Starting phenix.real_space_refine
on Wed Sep 17 17:52:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w0a_43706/09_2025/8w0a_43706.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w0a_43706/09_2025/8w0a_43706.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w0a_43706/09_2025/8w0a_43706.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w0a_43706/09_2025/8w0a_43706.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w0a_43706/09_2025/8w0a_43706.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w0a_43706/09_2025/8w0a_43706.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      14      5.49       5
     S      66      5.16       5
     C    6532      2.51       5
     N    1708      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10216
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 4968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 636, 4968
          Classifications: {'peptide': 636}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 616}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 49
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "D"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 140
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
  Restraints were copied for chains:
    A, B
  Time building chain proxies: 4.11, per 1000 atoms: 0.40
  Number of scatterers: 10216
  At special positions: 0
  Unit cell: (165.98, 93.74, 82.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      66     16.00
     P      14     15.00
     O    1896      8.00
     N    1708      7.00
     C    6532      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 424.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2380

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 13 sheets defined
      56.8% alpha, 6.1% beta
      0 base pairs and 6 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'C' and resid 77 through 88
      removed outlier: 3.616A  pdb=" N   LEU C  81 " --> pdb=" O   PRO C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 101
      removed outlier: 4.008A  pdb=" N   ALA C  97 " --> pdb=" O   PHE C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 107
      removed outlier: 4.325A  pdb=" N   LEU C 106 " --> pdb=" O   GLY C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 136
      removed outlier: 3.907A  pdb=" N   LEU C 130 " --> pdb=" O   GLU C 126 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LYS C 131 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG C 132 " --> pdb=" O   LEU C 128 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL C 133 " --> pdb=" O   ILE C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 165
      removed outlier: 4.145A  pdb=" N   GLU C 163 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 184
      removed outlier: 3.628A  pdb=" N   SER C 183 " --> pdb=" O   HIS C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 203
    Processing helix  chain 'C' and resid 217 through 222
      removed outlier: 3.568A  pdb=" N   LEU C 221 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   GLY C 222 " --> pdb=" O   HIS C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 244
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 3.776A  pdb=" N   VAL C 274 " --> pdb=" O   ASN C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 335
      removed outlier: 3.734A  pdb=" N   THR C 333 " --> pdb=" O   LEU C 329 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   CYS C 335 " --> pdb=" O   TYR C 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 363
      removed outlier: 3.512A  pdb=" N   ASP C 355 " --> pdb=" O   GLU C 351 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA C 358 " --> pdb=" O   ALA C 354 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 386 through 397
      removed outlier: 3.969A  pdb=" N   MET C 391 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG C 395 " --> pdb=" O   MET C 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 409
      removed outlier: 4.169A  pdb=" N   LYS C 407 " --> pdb=" O   SER C 403 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   THR C 408 " --> pdb=" O   VAL C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 435
      removed outlier: 3.693A  pdb=" N   GLU C 429 " --> pdb=" O   ARG C 425 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE C 432 " --> pdb=" O   ILE C 428 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG C 433 " --> pdb=" O   GLU C 429 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN C 434 " --> pdb=" O   GLY C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 449
      removed outlier: 3.904A  pdb=" N   SER C 448 " --> pdb=" O   SER C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 479
    Processing helix  chain 'C' and resid 500 through 509
    Processing helix  chain 'C' and resid 528 through 537
      removed outlier: 3.538A  pdb=" N   ARG C 533 " --> pdb=" O   GLY C 529 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA C 534 " --> pdb=" O   SER C 530 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU C 537 " --> pdb=" O   ARG C 533 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 546 through 556
      removed outlier: 3.765A  pdb=" N   THR C 552 " --> pdb=" O   GLN C 548 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR C 553 " --> pdb=" O   ASP C 549 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA C 554 " --> pdb=" O   MET C 550 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS C 556 " --> pdb=" O   THR C 552 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 557 through 562
      removed outlier: 3.823A  pdb=" N   ALA C 561 " --> pdb=" O   THR C 557 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 584 through 592
      removed outlier: 3.555A  pdb=" N   TRP C 588 " --> pdb=" O   ALA C 584 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU C 589 " --> pdb=" O   CYS C 585 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 612 through 622
      removed outlier: 3.839A  pdb=" N   LEU C 619 " --> pdb=" O   GLY C 615 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 624 through 639
