Starting phenix.real_space_refine
on Wed Aug  5 20:11:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xgc_66843/08_2026/9xgc_66843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xgc_66843/08_2026/9xgc_66843.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xgc_66843/08_2026/9xgc_66843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xgc_66843/08_2026/9xgc_66843.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xgc_66843/08_2026/9xgc_66843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xgc_66843/08_2026/9xgc_66843.map"
  }
  resolution = 3.37
  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=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    7261      2.51       5
     N    1936      2.21       5
     O    2164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11414
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2353
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 277}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "D"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 599
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 7860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 993, 7860
          Classifications: {'peptide': 993}
          Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 48, 'TRANS': 939}
          Chain breaks: 3
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU C  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU C  73 " occ=0.45
    residue:
      pdb=" N   ARG C  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG C  74 " occ=0.45
    residue:
      pdb=" N   GLY C  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY C  75 " occ=0.25
    residue:
      pdb=" N   GLY C  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY C  76 " occ=0.25
  Time building chain proxies: 1.71, per 1000 atoms: 0.15
  Number of scatterers: 11414
  At special positions: 0
  Unit cell: (107.464, 97.768, 118.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    2164      8.00
     N    1936      7.00
     C    7261      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 323.9 milliseconds
  

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2728

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 12 sheets defined
      44.2% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4524 through 4535
      removed outlier: 4.160A  pdb=" N   LYS B4534 " --> pdb=" O   ALA B4530 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B4535 " --> pdb=" O   VAL B4531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4559 through 4565
    Processing helix  chain 'B' and resid 4571 through 4588
      removed outlier: 3.644A  pdb=" N   ALA B4575 " --> pdb=" O   SER B4571 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   LEU B4578 " --> pdb=" O   ARG B4574 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL B4583 " --> pdb=" O   ALA B4579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4687 through 4698
      removed outlier: 3.700A  pdb=" N   VAL B4691 " --> pdb=" O   SER B4687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4703 through 4708
      removed outlier: 3.642A  pdb=" N   PHE B4706 " --> pdb=" O   GLU B4703 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU B4708 " --> pdb=" O   TYR B4705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4717 through 4739
      removed outlier: 3.847A  pdb=" N   GLY B4729 " --> pdb=" O   ARG B4725 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASN B4730 " --> pdb=" O   GLU B4726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4740 through 4746
      removed outlier: 3.664A  pdb=" N   ILE B4744 " --> pdb=" O   MET B4740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4748 through 4750
      No H-bonds generated for 'chain 'B' and resid 4748 through 4750'
    Processing helix  chain 'B' and resid 4751 through 4762
      removed outlier: 3.538A  pdb=" N   HIS B4758 " --> pdb=" O   VAL B4754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4762 through 4781
      removed outlier: 4.023A  pdb=" N   MET B4767 " --> pdb=" O   ARG B4763 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA B4768 " --> pdb=" O   VAL B4764 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA B4775 " --> pdb=" O   GLU B4771 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN B4779 " --> pdb=" O   ALA B4775 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TYR B4780 " --> pdb=" O   ASP B4776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4786 through 4811
      removed outlier: 3.922A  pdb=" N   ALA B4795 " --> pdb=" O   SER B4791 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA B4796 " --> pdb=" O   HIS B4792 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS B4800 " --> pdb=" O   ALA B4796 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 35
