.1805
Evaluate side-chains
  180 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  609 ILE
Chi-restraints excluded: chain B residue  676 TYR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9980
   chunk 124 optimal weight:    0.0570
   chunk 133 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    1.0100

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

Flipped N/Q/H residues before XYZ refinement:
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.141006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.100011 restraints weight = 21014.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.102730 restraints weight = 12497.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.104500 restraints weight = 9229.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.105611 restraints weight = 7720.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.106155 restraints weight = 6944.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12279  Z= 0.124
  Angle     :  0.556  10.050  16996  Z= 0.278
  Chirality :  0.039   0.168   2052
  Planarity :  0.003   0.041   1837
  Dihedral  : 16.275  82.039   2541
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 22.30 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.24), residues: 1292
  helix:  0.27 (0.23), residues: 543
  sheet: -2.35 (0.31), residues: 259
  loop : -1.42 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 164 
 TYR   0.022   0.001   TYR A 650 
 PHE   0.024   0.001   PHE B 591 
 TRP   0.011   0.001   TRP A 452 
 HIS   0.005   0.001   HIS B 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12268)
  covalent geometry    : angle       0.55577 (16986)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       1.21773 (   10)
  hydrogen bonds       : bond        0.03986 (  487)
  hydrogen bonds       : angle       4.27023 ( 1287)
  metal coordination   : bond        0.00254 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 163
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  676 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6281 (t80)
REVERT: B  680 MET cc_start: 0.8060 (mtp) cc_final: 0.7631 (mtt)
REVERT: A   88 ASP cc_start: 0.7477 (p0) cc_final: 0.6890 (p0)
REVERT: A  193 LYS cc_start: 0.8880 (tptt) cc_final: 0.8641 (pttt)
REVERT: A  219 TYR cc_start: 0.8033 (m-80) cc_final: 0.7677 (m-80)
REVERT: A  314 TYR cc_start: 0.8205 (m-80) cc_final: 0.7897 (m-80)
REVERT: A  450 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7240 (t70)
REVERT: A  484 ILE cc_start: 0.8853 (tp) cc_final: 0.8427 (tp)
REVERT: A  520 LEU cc_start: 0.8181 (mm) cc_final: 0.7748 (mt)
REVERT: A  522 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8053 (t0)
REVERT: A  533 SER cc_start: 0.8770 (t) cc_final: 0.8460 (t)
REVERT: A  637 MET cc_start: 0.7232 (ttp) cc_final: 0.6559 (ptt)
REVERT: A  675 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7183 (mmp)
REVERT: A  728 ASN cc_start: 0.8086 (p0) cc_final: 0.7543 (p0)
REVERT: A  741 ASP cc_start: 0.7948 (m-30) cc_final: 0.7595 (m-30)
  outliers start: 36
  outliers final: 26
  residues processed: 186
  average time/residue: 0.0807
  time to fit residues: 23.6788
Evaluate side-chains
  185 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  555 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  676 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 132 optimal weight:   30.0000
   chunk 108 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 128 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 GLN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.141001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.100109 restraints weight = 21086.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.102836 restraints weight = 12578.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.104643 restraints weight = 9239.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.105770 restraints weight = 7688.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.106176 restraints weight = 6911.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12279  Z= 0.124
  Angle     :  0.552  11.020  16996  Z= 0.277
  Chirality :  0.040   0.180   2052
  Planarity :  0.003   0.042   1837
  Dihedral  : 16.183  82.178   2541
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.03 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.24), residues: 1292
  helix:  0.45 (0.23), residues: 537
  sheet: -2.32 (0.31), residues: 256
  loop : -1.33 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 504 
 TYR   0.022   0.001   TYR A 650 
 PHE   0.025   0.001   PHE A 296 
 TRP   0.011   0.001   TRP A 452 
 HIS   0.006   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12268)
  covalent geometry    : angle       0.55173 (16986)
  SS BOND              : bond        0.00252 (    5)
  SS BOND              : angle       1.15906 (   10)
  hydrogen bonds       : bond        0.03980 (  487)
  hydrogen bonds       : angle       4.23470 ( 1287)
