Starting phenix.real_space_refine
on Fri Jul  3 05:34:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c5q_45218/07_2026/9c5q_45218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c5q_45218/07_2026/9c5q_45218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2026/9c5q_45218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2026/9c5q_45218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2026/9c5q_45218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c5q_45218/07_2026/9c5q_45218.cif"
  }
  resolution = 3.1
  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=   0.017
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      28      5.49       5
     S      70      5.16       5
     C    7818      2.51       5
     N    2068      2.21       5
     O    2340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12324
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 234
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {' DC:plan': 2, ' DC:plan2': 2, ' DG:plan': 3, ' DG:plan2': 3}
          Unresolved non-hydrogen planarities: 59
    Chain: "C"
      Number of atoms: 5928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 775, 5928
          Classifications: {'peptide': 775}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 23, 'TRANS': 751}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 180
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 148
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 10, 'HIS:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 113
  Restraints were copied for chains:
    B, A
  Time building chain proxies: 5.06, per 1000 atoms: 0.41
  Number of scatterers: 12324
  At special positions: 0
  Unit cell: (148.78, 128.14, 83.42, 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      70     16.00
     P      28     15.00
     O    2340      8.00
     N    2068      7.00
     C    7818      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 344 " - pdb=" SG  CYS C 350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 350 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 486.1 milliseconds
  

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2924

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 10 sheets defined
      54.6% alpha, 4.8% beta
      0 base pairs and 6 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'C' and resid 70 through 75
      removed outlier: 3.616A  pdb=" N   TRP C  74 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   GLY C  75 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 88
      removed outlier: 3.556A  pdb=" N   GLY C  88 " --> pdb=" O   TYR C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 101
      removed outlier: 3.592A  pdb=" N   ALA C  97 " --> pdb=" O   PHE C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 136
      removed outlier: 4.507A  pdb=" N   ALA C 125 " --> pdb=" O   LYS C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 161
    Processing helix  chain 'C' and resid 191 through 204
      removed outlier: 3.832A  pdb=" N   ASN C 195 " --> pdb=" O   ILE C 191 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY C 196 " --> pdb=" O   GLU C 192 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU C 197 " --> pdb=" O   ARG C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 208
      No H-bonds generated for 'chain 'C' and resid 206 through 208'
    Processing helix  chain 'C' and resid 217 through 222
      removed outlier: 3.535A  pdb=" N   MET C 220 " --> pdb=" O   GLU C 217 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY C 222 " --> pdb=" O   HIS C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 243
      removed outlier: 4.286A  pdb=" N   THR C 235 " --> pdb=" O   GLU C 231 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LYS C 236 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 3.799A  pdb=" N   VAL C 274 " --> pdb=" O   ASN C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 336
      removed outlier: 3.551A  pdb=" N   LEU C 329 " --> pdb=" O   HIS C 325 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS C 330 " --> pdb=" O   VAL C 326 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLU C 332 " --> pdb=" O   SER C 328 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR C 333 " --> pdb=" O   LEU C 329 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ASP C 336 " --> pdb=" O   GLU C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 364
      removed outlier: 3.528A  pdb=" N   GLU C 351 " --> pdb=" O   LYS C 347 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU C 360 " --> pdb=" O   ILE C 356 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU C 364 " --> pdb=" O   GLU C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 396
      removed outlier: 3.633A  pdb=" N   LEU C 388 " --> pdb=" O   GLN C 384 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU C 389 " --> pdb=" O   LYS C 385 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP C 392 " --> pdb=" O   LEU C 388 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLN C 393 " --> pdb=" O   GLU C 389 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG C 396 " --> pdb=" O   ASP C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 434
      removed outlier: 3.695A  pdb=" N   ILE C 428 " --> pdb=" O   GLU C 424 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   GLN C 434 " --> pdb=" O   GLY C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 448
      removed outlier: 3.726A  pdb=" N   SER C 448 " --> pdb=" O   THR C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 479
    Processing helix  chain 'C' and resid 501 through 509
    Processing helix  chain 'C' and resid 528 through 540
      removed outlier: 3.917A  pdb=" N   ILE C 538 " --> pdb=" O   ALA C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 546 through 554
      removed outlier: 3.502A  pdb=" N   THR C 552 " --> pdb=" O   GLN C 548 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 558 through 563
      removed outlier: 3.571A  pdb=" N   SER C 562 " --> pdb=" O   PHE C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 581 through 589
      removed outlier: 3.505A  pdb=" N   TRP C 588 " --> pdb=" O   ALA C 584 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU C 589 " --> pdb=" O   CYS C 585 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 612 through 622
    Processing helix  chain 'C' and resid 627 through 639
      removed outlier: 3.778A  pdb=" N   ALA C 633 " --> pdb=" O   LEU C 629 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET C 639 " --> pdb=" O   LEU C 635 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 648 through 653
      removed outlier: 3.830A  pdb=" N   LEU C 653 " --> pdb=" O   HIS C 649 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 665 through 675
      removed outlier: 3.611A  pdb=" N   PHE C 669 " --> pdb=" O   ASP C 665 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU C 674 " --> pdb=" O   PHE C 670 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS C 675 " --> pdb=" O   CYS C 671 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 677 through 688