      removed outlier: 3.539A  pdb=" N   LYS C  29 " --> pdb=" O   ASN C  25 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.639A  pdb=" N   LYS A  58 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 84
    Processing helix  chain 'A' and resid 108 through 115
      removed outlier: 3.694A  pdb=" N   VAL A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 128
      removed outlier: 3.614A  pdb=" N   VAL A 122 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   LYS A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   HIS A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 3.601A  pdb=" N   ASP A 152 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LYS A 153 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 176
      removed outlier: 3.513A  pdb=" N   LYS A 169 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 257
      removed outlier: 3.593A  pdb=" N   LEU A 256 " --> pdb=" O   MET A 253 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN A 257 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 257'
    Processing helix  chain 'A' and resid 301 through 308
      removed outlier: 4.389A  pdb=" N   LYS A 307 " --> pdb=" O   GLU A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 340
      removed outlier: 3.549A  pdb=" N   GLU A 324 " --> pdb=" O   GLU A 320 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 365
      removed outlier: 3.530A  pdb=" N   SER A 360 " --> pdb=" O   LYS A 356 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   SER A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU A 363 " --> pdb=" O   THR A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 382
      removed outlier: 3.672A  pdb=" N   VAL A 376 " --> pdb=" O   ASN A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 408
    Processing helix  chain 'A' and resid 421 through 427
      removed outlier: 4.338A  pdb=" N   VAL A 425 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   SER A 427 " --> pdb=" O   ASP A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 436
    Processing helix  chain 'A' and resid 443 through 451
    Processing helix  chain 'A' and resid 451 through 460
    Processing helix  chain 'A' and resid 469 through 483
      removed outlier: 3.535A  pdb=" N   LYS A 477 " --> pdb=" O   CYS A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.653A  pdb=" N   ASN A 507 " --> pdb=" O   SER A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 517
      removed outlier: 3.909A  pdb=" N   ILE A 517 " --> pdb=" O   PRO A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 533
    Processing helix  chain 'A' and resid 546 through 550
    Processing helix  chain 'A' and resid 554 through 561
    Processing helix  chain 'A' and resid 576 through 584
    Processing helix  chain 'A' and resid 623 through 629
      removed outlier: 3.544A  pdb=" N   LEU A 627 " --> pdb=" O   PRO A 623 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS A 628 " --> pdb=" O   PHE A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 650
      removed outlier: 4.077A  pdb=" N   THR A 637 " --> pdb=" O   ALA A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 663
      removed outlier: 3.540A  pdb=" N   TRP A 660 " --> pdb=" O   PHE A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 675
      removed outlier: 3.563A  pdb=" N   LYS A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 691
      removed outlier: 3.651A  pdb=" N   VAL A 685 " --> pdb=" O   GLY A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 712
      removed outlier: 3.529A  pdb=" N   CYS A 699 " --> pdb=" O   ASN A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 722
    Processing helix  chain 'A' and resid 751 through 769
      removed outlier: 3.792A  pdb=" N   LEU A 755 " --> pdb=" O   GLU A 751 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER A 756 " --> pdb=" O   PRO A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 778
    Processing helix  chain 'A' and resid 779 through 788
      removed outlier: 3.678A  pdb=" N   LEU A 783 " --> pdb=" O   SER A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 834
      removed outlier: 3.961A  pdb=" N   PHE A 826 " --> pdb=" O   ARG A 822 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LYS A 830 " --> pdb=" O   PHE A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 873
    Processing helix  chain 'A' and resid 879 through 889
      removed outlier: 3.882A  pdb=" N   ARG A 885 " --> pdb=" O   PHE A 881 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ILE A 886 " --> pdb=" O   LYS A 882 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA A 887 " --> pdb=" O   THR A 883 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLY A 888 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 914