  metal coordination   : bond        0.00248 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 162
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.8971 (mt) cc_final: 0.8598 (tt)
REVERT: B  260 ASP cc_start: 0.8577 (m-30) cc_final: 0.8194 (m-30)
REVERT: B  676 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6357 (t80)
REVERT: B  680 MET cc_start: 0.8065 (mtp) cc_final: 0.7623 (mtt)
REVERT: A   88 ASP cc_start: 0.7466 (p0) cc_final: 0.6876 (p0)
REVERT: A  168 THR cc_start: 0.9217 (p) cc_final: 0.8960 (t)
REVERT: A  219 TYR cc_start: 0.8025 (m-80) cc_final: 0.7676 (m-80)
REVERT: A  299 LYS cc_start: 0.8108 (tttp) cc_final: 0.7456 (ttmt)
REVERT: A  450 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7241 (t70)
REVERT: A  484 ILE cc_start: 0.8812 (tp) cc_final: 0.8450 (tp)
REVERT: A  520 LEU cc_start: 0.8172 (mm) cc_final: 0.7751 (mt)
REVERT: A  522 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8018 (t0)
REVERT: A  533 SER cc_start: 0.8774 (t) cc_final: 0.8472 (t)
REVERT: A  637 MET cc_start: 0.7237 (ttp) cc_final: 0.6559 (ptt)
REVERT: A  675 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7133 (mmp)
REVERT: A  728 ASN cc_start: 0.8072 (p0) cc_final: 0.7569 (p0)
  outliers start: 38
  outliers final: 32
  residues processed: 185
  average time/residue: 0.0816
  time to fit residues: 24.1434
Evaluate side-chains
  192 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 156
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  555 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  676 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   chunk 126 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0470
   chunk 17 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 120 optimal weight:   10.0000
   chunk 111 optimal weight:    0.6980
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.140702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.099980 restraints weight = 20962.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.102681 restraints weight = 12427.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.104407 restraints weight = 9221.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.105233 restraints weight = 7738.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.105950 restraints weight = 7046.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12279  Z= 0.129
  Angle     :  0.559  14.204  16996  Z= 0.280
  Chirality :  0.039   0.173   2052
  Planarity :  0.003   0.038   1837
  Dihedral  : 16.047  82.498   2541
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 22.93 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.24), residues: 1292
  helix:  0.61 (0.23), residues: 537
  sheet: -2.11 (0.32), residues: 247
  loop : -1.32 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 504 
 TYR   0.022   0.001   TYR A 650 
 PHE   0.027   0.001   PHE A 296 
 TRP   0.012   0.001   TRP A 452 
 HIS   0.006   0.001   HIS B 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12268)
  covalent geometry    : angle       0.55887 (16986)
  SS BOND              : bond        0.00256 (    5)
  SS BOND              : angle       1.21859 (   10)
  hydrogen bonds       : bond        0.03967 (  487)
  hydrogen bonds       : angle       4.21997 ( 1287)
  metal coordination   : bond        0.00319 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.8948 (mt) cc_final: 0.8598 (tt)
REVERT: B  100 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7583 (tpp80)
REVERT: B  260 ASP cc_start: 0.8761 (m-30) cc_final: 0.8412 (m-30)
REVERT: B  676 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6674 (t80)
REVERT: B  680 MET cc_start: 0.8058 (mtp) cc_final: 0.7846 (mtp)
REVERT: A   88 ASP cc_start: 0.7485 (p0) cc_final: 0.6952 (p0)
REVERT: A  168 THR cc_start: 0.9243 (p) cc_final: 0.8982 (t)
REVERT: A  219 TYR cc_start: 0.8022 (m-80) cc_final: 0.7675 (m-80)
REVERT: A  314 TYR cc_start: 0.8154 (m-80) cc_final: 0.7943 (m-80)
REVERT: A  450 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7243 (t70)
REVERT: A  484 ILE cc_start: 0.8796 (tp) cc_final: 0.8424 (tp)
REVERT: A  520 LEU cc_start: 0.8180 (mm) cc_final: 0.7778 (mt)
REVERT: A  522 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8005 (t0)
REVERT: A  533 SER cc_start: 0.8795 (t) cc_final: 0.8502 (t)
REVERT: A  637 MET cc_start: 0.7246 (ttp) cc_final: 0.6564 (ptt)
REVERT: A  728 ASN cc_start: 0.8098 (p0) cc_final: 0.7553 (p0)
  outliers start: 36
  outliers final: 31
  residues processed: 181
  average time/residue: 0.0804
  time to fit residues: 23.3818
Evaluate side-chains
  187 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  555 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  676 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 129 optimal weight:   20.0000
   chunk 86 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 131 optimal weight:   10.0000
   chunk 119 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0570