      removed outlier: 3.849A  pdb=" N   LEU C 629 " --> pdb=" O   PRO C 625 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ASP C 630 " --> pdb=" O   ALA C 626 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA C 633 " --> pdb=" O   LEU C 629 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG C 637 " --> pdb=" O   ALA C 633 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   MET C 639 " --> pdb=" O   LEU C 635 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 647 through 653
      removed outlier: 3.735A  pdb=" N   LEU C 653 " --> pdb=" O   HIS C 649 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 668 through 674
    Processing helix  chain 'C' and resid 677 through 686
      removed outlier: 3.707A  pdb=" N   ARG C 682 " --> pdb=" O   THR C 678 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   VAL C 683 " --> pdb=" O   SER C 679 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 710 through 730
      removed outlier: 3.620A  pdb=" N   HIS C 716 " --> pdb=" O   GLN C 712 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG C 718 " --> pdb=" O   ALA C 714 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   PHE C 719 " --> pdb=" O   ILE C 715 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE C 720 " --> pdb=" O   HIS C 716 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR C 721 " --> pdb=" O   LYS C 717 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU C 725 " --> pdb=" O   THR C 721 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASP C 727 " --> pdb=" O   LEU C 723 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU C 728 " --> pdb=" O   VAL C 724 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER C 730 " --> pdb=" O   LEU C 726 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 733 through 741
      removed outlier: 3.798A  pdb=" N   ILE C 737 " --> pdb=" O   PRO C 733 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN C 738 " --> pdb=" O   LEU C 734 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLN C 739 " --> pdb=" O   ARG C 735 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 744 through 768
      removed outlier: 4.206A  pdb=" N   GLN C 749 " --> pdb=" O   ARG C 745 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   SER C 750 " --> pdb=" O   GLY C 746 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN C 752 " --> pdb=" O   ILE C 748 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   GLN C 753 " --> pdb=" O   GLN C 749 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER C 754 " --> pdb=" O   SER C 750 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL C 757 " --> pdb=" O   GLN C 753 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR C 758 " --> pdb=" O   SER C 754 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY C 760 " --> pdb=" O   ALA C 756 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET C 761 " --> pdb=" O   VAL C 757 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE C 762 " --> pdb=" O   TYR C 758 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   THR C 763 " --> pdb=" O   ALA C 759 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   VAL C 764 " --> pdb=" O   GLY C 760 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 771 through 780
      removed outlier: 3.524A  pdb=" N   GLU C 775 " --> pdb=" O   TRP C 771 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU C 776 " --> pdb=" O   HIS C 772 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU C 777 " --> pdb=" O   ASN C 773 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 781 through 787
      removed outlier: 3.740A  pdb=" N   THR C 786 " --> pdb=" O   GLN C 782 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE C 787 " --> pdb=" O   LYS C 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 88
      removed outlier: 3.616A  pdb=" N   LEU A  81 " --> pdb=" O   PRO A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 101
      removed outlier: 4.009A  pdb=" N   ALA A  97 " --> pdb=" O   PHE A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 107
      removed outlier: 4.326A  pdb=" N   LEU A 106 " --> pdb=" O   GLY A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 136
      removed outlier: 3.908A  pdb=" N   LEU A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LYS A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 133 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 165
      removed outlier: 4.144A  pdb=" N   GLU A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 3.628A  pdb=" N   SER A 183 " --> pdb=" O   HIS A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 203
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 3.568A  pdb=" N   LEU A 221 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLY A 222 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 244
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.776A  pdb=" N   VAL A 274 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 335
      removed outlier: 3.735A  pdb=" N   THR A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   CYS A 335 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 363
      removed outlier: 3.512A  pdb=" N   ASP A 355 " --> pdb=" O   GLU A 351 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ALA A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 397
      removed outlier: 3.970A  pdb=" N   MET A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG A 395 " --> pdb=" O   MET A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 409
      removed outlier: 4.169A  pdb=" N   LYS A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   THR A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 435
      removed outlier: 3.693A  pdb=" N   GLU A 429 " --> pdb=" O   ARG A 425 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE A 432 " --> pdb=" O   ILE A 428 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 449
      removed outlier: 3.905A  pdb=" N   SER A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
    Processing helix  chain 'A' and resid 500 through 509
    Processing helix  chain 'A' and resid 528 through 537
      removed outlier: 3.538A  pdb=" N   ARG A 533 " --> pdb=" O   GLY A 529 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU A 537 " --> pdb=" O   ARG A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 556