      removed outlier: 3.765A  pdb=" N   GLY A 903 " --> pdb=" O   ALA A 899 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE A 910 " --> pdb=" O   ALA A 906 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS A 911 " --> pdb=" O   LEU A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 979
      removed outlier: 3.642A  pdb=" N   LYS A 976 " --> pdb=" O   ILE A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1000 through 1005
      removed outlier: 3.668A  pdb=" N   ARG A1004 " --> pdb=" O   GLY A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1014
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4537 through 4540
      removed outlier: 3.520A  pdb=" N   ASP B4602 " --> pdb=" O   ILE B4608 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   ILE B4608 " --> pdb=" O   ASP B4602 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 4543 through 4545
    Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 16
      removed outlier: 9.109A  pdb=" N   LEU C  67 " --> pdb=" O   GLN C   2 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   PHE C   4 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42
    Processing sheet with id=AA5, first strand: chain 'C' and resid 44 through 45
    Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 16
    Processing sheet with id=AA7, first strand: chain 'A' and resid 134 through 136
      removed outlier: 3.972A  pdb=" N   CYS A 156 " --> pdb=" O   HIS A  63 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 205
    Processing sheet with id=AA9, first strand: chain 'A' and resid 260 through 262
      removed outlier: 6.421A  pdb=" N   LEU A 245 " --> pdb=" O   GLN A 290 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   GLN A 290 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   PHE A 247 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ALA A 288 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   GLU A 249 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   GLY A 286 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 541
      removed outlier: 6.010A  pdb=" N   ILE A 493 " --> pdb=" O   ASP A 539 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   HIS A 541 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL A 495 " --> pdb=" O   HIS A 541 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A 563 " --> pdb=" O   ASN A 462 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   SER A 591 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   CYS A 924 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   VAL A 602 " --> pdb=" O   LYS A 922 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   LYS A 922 " --> pdb=" O   VAL A 602 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 947
      removed outlier: 6.425A  pdb=" N   ILE A 950 " --> pdb=" O   ILE A 946 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 958 through 961
      removed outlier: 6.154A  pdb=" N   TRP A 958 " --> pdb=" O   ARG A1044 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   TYR A1046 " --> pdb=" O   TRP A 958 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL A 960 " --> pdb=" O   TYR A1046 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   GLN A 988 " --> pdb=" O   MET A 992 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   MET A 992 " --> pdb=" O   GLN A 988 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1371 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 0.83 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: 3700
        1.34 -     1.46: 2125
        1.46 -     1.57: 5755
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 11658
  Sorted by residual:
  bond pdb=" C   ASP A 497 "
       pdb=" N   PRO A 498 "
    ideal  model  delta    sigma   weight residual
    1.331  1.314  0.018 7.90e-03 1.60e+04 4.99e+00
  bond pdb=" C   TYR B4631 "
       pdb=" N   PHE B4632 "
    ideal  model  delta    sigma   weight residual
    1.331  1.263  0.067 3.12e-02 1.03e+03 4.65e+00
  bond pdb=" C   SER A 388 "
       pdb=" N   PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.23e-02 6.61e+03 3.56e+00
  bond pdb=" CA  PHE B4632 "
       pdb=" C   PHE B4632 "
    ideal  model  delta    sigma   weight residual
    1.528  1.507  0.021 1.18e-02 7.18e+03 3.20e+00
  bond pdb=" CB  THR A 938 "
       pdb=" CG2 THR A 938 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.17e+00
  ... (remaining 11653 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 15315
        2.20 -     4.40: 416