      removed outlier: 3.581A  pdb=" N   ARG C 682 " --> pdb=" O   THR C 678 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL C 683 " --> pdb=" O   SER C 679 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA C 684 " --> pdb=" O   MET C 680 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU C 685 " --> pdb=" O   LYS C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 690 through 697
      removed outlier: 3.821A  pdb=" N   LEU C 694 " --> pdb=" O   GLU C 690 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 707 through 730
      removed outlier: 3.509A  pdb=" N   PHE C 719 " --> pdb=" O   ILE C 715 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE C 720 " --> pdb=" O   HIS C 716 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR C 721 " --> pdb=" O   LYS C 717 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASP C 727 " --> pdb=" O   LEU C 723 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU C 728 " --> pdb=" O   VAL C 724 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE C 729 " --> pdb=" O   LEU C 725 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 733 through 741
      removed outlier: 3.612A  pdb=" N   ASN C 738 " --> pdb=" O   LEU C 734 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLN C 739 " --> pdb=" O   ARG C 735 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 744 through 770
      removed outlier: 3.613A  pdb=" N   GLN C 749 " --> pdb=" O   ARG C 745 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER C 750 " --> pdb=" O   GLY C 746 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA C 756 " --> pdb=" O   GLN C 752 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL C 757 " --> pdb=" O   GLN C 753 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY C 760 " --> pdb=" O   ALA C 756 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET C 761 " --> pdb=" O   VAL C 757 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR C 763 " --> pdb=" O   ALA C 759 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   VAL C 764 " --> pdb=" O   GLY C 760 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY C 770 " --> pdb=" O   SER C 766 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 772 through 781
      removed outlier: 3.625A  pdb=" N   LEU C 776 " --> pdb=" O   HIS C 772 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU C 777 " --> pdb=" O   ASN C 773 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE C 781 " --> pdb=" O   LEU C 777 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 781 through 786
      removed outlier: 3.515A  pdb=" N   LEU C 785 " --> pdb=" O   PHE C 781 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR C 786 " --> pdb=" O   GLN C 782 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 781 through 786'
    Processing helix  chain 'C' and resid 792 through 797
      removed outlier: 4.362A  pdb=" N   LEU C 796 " --> pdb=" O   GLU C 792 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 803 through 814
      removed outlier: 4.246A  pdb=" N   ARG C 808 " --> pdb=" O   ALA C 804 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   VAL C 809 " --> pdb=" O   GLN C 805 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA C 812 " --> pdb=" O   ARG C 808 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   SER C 813 " --> pdb=" O   VAL C 809 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 826 through 835
    Processing helix  chain 'C' and resid 849 through 858
    Processing helix  chain 'C' and resid 871 through 891
      removed outlier: 3.841A  pdb=" N   ALA C 876 " --> pdb=" O   GLU C 872 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA C 877 " --> pdb=" O   ARG C 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 75
      removed outlier: 3.616A  pdb=" N   TRP A  74 " --> pdb=" O   LEU A  71 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLY A  75 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 88
      removed outlier: 3.556A  pdb=" N   GLY A  88 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 101
      removed outlier: 3.592A  pdb=" N   ALA A  97 " --> pdb=" O   PHE A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 136
      removed outlier: 4.508A  pdb=" N   ALA A 125 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 161
    Processing helix  chain 'A' and resid 191 through 204
      removed outlier: 3.832A  pdb=" N   ASN A 195 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU A 197 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 3.535A  pdb=" N   MET A 220 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY A 222 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 243
      removed outlier: 4.286A  pdb=" N   THR A 235 " --> pdb=" O   GLU A 231 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LYS A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.799A  pdb=" N   VAL A 274 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 336
      removed outlier: 3.550A  pdb=" N   LEU A 329 " --> pdb=" O   HIS A 325 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS A 330 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLU A 332 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ASP A 336 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 364
      removed outlier: 3.528A  pdb=" N   GLU A 351 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 396
      removed outlier: 3.633A  pdb=" N   LEU A 388 " --> pdb=" O   GLN A 384 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU A 389 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASP A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN A 393 " --> pdb=" O   GLU A 389 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG A 396 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 434
      removed outlier: 3.696A  pdb=" N   ILE A 428 " --> pdb=" O   GLU A 424 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLN A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 448
      removed outlier: 3.727A  pdb=" N   SER A 448 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
    Processing helix  chain 'A' and resid 501 through 509
    Processing helix  chain 'A' and resid 528 through 540
      removed outlier: 3.918A  pdb=" N   ILE A 538 " --> pdb=" O   ALA A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 554
      removed outlier: 3.502A  pdb=" N   THR A 552 " --> pdb=" O   GLN A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 563
      removed outlier: 3.571A  pdb=" N   SER A 562 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 589
      removed outlier: 3.504A  pdb=" N   TRP A 588 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 622
    Processing helix  chain 'A' and resid 627 through 639
      removed outlier: 3.778A  pdb=" N   ALA A 633 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET A 639 " --> pdb=" O   LEU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 653
      removed outlier: 3.830A  pdb=" N   LEU A 653 " --> pdb=" O   HIS A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 675
      removed outlier: 3.611A  pdb=" N   PHE A 669 " --> pdb=" O   ASP A 665 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU A 674 " --> pdb=" O   PHE A 670 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS A 675 " --> pdb=" O   CYS A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 688