      removed outlier: 3.765A  pdb=" N   THR A 552 " --> pdb=" O   GLN A 548 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR A 553 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 554 " --> pdb=" O   MET A 550 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   CYS A 556 " --> pdb=" O   THR A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 562
      removed outlier: 3.823A  pdb=" N   ALA A 561 " --> pdb=" O   THR A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 592
      removed outlier: 3.555A  pdb=" N   TRP A 588 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 622
      removed outlier: 3.838A  pdb=" N   LEU A 619 " --> pdb=" O   GLY A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 639
      removed outlier: 3.848A  pdb=" N   LEU A 629 " --> pdb=" O   PRO A 625 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ASP A 630 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA A 633 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 637 " --> pdb=" O   ALA A 633 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   MET A 639 " --> pdb=" O   LEU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 653
      removed outlier: 3.735A  pdb=" N   LEU A 653 " --> pdb=" O   HIS A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 674
    Processing helix  chain 'A' and resid 677 through 686
      removed outlier: 3.707A  pdb=" N   ARG A 682 " --> pdb=" O   THR A 678 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL A 683 " --> pdb=" O   SER A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 730
      removed outlier: 3.620A  pdb=" N   HIS A 716 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 718 " --> pdb=" O   ALA A 714 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   PHE A 719 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE A 720 " --> pdb=" O   HIS A 716 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR A 721 " --> pdb=" O   LYS A 717 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 725 " --> pdb=" O   THR A 721 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASP A 727 " --> pdb=" O   LEU A 723 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 728 " --> pdb=" O   VAL A 724 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 730 " --> pdb=" O   LEU A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 741
      removed outlier: 3.797A  pdb=" N   ILE A 737 " --> pdb=" O   PRO A 733 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A 738 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLN A 739 " --> pdb=" O   ARG A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 768
      removed outlier: 4.207A  pdb=" N   GLN A 749 " --> pdb=" O   ARG A 745 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   SER A 750 " --> pdb=" O   GLY A 746 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN A 752 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   GLN A 753 " --> pdb=" O   GLN A 749 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER A 754 " --> pdb=" O   SER A 750 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 757 " --> pdb=" O   GLN A 753 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR A 758 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 760 " --> pdb=" O   ALA A 756 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET A 761 " --> pdb=" O   VAL A 757 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A 762 " --> pdb=" O   TYR A 758 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   THR A 763 " --> pdb=" O   ALA A 759 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   VAL A 764 " --> pdb=" O   GLY A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 780
      removed outlier: 3.524A  pdb=" N   GLU A 775 " --> pdb=" O   TRP A 771 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU A 776 " --> pdb=" O   HIS A 772 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 777 " --> pdb=" O   ASN A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 787
      removed outlier: 3.740A  pdb=" N   THR A 786 " --> pdb=" O   GLN A 782 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A 787 " --> pdb=" O   LYS A 783 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 263 through 264
      removed outlier: 6.425A  pdb=" N   LEU C 111 " --> pdb=" O   GLY C 263 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   ASN C 110 " --> pdb=" O   GLU C 281 " (cutoff:3.500A)
      removed outlier: 8.991A  pdb=" N   TYR C 283 " --> pdb=" O   ASN C 110 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL C 112 " --> pdb=" O   TYR C 283 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 189
      removed outlier: 6.094A  pdb=" N   PHE C 142 " --> pdb=" O   CYS C 189 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL C 214 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 301 through 304
      removed outlier: 6.421A  pdb=" N   VAL C 457 " --> pdb=" O   ILE C 493 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LEU C 341 " --> pdb=" O   ILE C 458 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 414 through 415
      removed outlier: 7.444A  pdb=" N   ALA C 414 " --> pdb=" O   ALA C 441 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 463 through 464
    Processing sheet with id=AA6, first strand: chain 'C' and resid 595 through 596
    Processing sheet with id=AA7, first strand: chain 'C' and resid 640 through 643
    Processing sheet with id=AA8, first strand: chain 'A' and resid 263 through 264
      removed outlier: 6.426A  pdb=" N   LEU A 111 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   ASN A 110 " --> pdb=" O   GLU A 281 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   TYR A 283 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL A 112 " --> pdb=" O   TYR A 283 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 188 through 189
      removed outlier: 6.093A  pdb=" N   PHE A 142 " --> pdb=" O   CYS A 189 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL A 214 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 304
      removed outlier: 6.421A  pdb=" N   VAL A 457 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   LEU A 341 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 414 through 415
      removed outlier: 7.444A  pdb=" N   ALA A 414 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 463 through 464
    Processing sheet with id=AB4, first strand: chain 'A' and resid 595 through 596

    352 hydrogen bonds defined for protein.