        4.40 -     6.59: 47
        6.59 -     8.79: 7
        8.79 -    10.99: 2
  Bond angle restraints: 15787
  Sorted by residual:
  angle pdb=" C   ILE A 930 "
        pdb=" N   PRO A 931 "
        pdb=" CA  PRO A 931 "
      ideal   model   delta    sigma   weight residual
     127.00  137.99  -10.99 2.40e+00 1.74e-01 2.10e+01
  angle pdb=" C   ILE A 930 "
        pdb=" N   PRO A 931 "
        pdb=" CD  PRO A 931 "
      ideal   model   delta    sigma   weight residual
     120.60  110.99    9.61 2.20e+00 2.07e-01 1.91e+01
  angle pdb=" C   LYS A 163 "
        pdb=" N   LEU A 164 "
        pdb=" CA  LEU A 164 "
      ideal   model   delta    sigma   weight residual
     120.58  125.66   -5.08 1.32e+00 5.74e-01 1.48e+01
  angle pdb=" C   SER A 818 "
        pdb=" N   GLU A 819 "
        pdb=" CA  GLU A 819 "
      ideal   model   delta    sigma   weight residual
     121.54  128.80   -7.26 1.91e+00 2.74e-01 1.44e+01
  angle pdb=" N   PRO A 412 "
        pdb=" CA  PRO A 412 "
        pdb=" C   PRO A 412 "
      ideal   model   delta    sigma   weight residual
     110.40  116.01   -5.61 1.61e+00 3.86e-01 1.22e+01
  ... (remaining 15782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.45: 6816
       14.45 -    28.90: 220
       28.90 -    43.34: 48
       43.34 -    57.79: 7
       57.79 -    72.24: 1
  Dihedral angle restraints: 7092
    sinusoidal: 2894
      harmonic: 4198
  Sorted by residual:
  dihedral pdb=" CA  ASN B4656 "
           pdb=" C   ASN B4656 "
           pdb=" N   PRO B4657 "
           pdb=" CA  PRO B4657 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.53   23.47     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  ASN A 460 "
           pdb=" C   ASN A 460 "
           pdb=" N   LEU A 461 "
           pdb=" CA  LEU A 461 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.84  -22.16     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  ALA B4569 "
           pdb=" C   ALA B4569 "
           pdb=" N   ASN B4570 "
           pdb=" CA  ASN B4570 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.92   22.08     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 7089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1176
       0.044 -    0.088: 450
       0.088 -    0.131: 133
       0.131 -    0.175: 16
       0.175 -    0.219: 4
  Chirality restraints: 1779
  Sorted by residual:
  chirality pdb=" CB  ILE A 981 "
            pdb=" CA  ILE A 981 "
            pdb=" CG1 ILE A 981 "
            pdb=" CG2 ILE A 981 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  ILE A 538 "
            pdb=" CA  ILE A 538 "
            pdb=" CG1 ILE A 538 "
            pdb=" CG2 ILE A 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  ILE A 634 "
            pdb=" CA  ILE A 634 "
            pdb=" CG1 ILE A 634 "
            pdb=" CG2 ILE A 634 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.44e-01
  ... (remaining 1776 not shown)

  Planarity restraints: 2039
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B4656 "    0.041 5.00e-02 4.00e+02   6.24e-02 6.22e+00
        pdb=" N   PRO B4657 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B4657 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B4657 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 267 "    0.040 5.00e-02 4.00e+02   6.07e-02 5.90e+00
        pdb=" N   PRO A 268 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 268 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 268 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B4677 "    0.012 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   PRO B4677 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   PRO B4677 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU B4678 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2036 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3445
        2.81 -     3.33: 10618
        3.33 -     3.85: 19860
        3.85 -     4.38: 23227
        4.38 -     4.90: 37921
  Nonbonded interactions: 95071
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B4621 "
            pdb=" O   PHE B4655 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   TYR A 576 "
            pdb=" OG  SER A 579 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OD1 ASN A 143 "
            pdb=" OG1 THR A 146 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OXT GLY C  76 "
            pdb=" SG  CYS A 625 "
     model   vdw
     2.302 3.400
  nonbonded pdb=" O   ALA A 525 "
            pdb=" OG1 THR A 529 "
     model   vdw
     2.314 3.040
  ... (remaining 95066 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 71 through 75 or (resid 76 and (name N or name \ 
 CA or name C or name O ))))