      removed outlier: 3.582A  pdb=" N   ARG A 682 " --> pdb=" O   THR A 678 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL A 683 " --> pdb=" O   SER A 679 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA A 684 " --> pdb=" O   MET A 680 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU A 685 " --> pdb=" O   LYS A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 697
      removed outlier: 3.821A  pdb=" N   LEU A 694 " --> pdb=" O   GLU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 730
      removed outlier: 3.509A  pdb=" N   PHE A 719 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE A 720 " --> pdb=" O   HIS A 716 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 721 " --> pdb=" O   LYS A 717 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A 727 " --> pdb=" O   LEU A 723 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 728 " --> pdb=" O   VAL A 724 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 741
      removed outlier: 3.612A  pdb=" N   ASN A 738 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLN A 739 " --> pdb=" O   ARG A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 770
      removed outlier: 3.613A  pdb=" N   GLN A 749 " --> pdb=" O   ARG A 745 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER A 750 " --> pdb=" O   GLY A 746 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A 756 " --> pdb=" O   GLN A 752 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 757 " --> pdb=" O   GLN A 753 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 760 " --> pdb=" O   ALA A 756 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET A 761 " --> pdb=" O   VAL A 757 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 763 " --> pdb=" O   ALA A 759 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   VAL A 764 " --> pdb=" O   GLY A 760 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY A 770 " --> pdb=" O   SER A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 781
      removed outlier: 3.625A  pdb=" N   LEU A 776 " --> pdb=" O   HIS A 772 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU A 777 " --> pdb=" O   ASN A 773 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE A 781 " --> pdb=" O   LEU A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 786
      removed outlier: 3.515A  pdb=" N   LEU A 785 " --> pdb=" O   PHE A 781 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR A 786 " --> pdb=" O   GLN A 782 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 781 through 786'
    Processing helix  chain 'A' and resid 792 through 797
      removed outlier: 4.362A  pdb=" N   LEU A 796 " --> pdb=" O   GLU A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 814
      removed outlier: 4.246A  pdb=" N   ARG A 808 " --> pdb=" O   ALA A 804 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   VAL A 809 " --> pdb=" O   GLN A 805 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA A 812 " --> pdb=" O   ARG A 808 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   SER A 813 " --> pdb=" O   VAL A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 835
    Processing helix  chain 'A' and resid 849 through 858
    Processing helix  chain 'A' and resid 871 through 891
      removed outlier: 3.841A  pdb=" N   ALA A 876 " --> pdb=" O   GLU A 872 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A 877 " --> pdb=" O   ARG A 873 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 169 through 170
      removed outlier: 6.738A  pdb=" N   ASP C 169 " --> pdb=" O   VAL C 188 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ALA C 140 " --> pdb=" O   ALA C 187 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS C 139 " --> pdb=" O   MET C 212 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   VAL C 214 " --> pdb=" O   LYS C 139 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   LEU C 141 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN C 260 " --> pdb=" O   GLY C 211 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 298
      removed outlier: 6.676A  pdb=" N   LYS C 297 " --> pdb=" O   CYS C 496 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 439 through 442
      removed outlier: 6.471A  pdb=" N   VAL C 340 " --> pdb=" O   LEU C 440 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ALA C 442 " --> pdb=" O   VAL C 340 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LEU C 342 " --> pdb=" O   ALA C 442 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   LEU C 341 " --> pdb=" O   ILE C 458 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   VAL C 457 " --> pdb=" O   ILE C 493 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 463 through 464
    Processing sheet with id=AA5, first strand: chain 'C' and resid 595 through 597
    Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170
      removed outlier: 6.738A  pdb=" N   ASP A 169 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ALA A 140 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS A 139 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   VAL A 214 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN A 260 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 298
      removed outlier: 6.677A  pdb=" N   LYS A 297 " --> pdb=" O   CYS A 496 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 442
      removed outlier: 6.471A  pdb=" N   VAL A 340 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   ALA A 442 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LEU A 342 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   LEU A 341 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   VAL A 457 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 463 through 464
    Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597

    438 hydrogen bonds defined for protein.
    1278 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: 1.75

  Time building geometry restraints manager: 1.08 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: 3639
        1.34 -     1.46: 1820
        1.46 -     1.57: 6947
        1.57 -     1.69: 54
        1.69 -     1.81: 112
  Bond restraints: 12572
  Sorted by residual:
  bond pdb=" C3'  DT B   8 "
       pdb=" C2'  DT B   8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 8.00e-03 1.56e+04 6.83e+00
  bond pdb=" C3'  DT D   8 "
       pdb=" C2'  DT D   8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 8.00e-03 1.56e+04 6.52e+00
  bond pdb=" C3'  DT D   4 "
       pdb=" C2'  DT D   4 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 8.00e-03 1.56e+04 5.25e+00
  bond pdb=" C3'  DT B   4 "
       pdb=" C2'  DT B   4 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 8.00e-03 1.56e+04 5.23e+00
  bond pdb=" C3'  DT D   8 "
       pdb=" O3'  DT D   8 "
    ideal  model  delta    sigma   weight residual
    1.435  1.461 -0.026 1.30e-02 5.92e+03 4.06e+00
  ... (remaining 12567 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 16698
        1.76 -     3.51: 365
        3.51 -     5.27: 41
        5.27 -     7.03: 10
        7.03 -     8.79: 2
  Bond angle restraints: 17116
  Sorted by residual:
  angle pdb=" N3   DT B   8 "
        pdb=" C4   DT B   8 "
        pdb=" O4   DT B   8 "
      ideal   model   delta    sigma   weight residual
     119.90  122.42   -2.52 6.00e-01 2.78e+00 1.76e+01