   chunk 32 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.4106

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

Flipped N/Q/H residues before XYZ refinement:
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.140190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.099423 restraints weight = 21312.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.102030 restraints weight = 12783.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.103739 restraints weight = 9545.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.104537 restraints weight = 8045.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.105386 restraints weight = 7342.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12279  Z= 0.146
  Angle     :  0.569  12.820  16996  Z= 0.286
  Chirality :  0.040   0.189   2052
  Planarity :  0.003   0.041   1837
  Dihedral  : 16.057  82.767   2541
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.93 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.24), residues: 1292
  helix:  0.59 (0.23), residues: 537
  sheet: -2.11 (0.32), residues: 245
  loop : -1.33 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 504 
 TYR   0.022   0.001   TYR A 650 
 PHE   0.037   0.001   PHE A 496 
 TRP   0.013   0.001   TRP A 452 
 HIS   0.005   0.001   HIS B 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (12268)
  covalent geometry    : angle       0.56853 (16986)
  SS BOND              : bond        0.00285 (    5)
  SS BOND              : angle       1.29243 (   10)
  hydrogen bonds       : bond        0.04028 (  487)
  hydrogen bonds       : angle       4.23562 ( 1287)
  metal coordination   : bond        0.00384 (    6)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.8948 (mt) cc_final: 0.8600 (tt)
REVERT: B   97 SER cc_start: 0.9156 (t) cc_final: 0.8915 (m)
REVERT: B  100 ARG cc_start: 0.8025 (tpp80) cc_final: 0.7619 (tpp80)
REVERT: B  260 ASP cc_start: 0.8693 (m-30) cc_final: 0.8456 (m-30)
REVERT: A   88 ASP cc_start: 0.7479 (p0) cc_final: 0.6970 (p0)
REVERT: A  168 THR cc_start: 0.9250 (p) cc_final: 0.8974 (t)
REVERT: A  219 TYR cc_start: 0.8052 (m-80) cc_final: 0.7714 (m-80)
REVERT: A  314 TYR cc_start: 0.8247 (m-80) cc_final: 0.8016 (m-80)
REVERT: A  450 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7261 (t70)
REVERT: A  484 ILE cc_start: 0.8823 (tp) cc_final: 0.8473 (tp)
REVERT: A  520 LEU cc_start: 0.8174 (mm) cc_final: 0.7773 (mt)
REVERT: A  522 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8008 (t0)
REVERT: A  637 MET cc_start: 0.7265 (ttp) cc_final: 0.6575 (ptt)
REVERT: A  649 MET cc_start: 0.8235 (mmt) cc_final: 0.7908 (mpp)
REVERT: A  728 ASN cc_start: 0.8097 (p0) cc_final: 0.7560 (p0)
  outliers start: 37
  outliers final: 33
  residues processed: 180
  average time/residue: 0.0769
  time to fit residues: 22.5878
Evaluate side-chains
  189 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  555 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  701 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  618 CYS
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  749 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 79 optimal weight:    8.9990
   chunk 99 optimal weight:    6.9990
   chunk 103 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0980
   chunk 41 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.142325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102278 restraints weight = 20965.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.104978 restraints weight = 13532.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.106087 restraints weight = 9414.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.106128 restraints weight = 8259.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.106380 restraints weight = 8169.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12279  Z= 0.107
  Angle     :  0.547  12.274  16996  Z= 0.273
  Chirality :  0.039   0.263   2052
  Planarity :  0.003   0.039   1837
  Dihedral  : 15.925  83.287   2541
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.17 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.24), residues: 1292
  helix:  0.71 (0.23), residues: 537
  sheet: -1.88 (0.33), residues: 243
  loop : -1.28 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 504 
 TYR   0.024   0.001   TYR A 650 
 PHE   0.025   0.001   PHE A 296 
 TRP   0.011   0.001   TRP A 703 
 HIS   0.009   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (12268)
  covalent geometry    : angle       0.54701 (16986)
  SS BOND              : bond        0.00199 (    5)
  SS BOND              : angle       0.99255 (   10)
  hydrogen bonds       : bond        0.03979 (  487)
  hydrogen bonds       : angle       4.19651 ( 1287)
  metal coordination   : bond        0.00182 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1897.70 seconds
wall clock time: 33 minutes 41.99 seconds (2021.99 seconds total)