    1020 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      6 stacking parallelities
  Total time for adding SS restraints: 1.42

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3222
        1.34 -     1.46: 1698
        1.46 -     1.58: 5376
        1.58 -     1.70: 26
        1.70 -     1.82: 104
  Bond restraints: 10426
  Sorted by residual:
  bond pdb=" O3'  DT D   4 "
       pdb=" P    DT D   5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.584  0.023 1.50e-02 4.44e+03 2.34e+00
  bond pdb=" O3'  DT B   4 "
       pdb=" P    DT B   5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.584  0.023 1.50e-02 4.44e+03 2.34e+00
  bond pdb=" O3'  DT B   3 "
       pdb=" P    DT B   4 "
    ideal  model  delta    sigma   weight residual
    1.607  1.589  0.018 1.50e-02 4.44e+03 1.43e+00
  bond pdb=" O3'  DT D   3 "
       pdb=" P    DT D   4 "
    ideal  model  delta    sigma   weight residual
    1.607  1.589  0.018 1.50e-02 4.44e+03 1.43e+00
  bond pdb=" CB  ASN A 279 "
       pdb=" CG  ASN A 279 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.11e-01
  ... (remaining 10421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 13940
        1.99 -     3.98: 188
        3.98 -     5.97: 18
        5.97 -     7.96: 6
        7.96 -     9.95: 6
  Bond angle restraints: 14158
  Sorted by residual:
  angle pdb=" CA  LEU C 273 "
        pdb=" CB  LEU C 273 "
        pdb=" CG  LEU C 273 "
      ideal   model   delta    sigma   weight residual
     116.30  126.25   -9.95 3.50e+00 8.16e-02 8.08e+00
  angle pdb=" CA  LEU A 273 "
        pdb=" CB  LEU A 273 "
        pdb=" CG  LEU A 273 "
      ideal   model   delta    sigma   weight residual
     116.30  126.23   -9.93 3.50e+00 8.16e-02 8.06e+00
  angle pdb=" C   ASP A 336 "
        pdb=" N   ASN A 337 "
        pdb=" CA  ASN A 337 "
      ideal   model   delta    sigma   weight residual
     121.54  126.67   -5.13 1.91e+00 2.74e-01 7.21e+00
  angle pdb=" CB  MET A 391 "
        pdb=" CG  MET A 391 "
        pdb=" SD  MET A 391 "
      ideal   model   delta    sigma   weight residual
     112.70  120.71   -8.01 3.00e+00 1.11e-01 7.14e+00
  angle pdb=" CB  MET C 391 "
        pdb=" CG  MET C 391 "
        pdb=" SD  MET C 391 "
      ideal   model   delta    sigma   weight residual
     112.70  120.69   -7.99 3.00e+00 1.11e-01 7.10e+00
  ... (remaining 14153 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 5019
       17.45 -    34.91: 805
       34.91 -    52.36: 288
       52.36 -    69.81: 62
       69.81 -    87.27: 14
  Dihedral angle restraints: 6188
    sinusoidal: 2516
      harmonic: 3672
  Sorted by residual:
  dihedral pdb=" CA  PRO A 656 "
           pdb=" C   PRO A 656 "
           pdb=" N   MET A 657 "
           pdb=" CA  MET A 657 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.79  -18.21     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  PRO C 656 "
           pdb=" C   PRO C 656 "
           pdb=" N   MET C 657 "
           pdb=" CA  MET C 657 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.85  -18.15     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  MET A 657 "
           pdb=" C   MET A 657 "
           pdb=" N   PHE A 658 "
           pdb=" CA  PHE A 658 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.82   17.18     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 6185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1131
       0.035 -    0.070: 402
       0.070 -    0.105: 93
       0.105 -    0.140: 30
       0.140 -    0.175: 4
  Chirality restraints: 1660
  Sorted by residual:
  chirality pdb=" CB  ILE C 261 "
            pdb=" CA  ILE C 261 "
            pdb=" CG1 ILE C 261 "
            pdb=" CG2 ILE C 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.64e-01
  chirality pdb=" CB  THR A 235 "
            pdb=" CA  THR A 235 "
            pdb=" OG1 THR A 235 "
            pdb=" CG2 THR A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.63e-01
  chirality pdb=" CB  THR C 235 "
            pdb=" CA  THR C 235 "
            pdb=" OG1 THR C 235 "
            pdb=" CG2 THR C 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.39e-01
  ... (remaining 1657 not shown)

  Planarity restraints: 1720
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 781 "    0.007 2.00e-02 2.50e+03   1.48e-02 3.82e+00
        pdb=" CG  PHE A 781 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 781 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 781 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 781 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 781 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 781 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 781 "    0.007 2.00e-02 2.50e+03   1.47e-02 3.80e+00
        pdb=" CG  PHE C 781 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 781 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 781 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 781 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 781 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 781 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 279 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   ASN A 279 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ASN A 279 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA A 280 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1717 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.23: 4
        2.23 -     2.90: 4052
        2.90 -     3.56: 14094
        3.56 -     4.23: 22123
        4.23 -     4.90: 37741
  Nonbonded interactions: 78014
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN C 773 "
            pdb=" O   LEU A 644 "
     model   vdw
     1.561 3.120
  nonbonded pdb=" O   LEU C 644 "
            pdb=" ND2 ASN A 773 "
     model   vdw
     1.566 3.120
  nonbonded pdb=" CD1 LEU C 776 "
            pdb=" NE2 GLN A 780 "
     model   vdw
     1.935 3.540
  nonbonded pdb=" NE2 GLN C 780 "
            pdb=" CD1 LEU A 776 "
     model   vdw
     1.940 3.540
  nonbonded pdb=" ND2 ASN A 110 "
            pdb=" O   LEU A 278 "
     model   vdw
     2.252 3.120
  ... (remaining 78009 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
}
ncs_group {
  reference = chain 'D'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.960
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10426  Z= 0.126
  Angle     :  0.593   9.952  14158  Z= 0.309
  Chirality :  0.040   0.175   1660
  Planarity :  0.003   0.029   1720
  Dihedral  : 19.614  87.266   3808
  Min Nonbonded Distance : 1.561

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 36.76 %