  angle pdb=" N3   DT D   8 "
        pdb=" C4   DT D   8 "
        pdb=" O4   DT D   8 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT D   3 "
        pdb=" C4   DT D   3 "
        pdb=" O4   DT D   3 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT B   6 "
        pdb=" C4   DT B   6 "
        pdb=" O4   DT B   6 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  angle pdb=" N3   DT D   4 "
        pdb=" C4   DT D   4 "
        pdb=" O4   DT D   4 "
      ideal   model   delta    sigma   weight residual
     119.90  122.37   -2.47 6.00e-01 2.78e+00 1.70e+01
  ... (remaining 17111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.93: 6553
       22.93 -    45.87: 798
       45.87 -    68.80: 166
       68.80 -    91.73: 21
       91.73 -   114.66: 2
  Dihedral angle restraints: 7540
    sinusoidal: 3042
      harmonic: 4498
  Sorted by residual:
  dihedral pdb=" CA  ASN C 337 "
           pdb=" C   ASN C 337 "
           pdb=" N   HIS C 338 "
           pdb=" CA  HIS C 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.73  -21.27     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" SG  CYS A 344 "
           pdb=" CB  CYS A 350 "
           pdb=" SG  CYS A 350 "
           pdb=" CA  CYS A 350 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    3.31   75.69     1      2.00e+01 2.50e-03 1.81e+01
  dihedral pdb=" SG  CYS C 344 "
           pdb=" CB  CYS C 350 "
           pdb=" SG  CYS C 350 "
           pdb=" CA  CYS C 350 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    3.35   75.65     1      2.00e+01 2.50e-03 1.81e+01
  ... (remaining 7537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1500
       0.038 -    0.076: 417
       0.076 -    0.113: 101
       0.113 -    0.151: 16
       0.151 -    0.189: 2
  Chirality restraints: 2036
  Sorted by residual:
  chirality pdb=" CB  ILE C 302 "
            pdb=" CA  ILE C 302 "
            pdb=" CG1 ILE C 302 "
            pdb=" CG2 ILE C 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.92e-01
  chirality pdb=" CB  ILE A 302 "
            pdb=" CA  ILE A 302 "
            pdb=" CG1 ILE A 302 "
            pdb=" CG2 ILE A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" C3'  DT D   8 "
            pdb=" C4'  DT D   8 "
            pdb=" O3'  DT D   8 "
            pdb=" C2'  DT D   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.59   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2033 not shown)

  Planarity restraints: 2074
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 624 "    0.052 5.00e-02 4.00e+02   8.04e-02 1.04e+01
        pdb=" N   PRO C 625 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO C 625 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 625 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 624 "   -0.052 5.00e-02 4.00e+02   8.03e-02 1.03e+01
        pdb=" N   PRO A 625 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 625 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 625 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  76 "   -0.030 5.00e-02 4.00e+02   4.63e-02 3.44e+00
        pdb=" N   PRO A  77 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A  77 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  77 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 2071 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2592
        2.78 -     3.31: 11250
        3.31 -     3.84: 18538
        3.84 -     4.37: 20706
        4.37 -     4.90: 36570
  Nonbonded interactions: 89656
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 217 "
            pdb=" NE2 HIS C 219 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OE1 GLU A 217 "
            pdb=" NE2 HIS A 219 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   SER A 624 "
            pdb=" OG1 THR A 628 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   SER C 624 "
            pdb=" OG1 THR C 628 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OH  TYR A 331 "
            pdb=" NE2 HIS A 365 "
     model   vdw
     2.293 3.120
  ... (remaining 89651 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
}

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:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.460
  Find NCS groups from input model:        0.070
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
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   0.050  12574  Z= 0.187
  Angle     :  0.591   8.786  17120  Z= 0.373
  Chirality :  0.038   0.189   2036
  Planarity :  0.004   0.080   2074
  Dihedral  : 19.490 114.664   4610
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.41 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 35.30 %
    Favored  : 64.05 %
  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 are not related in a simple way.
  whole: -2.00 (0.21), residues: 1522
  helix: -0.60 (0.19), residues: 720
  sheet: -0.71 (0.51), residues: 130
  loop : -2.24 (0.23), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 456 
 TYR   0.009   0.001   TYR A 362 
 PHE   0.006   0.001   PHE A 161 
 TRP   0.007   0.001   TRP A 349 
 HIS   0.003   0.001   HIS C 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.19 (12572)
  covalent geometry    : angle       0.59045 /  0.37 (17116)
  SS BOND              : bond        0.00040 /  0.02 (    2)
  SS BOND              : angle       1.28495 /  1.83 (    4)
  hydrogen bonds       : bond        0.30083 / 26.13 (  438)
  hydrogen bonds       : angle       7.00693 /  5.43 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.360 
Fit side-chains
REVERT: C  295 SER cc_start: 0.8397 (t) cc_final: 0.7964 (p)
REVERT: C  317 LEU cc_start: 0.6943 (pt) cc_final: 0.6302 (tt)
REVERT: A  295 SER cc_start: 0.8358 (t) cc_final: 0.8129 (t)
REVERT: A  317 LEU cc_start: 0.6917 (pt) cc_final: 0.6324 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 128
  average time/residue: 0.1178
  time to fit residues: 21.2354
Evaluate side-chains
  112 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  803 ASN
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  803 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    0.4980
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    0.3980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0870
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0270
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:    0.1980
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    0.2216

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
C 498 ASN
C 752 GLN
C 767 ASN
C 835 ASN
A 325 HIS
A 498 ASN
A 752 GLN
A 767 ASN
A 835 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.151847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.114812 restraints weight = 20885.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 3.46
r_work: 0.3455 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12574  Z= 0.125
  Angle     :  0.580   7.765  17120  Z= 0.309
  Chirality :  0.039   0.232   2036
  Planarity :  0.005   0.060   2074
  Dihedral  : 13.395 113.543   1924
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.15 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 31.66 %
    Favored  : 65.02 %
  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 are not related in a simple way.
