Starting phenix.real_space_refine
on Tue Jun 10 22:25:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hke_34850/06_2025/8hke_34850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hke_34850/06_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_34850/06_2025/8hke_34850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hke_34850/06_2025/8hke_34850.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hke_34850/06_2025/8hke_34850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hke_34850/06_2025/8hke_34850.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 3, 'ASP:plan': 8, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS: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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 8, 'HIS:plan': 3}
          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: 8.01, per 1000 atoms: 0.68
  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: 3.14
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  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: 4.06
  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: 4.39

  Time building geometry restraints manager: 3.73 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 776 or resid 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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.660
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     35.970
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.040
-------------------------------------------------------------------------------
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 : 16.52
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.020   0.002   TRP A 452 
 HIS   0.008   0.002   HIS A 744 
 PHE   0.033   0.002   PHE A 639 
 TYR   0.020   0.002   TYR A 650 
 ARG   0.004   0.000   ARG A 135 

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

*********************** 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  : 1.229 
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: 0.2548
  time to fit residues: 73.2827
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  : 1.129 
-------------------------------------------------------------------------------
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 113 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 122 optimal weight:   10.0000
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.142035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.100494 restraints weight = 20850.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.103193 restraints weight = 12243.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.104988 restraints weight = 9063.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12279  Z= 0.137
  Angle     :  0.610   8.245  16996  Z= 0.312
  Chirality :  0.042   0.159   2052
  Planarity :  0.004   0.048   1837
  Dihedral  : 17.345  92.931   2543
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.01 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.22), residues: 1292
  helix: -1.11 (0.21), residues: 527
  sheet: -3.30 (0.29), residues: 243
  loop : -2.30 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 567 
 HIS   0.006   0.001   HIS B 166 
 PHE   0.026   0.001   PHE B 324 
 TYR   0.024   0.001   TYR A 650 
 ARG   0.007   0.001   ARG B 769 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05657 (  487)
  hydrogen bonds       : angle       5.13728 ( 1287)
  metal coordination   : bond        0.00502 (    6)
  SS BOND              : bond        0.00274 (    5)
  SS BOND              : angle       1.45629 (   10)
  covalent geometry    : bond        0.00294 (12268)
  covalent geometry    : angle       0.60900 (16986)

*********************** 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
  199 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7419 (pm20)
REVERT: B  322 MET cc_start: 0.8144 (mmt) cc_final: 0.7928 (mmt)
REVERT: B  484 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8887 (tp)
REVERT: B  563 MET cc_start: 0.7245 (mtt) cc_final: 0.6796 (mmm)
REVERT: A  193 LYS cc_start: 0.9169 (tptt) cc_final: 0.8943 (tttp)
REVERT: A  219 TYR cc_start: 0.8087 (m-80) cc_final: 0.7597 (m-10)
REVERT: A  261 ILE cc_start: 0.9167 (mt) cc_final: 0.8924 (mm)
REVERT: A  484 ILE cc_start: 0.9199 (tp) cc_final: 0.8638 (tp)
REVERT: A  637 MET cc_start: 0.7311 (ttp) cc_final: 0.6123 (tmm)
REVERT: A  641 MET cc_start: 0.5246 (ptt) cc_final: 0.4834 (ptt)
REVERT: A  681 LYS cc_start: 0.9002 (tttp) cc_final: 0.8089 (tttt)
REVERT: A  728 ASN cc_start: 0.8089 (p0) cc_final: 0.7510 (p0)
  outliers start: 15
  outliers final: 8
  residues processed: 192
  average time/residue: 0.2034
  time to fit residues: 58.8291
Evaluate side-chains
  151 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
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  700 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  731 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0870
   chunk 115 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 120 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 89 optimal weight:    0.3980
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.6160