    Favored  : 63.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.24), residues: 1240
  helix: -0.95 (0.21), residues: 596
  sheet: -2.43 (0.66), residues: 68
  loop : -1.10 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 480 
 TYR   0.011   0.001   TYR A 283 
 PHE   0.032   0.001   PHE A 781 
 TRP   0.021   0.001   TRP A 277 
 HIS   0.002   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10426)
  covalent geometry    : angle       0.59322 (14158)
  hydrogen bonds       : bond        0.28397 (  352)
  hydrogen bonds       : angle       7.89477 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  402 ASP cc_start: 0.3212 (m-30) cc_final: 0.2381 (p0)
REVERT: C  538 ILE cc_start: 0.6187 (pt) cc_final: 0.5882 (pt)
REVERT: A  402 ASP cc_start: 0.3275 (m-30) cc_final: 0.2469 (p0)
REVERT: A  538 ILE cc_start: 0.6177 (pt) cc_final: 0.5894 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1020
  time to fit residues: 20.7907
Evaluate side-chains
  112 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
C 260 GLN
** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 749 GLN
C 752 GLN
A 260 GLN
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 752 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.166903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.145027 restraints weight = 19640.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 3.15
r_work: 0.3974 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10426  Z= 0.184
  Angle     :  0.624   5.878  14158  Z= 0.333
  Chirality :  0.042   0.153   1660
  Planarity :  0.004   0.032   1720
  Dihedral  : 10.783  87.964   1486
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 32.87 %
    Favored  : 61.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.23), residues: 1240
  helix: -1.14 (0.19), residues: 650
  sheet: -1.43 (0.50), residues: 120
  loop : -1.61 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 668 
 TYR   0.012   0.001   TYR A 228 
 PHE   0.035   0.002   PHE A  87 
 TRP   0.006   0.001   TRP A 771 
 HIS   0.005   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (10426)
  covalent geometry    : angle       0.62427 (14158)
  hydrogen bonds       : bond        0.05832 (  352)
  hydrogen bonds       : angle       5.39652 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 123
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  402 ASP cc_start: 0.4071 (m-30) cc_final: 0.2459 (p0)
REVERT: C  538 ILE cc_start: 0.6693 (pt) cc_final: 0.6425 (pt)
REVERT: C  752 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6772 (tm-30)
REVERT: A  402 ASP cc_start: 0.4053 (m-30) cc_final: 0.2484 (p0)
REVERT: A  538 ILE cc_start: 0.6689 (pt) cc_final: 0.6409 (pt)
REVERT: A  752 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6785 (tm-30)
  outliers start: 57
  outliers final: 35
  residues processed: 169
  average time/residue: 0.0826
  time to fit residues: 21.1332
Evaluate side-chains
  144 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  189 CYS
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  411 TRP
Chi-restraints excluded: chain C residue  417 HIS
Chi-restraints excluded: chain C residue  445 THR
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  586 VAL
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  654 VAL
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  676 LEU
Chi-restraints excluded: chain C residue  715 ILE
Chi-restraints excluded: chain C residue  749 GLN
Chi-restraints excluded: chain C residue  752 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  411 TRP
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue  752 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 32 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
C 384 GLN
** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 749 GLN
A 384 GLN
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.168759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.146877 restraints weight = 19643.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4119 rms_B_bonded: 3.19
r_work: 0.3996 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10426  Z= 0.122
  Angle     :  0.552   5.097  14158  Z= 0.294
  Chirality :  0.040   0.154   1660
  Planarity :  0.004   0.031   1720
  Dihedral  : 10.620  88.076   1486
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 34.07 %
    Favored  : 61.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.23), residues: 1240
  helix: -1.00 (0.19), residues: 666
  sheet: -1.45 (0.50), residues: 118
  loop : -1.55 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 745 
 TYR   0.008   0.001   TYR A 474 
 PHE   0.013   0.001   PHE A 287 
 TRP   0.005   0.001   TRP A 349 
 HIS   0.003   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10426)
  covalent geometry    : angle       0.55168 (14158)
  hydrogen bonds       : bond        0.04715 (  352)
  hydrogen bonds       : angle       5.03990 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 123
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  209 LEU cc_start: 0.6345 (mm) cc_final: 0.6109 (tp)
REVERT: C  212 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6938 (ttm)
REVERT: C  384 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.5809 (tm-30)
REVERT: C  402 ASP cc_start: 0.3868 (m-30) cc_final: 0.2414 (p0)
REVERT: C  752 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6679 (tm-30)
REVERT: A  209 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6100 (tp)
REVERT: A  212 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6939 (ttm)
REVERT: A  384 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.5786 (tm-30)
REVERT: A  402 ASP cc_start: 0.3827 (m-30) cc_final: 0.2423 (p0)
REVERT: A  752 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6686 (tm-30)
  outliers start: 45
  outliers final: 26
  residues processed: 155
  average time/residue: 0.0795
  time to fit residues: 18.9496
Evaluate side-chains
  142 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  212 MET
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  384 GLN
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  411 TRP
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  596 GLN
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  752 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  411 TRP
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  596 GLN
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  752 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 116 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 101 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 ASN
C 747 GLN
C 752 GLN
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 744 ASN