  whole: -1.59 (0.21), residues: 1522
  helix: -0.16 (0.18), residues: 768
  sheet: -0.74 (0.50), residues: 130
  loop : -2.25 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 433 
 TYR   0.009   0.001   TYR A 553 
 PHE   0.010   0.001   PHE C 422 
 TRP   0.006   0.001   TRP C 771 
 HIS   0.005   0.001   HIS C 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.13 (12572)
  covalent geometry    : angle       0.58000 /  0.31 (17116)
  SS BOND              : bond        0.00147 /  0.07 (    2)
  SS BOND              : angle       1.16246 /  1.57 (    4)
  hydrogen bonds       : bond        0.05735 /  4.90 (  438)
  hydrogen bonds       : angle       4.70817 /  3.75 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 112
  time to evaluate  : 0.291 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6104 (t80)
REVERT: C  295 SER cc_start: 0.7593 (t) cc_final: 0.7223 (p)
REVERT: C  351 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6856 (mm-30)
REVERT: A   84 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6123 (t80)
REVERT: A  295 SER cc_start: 0.7599 (t) cc_final: 0.7386 (t)
REVERT: A  351 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6862 (mm-30)
  outliers start: 41
  outliers final: 24
  residues processed: 144
  average time/residue: 0.1134
  time to fit residues: 22.9898
Evaluate side-chains
  129 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  539 ILE
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  761 MET
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 143 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 147 optimal weight:   10.0000
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.150516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.113330 restraints weight = 21138.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 3.47
r_work: 0.3433 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12574  Z= 0.115
  Angle     :  0.538   6.399  17120  Z= 0.282
  Chirality :  0.039   0.247   2036
  Planarity :  0.004   0.049   2074
  Dihedral  : 13.493 114.862   1920
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.74 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 30.21 %
    Favored  : 64.94 %
  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 are not related in a simple way.
  whole: -1.25 (0.22), residues: 1522
  helix:  0.27 (0.19), residues: 780
  sheet: -0.78 (0.50), residues: 128
  loop : -2.30 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 433 
 TYR   0.007   0.001   TYR C 741 
 PHE   0.009   0.001   PHE C 693 
 TRP   0.004   0.001   TRP A 673 
 HIS   0.003   0.000   HIS A 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 (12572)
  covalent geometry    : angle       0.53763 /  0.28 (17116)
  SS BOND              : bond        0.00382 /  0.19 (    2)
  SS BOND              : angle       1.27159 /  1.71 (    4)
  hydrogen bonds       : bond        0.04886 /  4.24 (  438)
  hydrogen bonds       : angle       4.27852 /  3.46 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 107
  time to evaluate  : 0.395 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6484 (t80)
REVERT: C  295 SER cc_start: 0.7686 (t) cc_final: 0.7478 (t)
REVERT: C  316 MET cc_start: 0.4722 (tpp) cc_final: 0.4426 (tpt)
REVERT: C  351 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6821 (mm-30)
REVERT: C  550 MET cc_start: 0.6369 (tmm) cc_final: 0.6090 (tmm)
REVERT: A   84 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.6463 (t80)
REVERT: A  295 SER cc_start: 0.7690 (t) cc_final: 0.7468 (t)
REVERT: A  316 MET cc_start: 0.4783 (tpp) cc_final: 0.4505 (tpt)
REVERT: A  351 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6880 (mm-30)
REVERT: A  550 MET cc_start: 0.6366 (tmm) cc_final: 0.6085 (tmm)
  outliers start: 60
  outliers final: 32
  residues processed: 155
  average time/residue: 0.0969
  time to fit residues: 22.1218
Evaluate side-chains
  136 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  539 ILE
Chi-restraints excluded: chain C residue  552 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  657 MET
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 106 optimal weight:    0.7980
   chunk 128 optimal weight:    0.4980
   chunk 41 optimal weight:    7.9990
   chunk 110 optimal weight:    0.0970
   chunk 86 optimal weight:    1.9990
   chunk 127 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 117 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.151477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.114338 restraints weight = 21026.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 3.47
r_work: 0.3451 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12574  Z= 0.099
  Angle     :  0.511   6.569  17120  Z= 0.270
  Chirality :  0.038   0.246   2036
  Planarity :  0.004   0.044   2074
  Dihedral  : 13.535 114.902   1920
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.88 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 31.34 %
    Favored  : 64.46 %
  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 are not related in a simple way.
  whole: -1.09 (0.22), residues: 1522
  helix:  0.46 (0.19), residues: 780
  sheet: -0.79 (0.49), residues: 128
  loop : -2.30 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 433 
 TYR   0.007   0.001   TYR A 113 
 PHE   0.006   0.001   PHE A 787 
 TRP   0.004   0.001   TRP A 863 
 HIS   0.002   0.000   HIS A 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00205 /  0.10 (12572)
  covalent geometry    : angle       0.51092 /  0.27 (17116)
  SS BOND              : bond        0.00240 /  0.12 (    2)
  SS BOND              : angle       1.24173 /  1.73 (    4)
  hydrogen bonds       : bond        0.03828 /  3.30 (  438)
  hydrogen bonds       : angle       4.05682 /  3.28 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 108
  time to evaluate  : 0.389 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.6650 (t80)
REVERT: C  316 MET cc_start: 0.4833 (tpp) cc_final: 0.4537 (tpt)
REVERT: C  351 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6746 (mm-30)
REVERT: C  563 MET cc_start: 0.4850 (mtt) cc_final: 0.4531 (mtt)
REVERT: A   84 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6638 (t80)
REVERT: A  316 MET cc_start: 0.4842 (tpp) cc_final: 0.4541 (tpt)
REVERT: A  351 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6787 (mm-30)
REVERT: A  563 MET cc_start: 0.4792 (mtt) cc_final: 0.4487 (mtt)
  outliers start: 52
  outliers final: 33
  residues processed: 149
  average time/residue: 0.0891
  time to fit residues: 19.7410
Evaluate side-chains
  139 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  539 ILE
Chi-restraints excluded: chain C residue  552 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  645 GLU
Chi-restraints excluded: chain C residue  657 MET
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 118 optimal weight:    9.9990
   chunk 119 optimal weight:    3.9990
   chunk 139 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 102 optimal weight:    9.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.145623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.107692 restraints weight = 21292.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 3.52
r_work: 0.3363 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12574  Z= 0.216
  Angle     :  0.634   7.899  17120  Z= 0.331
  Chirality :  0.043   0.279   2036
  Planarity :  0.004   0.048   2074
  Dihedral  : 13.630 114.445   1920
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.71 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 31.18 %
    Favored  : 63.41 %
  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 are not related in a simple way.