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.140180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.098530 restraints weight = 21273.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.101142 restraints weight = 12539.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.102880 restraints weight = 9323.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12279  Z= 0.166
  Angle     :  0.590   9.695  16996  Z= 0.299
  Chirality :  0.041   0.156   2052
  Planarity :  0.004   0.045   1837
  Dihedral  : 17.143  92.415   2543
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.41 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.23), residues: 1292
  helix: -0.42 (0.23), residues: 541
  sheet: -2.98 (0.30), residues: 245
  loop : -2.10 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 452 
 HIS   0.005   0.001   HIS B 166 
 PHE   0.021   0.001   PHE A 755 
 TYR   0.022   0.001   TYR A 650 
 ARG   0.005   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04801 (  487)
  hydrogen bonds       : angle       4.71252 ( 1287)
  metal coordination   : bond        0.00486 (    6)
  SS BOND              : bond        0.00356 (    5)
  SS BOND              : angle       1.70158 (   10)
  covalent geometry    : bond        0.00382 (12268)
  covalent geometry    : angle       0.58859 (16986)

*********************** 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
  187 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7636 (pm20)
REVERT: B  461 ASP cc_start: 0.8410 (m-30) cc_final: 0.7947 (m-30)
REVERT: B  484 ILE cc_start: 0.9059 (tp) cc_final: 0.8756 (tp)
REVERT: B  487 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8423 (tp)
REVERT: B  563 MET cc_start: 0.7492 (mtt) cc_final: 0.6217 (tmm)
REVERT: A   80 ASP cc_start: 0.7999 (m-30) cc_final: 0.7692 (t0)
REVERT: A  193 LYS cc_start: 0.9183 (tptt) cc_final: 0.8959 (tttp)
REVERT: A  219 TYR cc_start: 0.8109 (m-80) cc_final: 0.7662 (m-10)
REVERT: A  484 ILE cc_start: 0.8922 (tp) cc_final: 0.8490 (tp)
REVERT: A  520 LEU cc_start: 0.8084 (mm) cc_final: 0.7779 (mt)
REVERT: A  637 MET cc_start: 0.7249 (ttp) cc_final: 0.6667 (ptt)
REVERT: A  681 LYS cc_start: 0.8790 (tttp) cc_final: 0.8557 (tttt)
REVERT: A  728 ASN cc_start: 0.8154 (p0) cc_final: 0.7588 (p0)
REVERT: A  741 ASP cc_start: 0.7917 (m-30) cc_final: 0.7712 (m-30)
  outliers start: 31
  outliers final: 20
  residues processed: 176
  average time/residue: 0.1886
  time to fit residues: 51.4332
Evaluate side-chains
  166 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  487 ILE
Chi-restraints excluded: chain B residue  562 LEU
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 B residue  701 LEU
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  588 SER
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  618 CYS
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 123 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.140644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.099488 restraints weight = 21021.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.102013 restraints weight = 12704.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103681 restraints weight = 9559.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12279  Z= 0.145
  Angle     :  0.553   9.315  16996  Z= 0.283
  Chirality :  0.040   0.155   2052
  Planarity :  0.003   0.043   1837
  Dihedral  : 16.883  89.087   2543
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.11 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.24), residues: 1292
  helix: -0.14 (0.23), residues: 543
  sheet: -2.66 (0.31), residues: 245
  loop : -1.80 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 452 
 HIS   0.005   0.001   HIS B 610 
 PHE   0.027   0.001   PHE A 708 
 TYR   0.024   0.001   TYR A 650 
 ARG   0.004   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04361 (  487)
  hydrogen bonds       : angle       4.52953 ( 1287)
  metal coordination   : bond        0.00342 (    6)
  SS BOND              : bond        0.00325 (    5)
  SS BOND              : angle       1.48786 (   10)
  covalent geometry    : bond        0.00332 (12268)
  covalent geometry    : angle       0.55171 (16986)