A 747 GLN
A 752 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.168801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.146847 restraints weight = 19783.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.4121 rms_B_bonded: 3.20
r_work: 0.3995 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  10426  Z= 0.117
  Angle     :  0.537   5.939  14158  Z= 0.284
  Chirality :  0.040   0.143   1660
  Planarity :  0.003   0.030   1720
  Dihedral  : 10.450  88.737   1486
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 33.70 %
    Favored  : 60.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.23), residues: 1240
  helix: -0.82 (0.19), residues: 672
  sheet: -1.36 (0.50), residues: 118
  loop : -1.56 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 711 
 TYR   0.009   0.001   TYR C 228 
 PHE   0.040   0.001   PHE A  87 
 TRP   0.009   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10426)
  covalent geometry    : angle       0.53729 (14158)
  hydrogen bonds       : bond        0.04259 (  352)
  hydrogen bonds       : angle       4.77632 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 122
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  209 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6113 (tp)
REVERT: C  212 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6961 (ttm)
REVERT: C  402 ASP cc_start: 0.3768 (m-30) cc_final: 0.2416 (p0)
REVERT: A  209 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.6090 (tp)
REVERT: A  212 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6957 (ttm)
REVERT: A  402 ASP cc_start: 0.3696 (m-30) cc_final: 0.2397 (p0)
  outliers start: 58
  outliers final: 38
  residues processed: 164
  average time/residue: 0.0791
  time to fit residues: 19.9487
Evaluate side-chains
  149 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 107
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  189 CYS
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  212 MET
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  445 THR
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  596 GLN
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  654 VAL
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  596 GLN
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  728 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 116 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 109 optimal weight:    0.8980
   chunk 120 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 ASN
C 747 GLN
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** 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 = 0.4400 r_free = 0.4400 target = 0.168337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.146415 restraints weight = 19688.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.4114 rms_B_bonded: 3.18
r_work: 0.3992 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10426  Z= 0.122
  Angle     :  0.544   7.541  14158  Z= 0.286
  Chirality :  0.040   0.145   1660
  Planarity :  0.003   0.030   1720
  Dihedral  : 10.361  89.551   1486
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 32.31 %
    Favored  : 60.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.24), residues: 1240
  helix: -0.74 (0.20), residues: 674
  sheet: -1.32 (0.50), residues: 118
  loop : -1.55 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 438 
 TYR   0.010   0.001   TYR A 228 
 PHE   0.019   0.001   PHE A 287 
 TRP   0.013   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10426)
  covalent geometry    : angle       0.54404 (14158)
  hydrogen bonds       : bond        0.04222 (  352)
  hydrogen bonds       : angle       4.71244 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 112
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  209 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6128 (tp)
REVERT: C  402 ASP cc_start: 0.3747 (m-30) cc_final: 0.2465 (p0)
REVERT: A  209 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6106 (tp)
REVERT: A  238 CYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7425 (m)
REVERT: A  402 ASP cc_start: 0.3689 (m-30) cc_final: 0.2469 (p0)
  outliers start: 73
  outliers final: 51
  residues processed: 168
  average time/residue: 0.0770
  time to fit residues: 19.5995
Evaluate side-chains
  160 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 106
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  189 CYS
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  445 THR
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  595 ILE
Chi-restraints excluded: chain C residue  596 GLN
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  627 ASP
Chi-restraints excluded: chain C residue  654 VAL
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  627 ASP
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 120 optimal weight:    0.8980
   chunk 33 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 744 ASN
A 747 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.168708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.146981 restraints weight = 19797.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 3.17
r_work: 0.4003 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10426  Z= 0.118
  Angle     :  0.546   8.148  14158  Z= 0.284
  Chirality :  0.040   0.154   1660
  Planarity :  0.004   0.060   1720
  Dihedral  : 10.302  89.988   1486
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 32.41 %
    Favored  : 60.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.24), residues: 1240
  helix: -0.66 (0.20), residues: 678
  sheet: -1.26 (0.51), residues: 112
  loop : -1.52 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 132 
 TYR   0.011   0.001   TYR A 474 
 PHE   0.018   0.001   PHE C 415 
 TRP   0.013   0.001   TRP C  95 
 HIS   0.003   0.001   HIS C 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10426)
  covalent geometry    : angle       0.54561 (14158)
  hydrogen bonds       : bond        0.04050 (  352)
  hydrogen bonds       : angle       4.60408 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 117
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  209 LEU cc_start: 0.6562 (mm) cc_final: 0.6356 (tp)
REVERT: C  238 CYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7461 (m)
REVERT: C  402 ASP cc_start: 0.3728 (m-30) cc_final: 0.2532 (p0)
REVERT: A  209 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6353 (tp)
REVERT: A  238 CYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7465 (m)
REVERT: A  402 ASP cc_start: 0.3612 (m-30) cc_final: 0.2442 (p0)
  outliers start: 75
  outliers final: 54
  residues processed: 178
  average time/residue: 0.0827