  selection = chain 'D'
}

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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.070
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4970
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.076  11658  Z= 0.363
  Angle     :  0.873  10.990  15787  Z= 0.493
  Chirality :  0.050   0.219   1779
  Planarity :  0.007   0.062   2039
  Dihedral  :  8.313  72.240   4364
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.94 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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: -3.19 (0.19), residues: 1426
  helix: -3.03 (0.14), residues: 562
  sheet: -1.21 (0.32), residues: 234
  loop : -1.36 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B4576 
 TYR   0.021   0.003   TYR D  59 
 PHE   0.029   0.003   PHE A 410 
 TRP   0.023   0.004   TRP A 640 
 HIS   0.011   0.002   HIS A1001 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00765 /  0.36 (11658)
  covalent geometry    : angle       0.87339 /  0.49 (15787)
  hydrogen bonds       : bond        0.27146 / 17.91 (  483)
  hydrogen bonds       : angle      10.08530 /  6.85 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 258
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4565 ASN cc_start: 0.6531 (m-40) cc_final: 0.5885 (m110)
REVERT: B 4604 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6773 (tp30)
REVERT: B 4668 SER cc_start: 0.5288 (p) cc_final: 0.5020 (p)
REVERT: B 4686 SER cc_start: 0.6719 (m) cc_final: 0.6240 (m)
REVERT: B 4760 TYR cc_start: 0.4498 (t80) cc_final: 0.4203 (t80)
REVERT: D   21 ASP cc_start: 0.4714 (m-30) cc_final: 0.4472 (m-30)
REVERT: D   60 ASN cc_start: 0.6238 (t160) cc_final: 0.5634 (t0)
REVERT: A   62 SER cc_start: 0.7539 (m) cc_final: 0.7139 (p)
REVERT: A   69 MET cc_start: 0.6302 (mmp) cc_final: 0.6064 (mmp)
REVERT: A   94 GLU cc_start: 0.4525 (tp30) cc_final: 0.4273 (mt-10)
REVERT: A   97 GLN cc_start: 0.6160 (mt0) cc_final: 0.5561 (tt0)
REVERT: A  202 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6605 (mt-10)
REVERT: A  253 MET cc_start: 0.4880 (ttm) cc_final: 0.4525 (tpp)
REVERT: A  300 GLU cc_start: 0.6053 (mt-10) cc_final: 0.5786 (mt-10)
REVERT: A  368 LYS cc_start: 0.7364 (mttt) cc_final: 0.7049 (tmtt)
REVERT: A  427 SER cc_start: 0.7693 (m) cc_final: 0.7419 (t)
REVERT: A  490 LYS cc_start: 0.4944 (tttt) cc_final: 0.4684 (pttt)
REVERT: A  497 ASP cc_start: 0.7338 (t0) cc_final: 0.7098 (t0)
REVERT: A  535 GLN cc_start: 0.5429 (mm-40) cc_final: 0.4808 (mt0)
REVERT: A  557 PHE cc_start: 0.5744 (t80) cc_final: 0.5377 (t80)
REVERT: A  559 THR cc_start: 0.7323 (m) cc_final: 0.7039 (p)
REVERT: A  601 GLU cc_start: 0.6810 (tt0) cc_final: 0.6028 (tt0)
REVERT: A  609 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6036 (mm-30)
REVERT: A  624 PHE cc_start: 0.5604 (t80) cc_final: 0.5167 (t80)
REVERT: A  628 LYS cc_start: 0.7547 (ttmt) cc_final: 0.7061 (ttpp)
REVERT: A  940 GLU cc_start: 0.6531 (tt0) cc_final: 0.5796 (tm-30)
REVERT: A  943 LYS cc_start: 0.8099 (mttt) cc_final: 0.7290 (mptt)
REVERT: A  982 GLU cc_start: 0.7270 (tt0) cc_final: 0.7052 (tt0)
REVERT: A 1008 THR cc_start: 0.6763 (p) cc_final: 0.6430 (t)
REVERT: A 1010 HIS cc_start: 0.7302 (t-90) cc_final: 0.7062 (t70)
REVERT: A 1044 ARG cc_start: 0.6627 (ttm170) cc_final: 0.6070 (ttm110)
  outliers start: 1
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1006
  time to fit residues: 36.2316
Evaluate side-chains
  160 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4658 ASN
B4671 ASN
B4674 HIS
B4696 GLN
B4778 GLN
C  60 ASN
D  40 GLN
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
A  47 GLN
A 251 ASN
A 257 ASN
A 262 GLN
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 584 ASN
A 599 HIS
A 760 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.243487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.198877 restraints weight = 11403.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 2.28
r_work: 0.3772 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11658  Z= 0.131
  Angle     :  0.574   6.609  15787  Z= 0.303
  Chirality :  0.042   0.145   1779
  Planarity :  0.005   0.054   2039
  Dihedral  :  5.073  43.207   1530
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  4.32 %
    Favored  : 93.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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: 1426
  helix: -1.05 (0.19), residues: 585
  sheet: -0.90 (0.32), residues: 230
  loop : -0.77 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B4574 
 TYR   0.017   0.002   TYR A1045 
 PHE   0.018   0.002   PHE A 199 
 TRP   0.013   0.002   TRP A 378 
 HIS   0.004   0.001   HIS A 858 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 (11658)