*********************** 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
  193 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 155
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  484 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8769 (tp)
REVERT: B  487 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8466 (tp)
REVERT: A   88 ASP cc_start: 0.7535 (p0) cc_final: 0.6985 (p0)
REVERT: A  193 LYS cc_start: 0.9169 (tptt) cc_final: 0.8871 (tttt)
REVERT: A  219 TYR cc_start: 0.8074 (m-80) cc_final: 0.7613 (m-10)
REVERT: A  261 ILE cc_start: 0.9157 (mt) cc_final: 0.8937 (mm)
REVERT: A  484 ILE cc_start: 0.8882 (tp) cc_final: 0.8456 (tp)
REVERT: A  487 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (tp)
REVERT: A  520 LEU cc_start: 0.8111 (mm) cc_final: 0.7808 (mt)
REVERT: A  522 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8076 (t0)
REVERT: A  637 MET cc_start: 0.7343 (ttp) cc_final: 0.6684 (ptt)
REVERT: A  728 ASN cc_start: 0.8142 (p0) cc_final: 0.7595 (p0)
REVERT: A  741 ASP cc_start: 0.7945 (m-30) cc_final: 0.7615 (m-30)
  outliers start: 38
  outliers final: 25
  residues processed: 179
  average time/residue: 0.1852
  time to fit residues: 51.8574
Evaluate side-chains
  173 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
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  439 LEU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  487 ILE
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  700 LEU
Chi-restraints excluded: chain B residue  701 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  579 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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 123 optimal weight:    0.0570
   chunk 38 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0670
   chunk 83 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.1840

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

Flipped N/Q/H residues before XYZ refinement:
B 482 ASN
** 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 166 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.141227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.099637 restraints weight = 21080.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.102299 restraints weight = 12463.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.104039 restraints weight = 9278.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12279  Z= 0.132
  Angle     :  0.544  10.157  16996  Z= 0.275
  Chirality :  0.040   0.162   2052
  Planarity :  0.003   0.041   1837
  Dihedral  : 16.630  82.712   2543
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.00 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.24), residues: 1292
  helix:  0.09 (0.23), residues: 542
  sheet: -2.45 (0.32), residues: 248
  loop : -1.65 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 452 
 HIS   0.005   0.001   HIS B 610 
 PHE   0.024   0.001   PHE A 755 
 TYR   0.023   0.001   TYR A 650 
 ARG   0.004   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  487)
  hydrogen bonds       : angle       4.38152 ( 1287)
  metal coordination   : bond        0.00300 (    6)
  SS BOND              : bond        0.00295 (    5)
  SS BOND              : angle       1.38025 (   10)
  covalent geometry    : bond        0.00302 (12268)
  covalent geometry    : angle       0.54355 (16986)

*********************** 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
  200 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 160
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  484 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8748 (tp)
REVERT: B  487 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8460 (tp)
REVERT: A   80 ASP cc_start: 0.7916 (m-30) cc_final: 0.7549 (t0)
REVERT: A   88 ASP cc_start: 0.7556 (p0) cc_final: 0.7013 (p0)
REVERT: A  193 LYS cc_start: 0.9098 (tptt) cc_final: 0.8800 (tttt)
REVERT: A  219 TYR cc_start: 0.8055 (m-80) cc_final: 0.7593 (m-10)
REVERT: A  261 ILE cc_start: 0.9210 (mt) cc_final: 0.8971 (mm)
REVERT: A  484 ILE cc_start: 0.8857 (tp) cc_final: 0.8475 (tp)
REVERT: A  520 LEU cc_start: 0.8144 (mm) cc_final: 0.7759 (mt)
REVERT: A  522 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8103 (t0)
REVERT: A  637 MET cc_start: 0.7226 (ttp) cc_final: 0.6525 (ptt)
REVERT: A  728 ASN cc_start: 0.8155 (p0) cc_final: 0.7576 (p0)
  outliers start: 40
  outliers final: 28
  residues processed: 187
  average time/residue: 0.2245
  time to fit residues: 64.6063
Evaluate side-chains
  181 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 150
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
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  264 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  487 ILE
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  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  522 ASP
Chi-restraints excluded: chain A residue  561 LEU
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  641 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 56 optimal weight:    9.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 684 HIS
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 HIS
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.142201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.100963 restraints weight = 21110.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103677 restraints weight = 12391.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.105306 restraints weight = 9179.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3283

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= 0.111
  Angle     :  0.529  10.343  16996  Z= 0.267
  Chirality :  0.039   0.172   2052
  Planarity :  0.003   0.042   1837
  Dihedral  : 16.444  82.643   2543
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 20.34 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.24), residues: 1292
  helix:  0.30 (0.23), residues: 542
  sheet: -2.20 (0.32), residues: 249
  loop : -1.45 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 452 
 HIS   0.005   0.001   HIS B 610 
 PHE   0.031   0.001   PHE A 708 
 TYR   0.022   0.001   TYR A 650 
 ARG   0.004   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03921 (  487)
  hydrogen bonds       : angle       4.22625 ( 1287)
  metal coordination   : bond        0.00226 (    6)
  SS BOND              : bond        0.00239 (    5)
  SS BOND              : angle       1.11646 (   10)
  covalent geometry    : bond        0.00252 (12268)
  covalent geometry    : angle       0.52855 (16986)