  time to fit residues: 22.6250
Evaluate side-chains
  163 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 106
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  189 CYS
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  445 THR
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  595 ILE
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  627 ASP
Chi-restraints excluded: chain C residue  654 VAL
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  763 THR
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  627 ASP
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 5 optimal weight:    0.1980
   chunk 98 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** 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 = 0.4387 r_free = 0.4387 target = 0.167070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.145317 restraints weight = 19716.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 3.16
r_work: 0.3981 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10426  Z= 0.139
  Angle     :  0.576   7.637  14158  Z= 0.298
  Chirality :  0.041   0.161   1660
  Planarity :  0.004   0.046   1720
  Dihedral  : 10.322  89.383   1486
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 32.87 %
    Favored  : 60.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.24), residues: 1240
  helix: -0.69 (0.20), residues: 674
  sheet: -1.33 (0.52), residues: 112
  loop : -1.51 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 132 
 TYR   0.011   0.001   TYR A 228 
 PHE   0.043   0.002   PHE A  87 
 TRP   0.010   0.001   TRP A  95 
 HIS   0.003   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10426)
  covalent geometry    : angle       0.57569 (14158)
  hydrogen bonds       : bond        0.04314 (  352)
  hydrogen bonds       : angle       4.67847 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 109
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  238 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7525 (m)
REVERT: C  402 ASP cc_start: 0.3809 (m-30) cc_final: 0.2565 (p0)
REVERT: C  423 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6177 (mp0)
REVERT: C  694 LEU cc_start: 0.4385 (OUTLIER) cc_final: 0.4121 (mm)
REVERT: C  728 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7679 (mp)
REVERT: A  209 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6302 (tp)
REVERT: A  238 CYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7527 (m)
REVERT: A  402 ASP cc_start: 0.3750 (m-30) cc_final: 0.2510 (p0)
REVERT: A  423 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6184 (mp0)
REVERT: A  694 LEU cc_start: 0.4418 (OUTLIER) cc_final: 0.4149 (mm)
REVERT: A  728 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7634 (mp)
  outliers start: 72
  outliers final: 56
  residues processed: 169
  average time/residue: 0.0822
  time to fit residues: 21.6225
Evaluate side-chains
  169 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 106
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  189 CYS
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  417 HIS
Chi-restraints excluded: chain C residue  445 THR
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  586 VAL
Chi-restraints excluded: chain C residue  595 ILE
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  627 ASP
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  654 VAL
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  694 LEU
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  763 THR
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  627 ASP
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 47 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0980
   chunk 36 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
** C 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** 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 = 0.4409 r_free = 0.4409 target = 0.169074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.147320 restraints weight = 19599.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 3.17
r_work: 0.4006 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10426  Z= 0.107
  Angle     :  0.547   7.592  14158  Z= 0.283
  Chirality :  0.039   0.166   1660
  Planarity :  0.004   0.038   1720
  Dihedral  : 10.276  89.278   1486
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 34.91 %
    Favored  : 60.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.24), residues: 1240
  helix: -0.54 (0.20), residues: 676
  sheet: -1.35 (0.51), residues: 112
  loop : -1.42 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 132 
 TYR   0.007   0.001   TYR C 228 
 PHE   0.043   0.001   PHE A  87 
 TRP   0.013   0.001   TRP A  95 
 HIS   0.003   0.001   HIS C 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10426)
  covalent geometry    : angle       0.54704 (14158)
  hydrogen bonds       : bond        0.03818 (  352)
  hydrogen bonds       : angle       4.49488 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 117
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  238 CYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7439 (m)
REVERT: C  402 ASP cc_start: 0.3922 (m-30) cc_final: 0.2758 (p0)
REVERT: C  423 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6208 (mp0)
REVERT: C  694 LEU cc_start: 0.4422 (OUTLIER) cc_final: 0.4177 (mm)
REVERT: C  728 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7744 (mp)
REVERT: A  238 CYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7447 (m)
REVERT: A  402 ASP cc_start: 0.3887 (m-30) cc_final: 0.2726 (p0)
REVERT: A  423 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6253 (mp0)
REVERT: A  694 LEU cc_start: 0.4424 (OUTLIER) cc_final: 0.4187 (mm)
REVERT: A  728 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7730 (mp)
  outliers start: 54
  outliers final: 43
  residues processed: 161
  average time/residue: 0.0873
  time to fit residues: 21.1654
Evaluate side-chains
  160 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 111
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  238 CYS
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  608 VAL
Chi-restraints excluded: chain C residue  628 THR
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  654 VAL
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  694 LEU
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  763 THR
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 LEU
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0370
   chunk 113 optimal weight:    0.0870
   chunk 8 optimal weight:    0.0980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.3236

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