  covalent geometry    : angle       0.57356 /  0.30 (15787)
  hydrogen bonds       : bond        0.04326 /  2.85 (  483)
  hydrogen bonds       : angle       5.73899 /  3.86 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4565 ASN cc_start: 0.7389 (m-40) cc_final: 0.7174 (m-40)
REVERT: B 4629 ASP cc_start: 0.6830 (m-30) cc_final: 0.6598 (m-30)
REVERT: B 4705 TYR cc_start: 0.7300 (t80) cc_final: 0.7014 (t80)
REVERT: A  214 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8238 (mtmt)
REVERT: A  235 HIS cc_start: 0.7540 (m-70) cc_final: 0.7237 (m-70)
REVERT: A  249 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6710 (mt-10)
REVERT: A  320 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7668 (pp20)
REVERT: A  337 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6563 (pt0)
REVERT: A  353 GLU cc_start: 0.5031 (mt-10) cc_final: 0.4491 (mm-30)
REVERT: A  444 ASP cc_start: 0.7406 (m-30) cc_final: 0.7182 (m-30)
REVERT: A  456 GLN cc_start: 0.7717 (mt0) cc_final: 0.7318 (mt0)
REVERT: A  628 LYS cc_start: 0.8264 (ttmt) cc_final: 0.8024 (ttpp)
  outliers start: 22
  outliers final: 14
  residues processed: 184
  average time/residue: 0.0884
  time to fit residues: 23.6018
Evaluate side-chains
  148 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4687 SER
Chi-restraints excluded: chain D residue   33 LYS
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  844 MET
Chi-restraints excluded: chain A residue  939 THR
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 41 optimal weight:    0.8980
   chunk 132 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 117 optimal weight:   30.0000
   chunk 125 optimal weight:    6.9990
   overall best weight:    3.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4690 GLN
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 HIS
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 ASN
A 759 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.229932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.180856 restraints weight = 11709.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 2.94
r_work: 0.3505 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3476
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3476
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  11658  Z= 0.241
  Angle     :  0.673  10.477  15787  Z= 0.344
  Chirality :  0.046   0.162   1779
  Planarity :  0.005   0.061   2039
  Dihedral  :  5.038  37.613   1530
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  :  5.82 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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 (0.21), residues: 1426
  helix: -0.38 (0.20), residues: 583
  sheet: -1.09 (0.32), residues: 214
  loop : -0.84 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B4576 
 TYR   0.024   0.002   TYR A1045 
 PHE   0.027   0.003   PHE A 410 
 TRP   0.022   0.002   TRP A 192 
 HIS   0.008   0.001   HIS A  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00582 /  0.24 (11658)
  covalent geometry    : angle       0.67349 /  0.34 (15787)
  hydrogen bonds       : bond        0.04775 /  3.19 (  483)
  hydrogen bonds       : angle       5.61521 /  3.78 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4565 ASN cc_start: 0.8117 (m-40) cc_final: 0.7849 (m-40)
REVERT: B 4580 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7743 (mt0)
REVERT: B 4684 GLN cc_start: 0.7581 (mm110) cc_final: 0.7335 (mm-40)
REVERT: A   56 MET cc_start: 0.7575 (mtp) cc_final: 0.7298 (mtm)
REVERT: A  138 SER cc_start: 0.8800 (t) cc_final: 0.8455 (m)
REVERT: A  214 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8293 (mtmt)
REVERT: A  253 MET cc_start: 0.5421 (tpp) cc_final: 0.4778 (tpt)
REVERT: A  320 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (pt0)
REVERT: A  628 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8290 (ttpp)
  outliers start: 37
  outliers final: 25
  residues processed: 163
  average time/residue: 0.0853
  time to fit residues: 20.2682
Evaluate side-chains
  147 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4560 MET
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4586 SER
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4723 SER
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  844 MET
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  939 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0770
   chunk 40 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 120 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 123 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    1.9544

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B4567 ASN