*********************** 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
  203 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 165
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.8990 (mt) cc_final: 0.8586 (tt)
REVERT: B  676 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6579 (t80)
REVERT: B  680 MET cc_start: 0.7975 (mtt) cc_final: 0.7585 (mtp)
REVERT: A   80 ASP cc_start: 0.7919 (m-30) cc_final: 0.7503 (t0)
REVERT: A   88 ASP cc_start: 0.7527 (p0) cc_final: 0.6960 (p0)
REVERT: A  193 LYS cc_start: 0.9072 (tptt) cc_final: 0.8796 (tttt)
REVERT: A  219 TYR cc_start: 0.7951 (m-80) cc_final: 0.7530 (m-80)
REVERT: A  261 ILE cc_start: 0.9230 (mt) cc_final: 0.9012 (mm)
REVERT: A  484 ILE cc_start: 0.8794 (tp) cc_final: 0.8356 (tp)
REVERT: A  487 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7857 (tp)
REVERT: A  522 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8103 (t0)
REVERT: A  533 SER cc_start: 0.8763 (t) cc_final: 0.8466 (t)
REVERT: A  637 MET cc_start: 0.7228 (ttp) cc_final: 0.6534 (ptt)
REVERT: A  728 ASN cc_start: 0.8109 (p0) cc_final: 0.7558 (p0)
  outliers start: 38
  outliers final: 25
  residues processed: 188
  average time/residue: 0.1986
  time to fit residues: 57.6737
Evaluate side-chains
  182 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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  264 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  443 MET
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  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  487 ILE
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  605 ILE
Chi-restraints excluded: chain A residue  609 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  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 80 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 103 optimal weight:   20.0000
   chunk 128 optimal weight:    7.9990
   chunk 133 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    2.2984

-------------------------------------------------------------------------------
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 113 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 = 0.3920 r_free = 0.3920 target = 0.137913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.096714 restraints weight = 21142.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.099261 restraints weight = 12764.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.100902 restraints weight = 9530.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12279  Z= 0.207
  Angle     :  0.609  11.112  16996  Z= 0.307
  Chirality :  0.042   0.160   2052
  Planarity :  0.003   0.041   1837
  Dihedral  : 16.493  82.663   2543
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 20.87 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.24), residues: 1292
  helix:  0.21 (0.23), residues: 544
  sheet: -2.24 (0.32), residues: 245
  loop : -1.40 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 452 
 HIS   0.005   0.001   HIS A 468 
 PHE   0.034   0.002   PHE A 755 
 TYR   0.022   0.002   TYR A 650 
 ARG   0.004   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04305 (  487)
  hydrogen bonds       : angle       4.41515 ( 1287)
  metal coordination   : bond        0.00618 (    6)
  SS BOND              : bond        0.00417 (    5)
  SS BOND              : angle       1.77071 (   10)
  covalent geometry    : bond        0.00480 (12268)
  covalent geometry    : angle       0.60761 (16986)