  whole: -1.51 (0.21), residues: 1522
  helix:  0.18 (0.19), residues: 772
  sheet: -1.18 (0.47), residues: 136
  loop : -2.54 (0.23), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 433 
 TYR   0.009   0.001   TYR A 113 
 PHE   0.019   0.002   PHE C 839 
 TRP   0.009   0.001   TRP C 277 
 HIS   0.008   0.001   HIS C 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00518 /  0.22 (12572)
  covalent geometry    : angle       0.63345 /  0.33 (17116)
  SS BOND              : bond        0.00519 /  0.26 (    2)
  SS BOND              : angle       1.51346 /  1.99 (    4)
  hydrogen bonds       : bond        0.05755 /  4.97 (  438)
  hydrogen bonds       : angle       4.33659 /  3.55 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 101
  time to evaluate  : 0.520 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7062 (t80)
REVERT: C  316 MET cc_start: 0.5005 (tpp) cc_final: 0.4730 (tpt)
REVERT: C  351 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6818 (mm-30)
REVERT: C  429 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6278 (tt0)
REVERT: C  563 MET cc_start: 0.5140 (mtt) cc_final: 0.4832 (mtt)
REVERT: C  761 MET cc_start: 0.8335 (ptp) cc_final: 0.8109 (ptm)
REVERT: A   84 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7073 (t80)
REVERT: A  351 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6855 (mm-30)
REVERT: A  563 MET cc_start: 0.5116 (mtt) cc_final: 0.4823 (mtt)
REVERT: A  761 MET cc_start: 0.8330 (ptp) cc_final: 0.8104 (ptm)
  outliers start: 67
  outliers final: 42
  residues processed: 160
  average time/residue: 0.1091
  time to fit residues: 25.4880
Evaluate side-chains
  145 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 99
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue   99 CYS
Chi-restraints excluded: chain C residue  293 LEU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  539 ILE
Chi-restraints excluded: chain C residue  552 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  662 THR
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  447 SER
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 141 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 147 optimal weight:    6.9990
   chunk 151 optimal weight:    7.9990
   chunk 111 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.148120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.110668 restraints weight = 21197.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 3.47
r_work: 0.3392 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12574  Z= 0.124
  Angle     :  0.548   6.292  17120  Z= 0.286
  Chirality :  0.039   0.261   2036
  Planarity :  0.004   0.045   2074
  Dihedral  : 13.614 113.691   1920
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.66 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 31.91 %
    Favored  : 63.73 %
  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 are not related in a simple way.
  whole: -1.37 (0.22), residues: 1522
  helix:  0.28 (0.19), residues: 784
  sheet: -1.37 (0.47), residues: 124
  loop : -2.40 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 433 
 TYR   0.008   0.001   TYR A 113 
 PHE   0.006   0.001   PHE C 839 
 TRP   0.005   0.001   TRP A 673 
 HIS   0.003   0.000   HIS C 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 (12572)
  covalent geometry    : angle       0.54785 /  0.29 (17116)
  SS BOND              : bond        0.00333 /  0.17 (    2)
  SS BOND              : angle       1.41401 /  1.92 (    4)
  hydrogen bonds       : bond        0.04303 /  3.71 (  438)
  hydrogen bonds       : angle       4.12524 /  3.36 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 104
  time to evaluate  : 0.459 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7044 (t80)
REVERT: C  351 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6821 (mm-30)
REVERT: C  429 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6191 (tt0)
REVERT: C  563 MET cc_start: 0.4839 (mtt) cc_final: 0.4558 (mtt)
REVERT: C  761 MET cc_start: 0.8437 (ptp) cc_final: 0.8027 (ptm)
REVERT: A   84 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7046 (t80)
REVERT: A  351 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6875 (mm-30)
REVERT: A  563 MET cc_start: 0.4820 (mtt) cc_final: 0.4526 (mtt)
REVERT: A  761 MET cc_start: 0.8438 (ptp) cc_final: 0.8026 (ptm)
  outliers start: 54
  outliers final: 38
  residues processed: 152
  average time/residue: 0.0913
  time to fit residues: 20.3972
Evaluate side-chains
  143 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 101
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  539 ILE
Chi-restraints excluded: chain C residue  552 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  661 TRP
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  447 SER
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 122 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0870
   chunk 31 optimal weight:    0.0170
   chunk 85 optimal weight:    0.8980
   chunk 88 optimal weight:    6.9990
   chunk 153 optimal weight:    0.0980
   chunk 121 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.4198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.150639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.113482 restraints weight = 20842.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 3.44
r_work: 0.3439 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12574  Z= 0.095
  Angle     :  0.527   6.272  17120  Z= 0.272
  Chirality :  0.038   0.247   2036
  Planarity :  0.004   0.043   2074
  Dihedral  : 13.545 113.591   1920
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.00 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 31.58 %
    Favored  : 64.38 %
  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 are not related in a simple way.