Flipped N/Q/H residues before XYZ refinement:
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** 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 = 0.4429 r_free = 0.4429 target = 0.171187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.149495 restraints weight = 19488.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 3.15
r_work: 0.4033 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10426  Z= 0.094
  Angle     :  0.525   7.580  14158  Z= 0.273
  Chirality :  0.039   0.170   1660
  Planarity :  0.003   0.028   1720
  Dihedral  : 10.193  89.552   1486
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 35.09 %
    Favored  : 60.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.24), residues: 1240
  helix: -0.36 (0.20), residues: 680
  sheet: -1.19 (0.50), residues: 114
  loop : -1.44 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 438 
 TYR   0.011   0.001   TYR A 474 
 PHE   0.015   0.001   PHE A  87 
 TRP   0.012   0.001   TRP A  95 
 HIS   0.004   0.001   HIS C 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 (10426)
  covalent geometry    : angle       0.52521 (14158)
  hydrogen bonds       : bond        0.03450 (  352)
  hydrogen bonds       : angle       4.34016 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 122
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  402 ASP cc_start: 0.3881 (m-30) cc_final: 0.2906 (p0)
REVERT: C  423 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6153 (mp0)
REVERT: A  402 ASP cc_start: 0.3987 (m-30) cc_final: 0.3017 (p0)
REVERT: A  423 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6130 (mp0)
  outliers start: 49
  outliers final: 39
  residues processed: 162
  average time/residue: 0.0811
  time to fit residues: 20.2969
Evaluate side-chains
  151 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 112
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  627 ASP
Chi-restraints excluded: chain C residue  628 THR
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 119 optimal weight:    2.9990
   chunk 91 optimal weight:    0.2980
   chunk 84 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0670
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0670
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
C 384 GLN
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 GLN
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** 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 = 0.4420 r_free = 0.4420 target = 0.171133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.149267 restraints weight = 19301.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4159 rms_B_bonded: 3.18
r_work: 0.4034 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10426  Z= 0.094
  Angle     :  0.523   7.495  14158  Z= 0.271
  Chirality :  0.039   0.168   1660
  Planarity :  0.003   0.026   1720
  Dihedral  : 10.146  89.674   1486
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 35.46 %
    Favored  : 60.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.24), residues: 1240
  helix: -0.21 (0.21), residues: 668
  sheet: -1.09 (0.50), residues: 114
  loop : -1.49 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 745 
 TYR   0.009   0.001   TYR C 474 
 PHE   0.021   0.001   PHE C 415 
 TRP   0.011   0.001   TRP C  95 
 HIS   0.004   0.000   HIS C 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 (10426)
  covalent geometry    : angle       0.52282 (14158)
  hydrogen bonds       : bond        0.03340 (  352)
  hydrogen bonds       : angle       4.29927 ( 1020)

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

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

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2480 Ramachandran restraints generated.
    1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 117
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  384 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.5572 (tm-30)
REVERT: C  402 ASP cc_start: 0.3753 (m-30) cc_final: 0.3021 (p0)
REVERT: A  384 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.5663 (tm-30)
REVERT: A  402 ASP cc_start: 0.3909 (m-30) cc_final: 0.3117 (p0)
  outliers start: 45
  outliers final: 39
  residues processed: 156
  average time/residue: 0.0722
  time to fit residues: 18.1889
Evaluate side-chains
  153 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 112
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  202 ILE
Chi-restraints excluded: chain C residue  259 VAL
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  350 CYS
Chi-restraints excluded: chain C residue  384 GLN
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  461 THR
Chi-restraints excluded: chain C residue  493 ILE
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  527 VAL
Chi-restraints excluded: chain C residue  551 HIS
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  670 PHE
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  654 VAL
Chi-restraints excluded: chain A residue  670 PHE
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0010
   chunk 116 optimal weight:    0.0670
   chunk 11 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 105 optimal weight:    0.3980
   chunk 98 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.3124

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

Flipped N/Q/H residues before XYZ refinement:
** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 716 HIS ** 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 = 0.4426 r_free = 0.4426 target = 0.171552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.149506 restraints weight = 19469.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 3.18
r_work: 0.4041 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10426  Z= 0.096
  Angle     :  0.525   7.348  14158  Z= 0.274
  Chirality :  0.039   0.170   1660
  Planarity :  0.003   0.027   1720
  Dihedral  : 10.133  89.720   1486
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 36.30 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.24), residues: 1240
  helix: -0.20 (0.21), residues: 672
  sheet: -1.15 (0.50), residues: 120
  loop : -1.60 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 132 
 TYR   0.009   0.001   TYR A 474 
 PHE   0.063   0.001   PHE C  87 
 TRP   0.011   0.001   TRP C  95 
 HIS   0.003   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 (10426)
  covalent geometry    : angle       0.52514 (14158)
  hydrogen bonds       : bond        0.03286 (  352)
  hydrogen bonds       : angle       4.27632 ( 1020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2370.44 seconds
wall clock time: 41 minutes 26.76 seconds (2486.76 seconds total)