*********************** 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
  207 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 160
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7729 (tpp80)
REVERT: B  260 ASP cc_start: 0.8770 (m-30) cc_final: 0.8450 (m-30)
REVERT: B  487 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8299 (tp)
REVERT: B  563 MET cc_start: 0.7319 (mtm) cc_final: 0.6037 (tmm)
REVERT: B  676 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6678 (t80)
REVERT: B  680 MET cc_start: 0.7999 (mtt) cc_final: 0.7605 (mtt)
REVERT: A   88 ASP cc_start: 0.7647 (p0) cc_final: 0.7067 (p0)
REVERT: A  106 LYS cc_start: 0.8613 (mttt) cc_final: 0.8055 (mtmt)
REVERT: A  219 TYR cc_start: 0.8148 (m-80) cc_final: 0.7751 (m-10)
REVERT: A  450 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7238 (t70)
REVERT: A  487 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8134 (tp)
REVERT: A  520 LEU cc_start: 0.8260 (mm) cc_final: 0.7956 (mt)
REVERT: A  637 MET cc_start: 0.7358 (ttp) cc_final: 0.6661 (ptt)
REVERT: A  649 MET cc_start: 0.7996 (mtm) cc_final: 0.7559 (mpp)
REVERT: A  728 ASN cc_start: 0.8218 (p0) cc_final: 0.7610 (p0)
REVERT: A  741 ASP cc_start: 0.7964 (m-30) cc_final: 0.7725 (m-30)
  outliers start: 47
  outliers final: 34
  residues processed: 191
  average time/residue: 0.2170
  time to fit residues: 65.5688
Evaluate side-chains
  188 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
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  264 THR
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  487 ILE
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  676 TYR
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  211 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  487 ILE
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  561 LEU
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  641 MET
Chi-restraints excluded: chain A residue  651 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 126 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 130 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
A 174 GLN
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.141655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.100442 restraints weight = 21005.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.103155 restraints weight = 12425.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.104881 restraints weight = 9227.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12279  Z= 0.115
  Angle     :  0.547  12.176  16996  Z= 0.274
  Chirality :  0.039   0.176   2052
  Planarity :  0.003   0.041   1837
  Dihedral  : 16.214  82.993   2543
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.68 %
    Favored  : 75.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.24), residues: 1292
  helix:  0.42 (0.23), residues: 542
  sheet: -2.17 (0.32), residues: 257
  loop : -1.28 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 452 
 HIS   0.006   0.001   HIS B 610 
 PHE   0.057   0.001   PHE A 496 
 TYR   0.024   0.001   TYR A 650 
 ARG   0.003   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  487)
  hydrogen bonds       : angle       4.28721 ( 1287)
  metal coordination   : bond        0.00215 (    6)
  SS BOND              : bond        0.00255 (    5)
  SS BOND              : angle       1.12537 (   10)
  covalent geometry    : bond        0.00261 (12268)
  covalent geometry    : angle       0.54637 (16986)

*********************** 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: 37
    poor density    : 163
  time to evaluate  : 2.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.8977 (mt) cc_final: 0.8612 (tt)
REVERT: B   97 SER cc_start: 0.9162 (t) cc_final: 0.8893 (m)
REVERT: B  100 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7669 (tpp80)
REVERT: B  260 ASP cc_start: 0.8717 (m-30) cc_final: 0.8442 (m-30)
REVERT: B  676 TYR cc_start: 0.7474 (t80) cc_final: 0.6506 (t80)
REVERT: B  680 MET cc_start: 0.8044 (mtt) cc_final: 0.7629 (mtp)
REVERT: A   80 ASP cc_start: 0.7921 (m-30) cc_final: 0.7545 (t0)
REVERT: A   88 ASP cc_start: 0.7541 (p0) cc_final: 0.6942 (p0)
REVERT: A  168 THR cc_start: 0.9185 (p) cc_final: 0.8958 (t)
REVERT: A  193 LYS cc_start: 0.9049 (tptt) cc_final: 0.8735 (pttt)
REVERT: A  219 TYR cc_start: 0.7934 (m-80) cc_final: 0.7533 (m-80)
REVERT: A  314 TYR cc_start: 0.8188 (m-80) cc_final: 0.7928 (m-80)
REVERT: A  450 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7163 (t70)
REVERT: A  484 ILE cc_start: 0.8781 (tp) cc_final: 0.8313 (tp)
REVERT: A  487 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7866 (tp)
REVERT: A  533 SER cc_start: 0.8793 (t) cc_final: 0.8503 (t)
REVERT: A  637 MET cc_start: 0.7319 (ttp) cc_final: 0.6647 (ptt)
REVERT: A  649 MET cc_start: 0.7954 (mtm) cc_final: 0.7553 (mpp)
REVERT: A  728 ASN cc_start: 0.8106 (p0) cc_final: 0.7552 (p0)
  outliers start: 37
  outliers final: 31
  residues processed: 191
  average time/residue: 0.1859
  time to fit residues: 55.8236
Evaluate side-chains
  190 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
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  168 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  487 ILE
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  674 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  302 ILE
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  561 LEU
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  618 CYS
Chi-restraints excluded: chain A residue  639 PHE
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    1.0164