  whole: -1.19 (0.22), residues: 1522
  helix:  0.44 (0.19), residues: 788
  sheet: -1.26 (0.48), residues: 124
  loop : -2.36 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 433 
 TYR   0.007   0.001   TYR C 113 
 PHE   0.005   0.001   PHE C 415 
 TRP   0.005   0.001   TRP A 673 
 HIS   0.002   0.000   HIS A 716 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00200 /  0.10 (12572)
  covalent geometry    : angle       0.52662 /  0.27 (17116)
  SS BOND              : bond        0.00263 /  0.13 (    2)
  SS BOND              : angle       1.25369 /  1.73 (    4)
  hydrogen bonds       : bond        0.03434 /  2.98 (  438)
  hydrogen bonds       : angle       3.99800 /  3.22 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 108
  time to evaluate  : 0.365 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7040 (t80)
REVERT: C  351 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6667 (mm-30)
REVERT: C  360 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5556 (mp0)
REVERT: C  429 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6148 (tt0)
REVERT: C  563 MET cc_start: 0.4565 (mtt) cc_final: 0.4265 (mtt)
REVERT: A   84 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7053 (t80)
REVERT: A  351 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6668 (mm-30)
REVERT: A  360 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5556 (mp0)
REVERT: A  563 MET cc_start: 0.4505 (mtt) cc_final: 0.4202 (mtt)
  outliers start: 50
  outliers final: 32
  residues processed: 150
  average time/residue: 0.0930
  time to fit residues: 20.9322
Evaluate side-chains
  141 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 103
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  360 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  661 TRP
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 145 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 147 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0670
   chunk 25 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 127 optimal weight:    0.0470
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.8818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.149490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.112267 restraints weight = 20937.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 3.43
r_work: 0.3419 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12574  Z= 0.112
  Angle     :  0.539   6.199  17120  Z= 0.279
  Chirality :  0.038   0.253   2036
  Planarity :  0.004   0.044   2074
  Dihedral  : 13.500 113.680   1920
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.80 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 31.91 %
    Favored  : 63.97 %
  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 are not related in a simple way.
  whole: -1.15 (0.22), residues: 1522
  helix:  0.47 (0.19), residues: 786
  sheet: -1.28 (0.48), residues: 124
  loop : -2.33 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 433 
 TYR   0.008   0.001   TYR A 113 
 PHE   0.008   0.001   PHE C 839 
 TRP   0.005   0.001   TRP A 673 
 HIS   0.003   0.000   HIS C 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 (12572)
  covalent geometry    : angle       0.53900 /  0.28 (17116)
  SS BOND              : bond        0.00327 /  0.16 (    2)
  SS BOND              : angle       1.23369 /  1.73 (    4)
  hydrogen bonds       : bond        0.03730 /  3.23 (  438)
  hydrogen bonds       : angle       3.96218 /  3.22 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 100
  time to evaluate  : 0.427 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7079 (t80)
REVERT: C  351 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6708 (mm-30)
REVERT: C  360 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5641 (mp0)
REVERT: C  429 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6170 (tt0)
REVERT: C  563 MET cc_start: 0.4889 (mtt) cc_final: 0.4603 (mtt)
REVERT: C  761 MET cc_start: 0.8391 (ptp) cc_final: 0.7961 (ptm)
REVERT: A   84 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7117 (t80)
REVERT: A  351 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6713 (mm-30)
REVERT: A  360 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5632 (mp0)
REVERT: A  563 MET cc_start: 0.4882 (mtt) cc_final: 0.4600 (mtt)
REVERT: A  761 MET cc_start: 0.8393 (ptp) cc_final: 0.7960 (ptm)
  outliers start: 51
  outliers final: 39
  residues processed: 146
  average time/residue: 0.0976
  time to fit residues: 21.5920
Evaluate side-chains
  145 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 100
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  360 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  552 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  661 TRP
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  763 THR
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 121 optimal weight:    0.0060
   chunk 106 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 71 optimal weight:   20.0000
   chunk 87 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 140 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 134 optimal weight:    3.9990
   overall best weight:    0.7798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.149747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.112837 restraints weight = 20908.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 3.45
r_work: 0.3427 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12574  Z= 0.107
  Angle     :  0.538   6.864  17120  Z= 0.277
  Chirality :  0.038   0.251   2036
  Planarity :  0.004   0.043   2074
  Dihedral  : 13.470 113.553   1920
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.59 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 32.07 %
    Favored  : 64.22 %
  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 are not related in a simple way.