-------------------------------------------------------------------------------
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 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.141248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.100924 restraints weight = 20945.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.103376 restraints weight = 13432.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.104450 restraints weight = 9017.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.3652

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= 0.127
  Angle     :  0.560  13.037  16996  Z= 0.281
  Chirality :  0.040   0.178   2052
  Planarity :  0.003   0.039   1837
  Dihedral  : 16.093  83.371   2541
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.94 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.24), residues: 1292
  helix:  0.48 (0.23), residues: 536
  sheet: -2.08 (0.32), residues: 257
  loop : -1.27 (0.29), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 452 
 HIS   0.006   0.001   HIS B 610 
 PHE   0.072   0.001   PHE A 496 
 TYR   0.023   0.001   TYR A 650 
 ARG   0.003   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  487)
  hydrogen bonds       : angle       4.29746 ( 1287)
  metal coordination   : bond        0.00335 (    6)
  SS BOND              : bond        0.00264 (    5)
  SS BOND              : angle       1.20105 (   10)
  covalent geometry    : bond        0.00294 (12268)
  covalent geometry    : angle       0.55969 (16986)

*********************** 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
  202 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9003 (mt) cc_final: 0.8629 (tt)
REVERT: B   97 SER cc_start: 0.9143 (t) cc_final: 0.8907 (m)
REVERT: B  100 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7508 (tpp80)
REVERT: B  260 ASP cc_start: 0.8739 (m-30) cc_final: 0.8474 (m-30)
REVERT: B  676 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6606 (t80)
REVERT: B  680 MET cc_start: 0.7985 (mtt) cc_final: 0.7551 (mtp)
REVERT: A   80 ASP cc_start: 0.7963 (m-30) cc_final: 0.7515 (t0)
REVERT: A   88 ASP cc_start: 0.7637 (p0) cc_final: 0.7086 (p0)
REVERT: A  168 THR cc_start: 0.9166 (p) cc_final: 0.8941 (t)
REVERT: A  193 LYS cc_start: 0.8916 (tptt) cc_final: 0.8458 (ttmt)
REVERT: A  219 TYR cc_start: 0.7947 (m-80) cc_final: 0.7548 (m-80)
REVERT: A  314 TYR cc_start: 0.8250 (m-80) cc_final: 0.8016 (m-80)
REVERT: A  450 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7197 (t70)
REVERT: A  484 ILE cc_start: 0.8785 (tp) cc_final: 0.8335 (tp)
REVERT: A  487 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7874 (tp)
REVERT: A  533 SER cc_start: 0.8791 (t) cc_final: 0.8498 (t)
REVERT: A  637 MET cc_start: 0.7315 (ttp) cc_final: 0.6625 (ptt)
REVERT: A  649 MET cc_start: 0.8073 (mtm) cc_final: 0.7551 (mpp)
REVERT: A  728 ASN cc_start: 0.8140 (p0) cc_final: 0.7562 (p0)
  outliers start: 38
  outliers final: 29
  residues processed: 190
  average time/residue: 0.2425
  time to fit residues: 73.8965
Evaluate side-chains
  189 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
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  168 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  487 ILE
Chi-restraints excluded: chain B residue  555 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  674 LEU
Chi-restraints excluded: chain B residue  676 TYR
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  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  487 ILE
Chi-restraints excluded: chain A residue  561 LEU
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  618 CYS
Chi-restraints excluded: chain A residue  639 PHE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   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 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.141564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.101796 restraints weight = 20818.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.104053 restraints weight = 13986.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.105269 restraints weight = 9399.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3788

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= 0.131
  Angle     :  0.569  15.011  16996  Z= 0.283
  Chirality :  0.040   0.281   2052
  Planarity :  0.003   0.041   1837
  Dihedral  : 15.986  83.841   2541
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.86 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.24), residues: 1292
  helix:  0.45 (0.23), residues: 543
  sheet: -1.93 (0.32), residues: 258
  loop : -1.20 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 452 
 HIS   0.006   0.001   HIS B 610 
 PHE   0.029   0.001   PHE A 496 
 TYR   0.023   0.001   TYR A 650 
 ARG   0.003   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04001 (  487)
  hydrogen bonds       : angle       4.30041 ( 1287)
  metal coordination   : bond        0.01459 (    6)
  SS BOND              : bond        0.00208 (    5)
  SS BOND              : angle       1.14751 (   10)
  covalent geometry    : bond        0.00300 (12268)
  covalent geometry    : angle       0.56842 (16986)

********************** 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
  202 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 166
  time to evaluate  : 1.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.8996 (mt) cc_final: 0.8626 (tt)
REVERT: B   97 SER cc_start: 0.9158 (t) cc_final: 0.8924 (m)
REVERT: B  100 ARG cc_start: 0.8002 (tpp80) cc_final: 0.7511 (tpp80)
REVERT: B  162 ASP cc_start: 0.7134 (t0) cc_final: 0.6916 (t0)
REVERT: B  260 ASP cc_start: 0.8712 (m-30) cc_final: 0.8448 (m-30)
REVERT: B  676 TYR cc_start: 0.7529 (t80) cc_final: 0.6706 (t80)
REVERT: B  680 MET cc_start: 0.7941 (mtt) cc_final: 0.7543 (mtp)
REVERT: A   80 ASP cc_start: 0.7953 (m-30) cc_final: 0.7575 (t0)
REVERT: A   88 ASP cc_start: 0.7633 (p0) cc_final: 0.7064 (p0)
REVERT: A  168 THR cc_start: 0.9185 (p) cc_final: 0.8944 (t)
REVERT: A  193 LYS cc_start: 0.8800 (tptt) cc_final: 0.8427 (pttt)
REVERT: A  219 TYR cc_start: 0.7981 (m-80) cc_final: 0.7587 (m-80)
REVERT: A  314 TYR cc_start: 0.8289 (m-80) cc_final: 0.8046 (m-80)
REVERT: A  450 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7212 (t70)
REVERT: A  484 ILE cc_start: 0.8783 (tp) cc_final: 0.8318 (tp)
REVERT: A  487 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7725 (tp)
REVERT: A  520 LEU cc_start: 0.8139 (mm) cc_final: 0.7863 (mt)
REVERT: A  522 ASP cc_start: 0.7517 (t0) cc_final: 0.7247 (t0)
REVERT: A  533 SER cc_start: 0.8774 (t) cc_final: 0.8485 (t)
REVERT: A  637 MET cc_start: 0.7264 (ttp) cc_final: 0.6566 (ptt)
REVERT: A  649 MET cc_start: 0.8039 (mtm) cc_final: 0.7517 (mpp)
REVERT: A  728 ASN cc_start: 0.8132 (p0) cc_final: 0.7578 (p0)
  outliers start: 36
  outliers final: 31
  residues processed: 193
  average time/residue: 0.2110
  time to fit residues: 65.8326
Evaluate side-chains
  198 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 165
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
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   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  487 ILE
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  674 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  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  487 ILE
Chi-restraints excluded: chain A residue  561 LEU
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  618 CYS
Chi-restraints excluded: chain A residue  639 PHE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   chunk 127 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.142623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.102418 restraints weight = 20871.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.105159 restraints weight = 13123.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.106293 restraints weight = 8764.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3968

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= 0.115
  Angle     :  0.562  13.821  16996  Z= 0.279
  Chirality :  0.039   0.301   2052
  Planarity :  0.003   0.040   1837
  Dihedral  : 15.911  84.368   2541
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.75 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.24), residues: 1292
  helix:  0.62 (0.23), residues: 531
  sheet: -1.79 (0.32), residues: 258
  loop : -1.19 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 452 
 HIS   0.008   0.001   HIS B 540 
 PHE   0.058   0.001   PHE A 755 
 TYR   0.023   0.001   TYR A 650 
 ARG   0.003   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03959 (  487)
  hydrogen bonds       : angle       4.26908 ( 1287)
  metal coordination   : bond        0.01358 (    6)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       1.01972 (   10)
  covalent geometry    : bond        0.00265 (12268)
  covalent geometry    : angle       0.56174 (16986)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3908.33 seconds
wall clock time: 70 minutes 50.12 seconds (4250.12 seconds total)