  whole: -1.14 (0.22), residues: 1522
  helix:  0.50 (0.19), residues: 786
  sheet: -1.28 (0.48), residues: 124
  loop : -2.35 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 433 
 TYR   0.008   0.001   TYR C 113 
 PHE   0.006   0.001   PHE C 839 
 TRP   0.005   0.001   TRP A 673 
 HIS   0.003   0.000   HIS A 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 (12572)
  covalent geometry    : angle       0.53735 /  0.28 (17116)
  SS BOND              : bond        0.00297 /  0.15 (    2)
  SS BOND              : angle       1.21231 /  1.69 (    4)
  hydrogen bonds       : bond        0.03601 /  3.13 (  438)
  hydrogen bonds       : angle       3.95700 /  3.20 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 104
  time to evaluate  : 0.494 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7099 (t80)
REVERT: C  217 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8527 (mm-30)
REVERT: C  351 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6791 (mm-30)
REVERT: C  360 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5495 (mp0)
REVERT: C  429 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6184 (tt0)
REVERT: C  563 MET cc_start: 0.4754 (mtt) cc_final: 0.4456 (mtt)
REVERT: C  761 MET cc_start: 0.8398 (ptp) cc_final: 0.7996 (ptm)
REVERT: A   84 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7100 (t80)
REVERT: A  217 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8534 (mm-30)
REVERT: A  316 MET cc_start: 0.2333 (tmm) cc_final: 0.2063 (tmm)
REVERT: A  351 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6704 (mm-30)
REVERT: A  360 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5551 (mp0)
REVERT: A  563 MET cc_start: 0.4748 (mtt) cc_final: 0.4451 (mtt)
REVERT: A  761 MET cc_start: 0.8396 (ptp) cc_final: 0.7999 (ptm)
  outliers start: 46
  outliers final: 36
  residues processed: 144
  average time/residue: 0.0935
  time to fit residues: 20.2972
Evaluate side-chains
  143 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 101
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  360 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  661 TRP
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  763 THR
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  792 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 121 optimal weight:    0.0370
   chunk 60 optimal weight:    0.9980
   chunk 77 optimal weight:   20.0000
   chunk 104 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 139 optimal weight:    0.6980
   chunk 93 optimal weight:    0.4980
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.6458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.150174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.113449 restraints weight = 20975.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 3.44
r_work: 0.3436 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  12574  Z= 0.102
  Angle     :  0.535   6.520  17120  Z= 0.276
  Chirality :  0.038   0.247   2036
  Planarity :  0.004   0.043   2074
  Dihedral  : 13.429 113.347   1920
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.54 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 32.07 %
    Favored  : 63.89 %
  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 are not related in a simple way.
  whole: -1.09 (0.22), residues: 1522
  helix:  0.55 (0.19), residues: 786
  sheet: -1.24 (0.48), residues: 124
  loop : -2.35 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 433 
 TYR   0.008   0.001   TYR C 113 
 PHE   0.005   0.001   PHE C 839 
 TRP   0.005   0.001   TRP A 673 
 HIS   0.004   0.000   HIS C 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00224 /  0.10 (12572)
  covalent geometry    : angle       0.53506 /  0.28 (17116)
  SS BOND              : bond        0.00265 /  0.13 (    2)
  SS BOND              : angle       1.17566 /  1.66 (    4)
  hydrogen bonds       : bond        0.03416 /  2.98 (  438)
  hydrogen bonds       : angle       3.89579 /  3.16 ( 1278)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 103
  time to evaluate  : 0.443 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7113 (t80)
REVERT: C  217 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8528 (mm-30)
REVERT: C  351 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6750 (mm-30)
REVERT: C  360 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5469 (mp0)
REVERT: C  429 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6197 (tt0)
REVERT: C  563 MET cc_start: 0.4857 (mtt) cc_final: 0.4560 (mtt)
REVERT: C  761 MET cc_start: 0.8393 (ptp) cc_final: 0.8124 (ptm)
REVERT: A   84 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7126 (t80)
REVERT: A  217 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8570 (mm-30)
REVERT: A  351 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6775 (mm-30)
REVERT: A  360 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5501 (mp0)
REVERT: A  563 MET cc_start: 0.4840 (mtt) cc_final: 0.4539 (mtt)
REVERT: A  761 MET cc_start: 0.8388 (ptp) cc_final: 0.8119 (ptm)
  outliers start: 50
  outliers final: 40
  residues processed: 148
  average time/residue: 0.0830
  time to fit residues: 18.6560
Evaluate side-chains
  147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 101
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 TYR
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain C residue  348 LYS
Chi-restraints excluded: chain C residue  351 GLU
Chi-restraints excluded: chain C residue  360 GLU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  404 VAL
Chi-restraints excluded: chain C residue  444 SER
Chi-restraints excluded: chain C residue  515 VAL
Chi-restraints excluded: chain C residue  528 THR
Chi-restraints excluded: chain C residue  619 LEU
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  657 MET
Chi-restraints excluded: chain C residue  689 VAL
Chi-restraints excluded: chain C residue  725 LEU
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  763 THR
Chi-restraints excluded: chain C residue  792 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  351 GLU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 118 optimal weight:    0.0970
   chunk 69 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 60 optimal weight:    0.5980
   chunk 130 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 141 optimal weight:    1.9990
   overall best weight:    0.6378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 325 HIS
A 325 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.150330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.113692 restraints weight = 20908.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 3.44
r_work: 0.3438 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12574  Z= 0.102
  Angle     :  0.540   7.528  17120  Z= 0.278
  Chirality :  0.038   0.245   2036
  Planarity :  0.004   0.043   2074
  Dihedral  : 13.382 113.171   1920
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.20 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 32.07 %
    Favored  : 63.81 %
  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 are not related in a simple way.
  whole: -1.08 (0.22), residues: 1522
  helix:  0.57 (0.19), residues: 786
  sheet: -1.26 (0.48), residues: 124
  loop : -2.36 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 433 
 TYR   0.008   0.001   TYR C 113 
 PHE   0.005   0.001   PHE C 839 
 TRP   0.005   0.001   TRP A 673 
 HIS   0.004   0.000   HIS A 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00223 /  0.10 (12572)
  covalent geometry    : angle       0.54021 /  0.28 (17116)
  SS BOND              : bond        0.00257 /  0.13 (    2)
  SS BOND              : angle       1.15966 /  1.64 (    4)
  hydrogen bonds       : bond        0.03366 /  2.93 (  438)
  hydrogen bonds       : angle       3.89670 /  3.15 ( 1278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2602.15 seconds
wall clock time: 45 minutes 11.41 seconds (2711.41 seconds total)