** B4634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 GLN
A 130 ASN
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.231805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.182998 restraints weight = 11561.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 2.48
r_work: 0.3590 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11658  Z= 0.142
  Angle     :  0.532   5.900  15787  Z= 0.274
  Chirality :  0.042   0.147   1779
  Planarity :  0.004   0.053   2039
  Dihedral  :  4.694  33.904   1530
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  7.08 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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: -0.64 (0.22), residues: 1426
  helix:  0.16 (0.21), residues: 586
  sheet: -0.91 (0.33), residues: 215
  loop : -0.66 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B4713 
 TYR   0.018   0.002   TYR B4780 
 PHE   0.016   0.002   PHE A 217 
 TRP   0.010   0.001   TRP A 192 
 HIS   0.005   0.001   HIS A  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.14 (11658)
  covalent geometry    : angle       0.53224 /  0.27 (15787)
  hydrogen bonds       : bond        0.03574 /  2.38 (  483)
  hydrogen bonds       : angle       5.12960 /  3.46 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4565 ASN cc_start: 0.7836 (m-40) cc_final: 0.7564 (m-40)
REVERT: D   54 ARG cc_start: 0.6273 (mmt90) cc_final: 0.5981 (mtt180)
REVERT: A  138 SER cc_start: 0.8702 (t) cc_final: 0.8375 (m)
REVERT: A  214 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8297 (mtmt)
REVERT: A  253 MET cc_start: 0.5268 (tpp) cc_final: 0.4603 (tpt)
REVERT: A  415 GLN cc_start: 0.7697 (mt0) cc_final: 0.6659 (mt0)
REVERT: A  628 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8196 (ttpp)
REVERT: A  867 ASN cc_start: 0.7713 (m-40) cc_final: 0.6950 (m-40)
REVERT: A  891 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7956 (mm)
  outliers start: 32
  outliers final: 24
  residues processed: 148
  average time/residue: 0.0894
  time to fit residues: 19.6291
Evaluate side-chains
  142 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4560 MET
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4811 LEU
Chi-restraints excluded: chain D residue   33 LYS
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  844 MET
Chi-restraints excluded: chain A residue  891 ILE
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 90 optimal weight:    6.9990
   chunk 126 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 117 optimal weight:   10.0000
   chunk 101 optimal weight:    3.9990
   chunk 105 optimal weight:   20.0000
   chunk 66 optimal weight:    7.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B4634 GLN
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 GLN
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.229762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.179387 restraints weight = 11478.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 2.50
r_work: 0.3553 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11658  Z= 0.168
  Angle     :  0.561   8.017  15787  Z= 0.285
  Chirality :  0.043   0.145   1779
  Planarity :  0.004   0.051   2039
  Dihedral  :  4.620  34.425   1530
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  7.86 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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: -0.53 (0.22), residues: 1426
  helix:  0.29 (0.21), residues: 587
  sheet: -1.04 (0.32), residues: 225
  loop : -0.55 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1004 
 TYR   0.021   0.002   TYR A1045 
 PHE   0.015   0.002   PHE B4688 
 TRP   0.011   0.001   TRP A 192 
 HIS   0.005   0.001   HIS A 326 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.17 (11658)
  covalent geometry    : angle       0.56069 /  0.28 (15787)
  hydrogen bonds       : bond        0.03690 /  2.47 (  483)
  hydrogen bonds       : angle       5.12783 /  3.46 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4565 ASN cc_start: 0.7947 (m-40) cc_final: 0.7668 (m-40)
REVERT: B 4666 CYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7344 (t)
REVERT: B 4668 SER cc_start: 0.8467 (p) cc_final: 0.8247 (t)
REVERT: A  138 SER cc_start: 0.8780 (t) cc_final: 0.8452 (m)
REVERT: A  214 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8297 (mtmt)
REVERT: A  628 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8219 (ttpp)
REVERT: A  867 ASN cc_start: 0.7685 (m-40) cc_final: 0.6898 (m-40)
REVERT: A  875 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8230 (mt)
  outliers start: 36
  outliers final: 27
  residues processed: 144
  average time/residue: 0.0858
  time to fit residues: 18.5696
Evaluate side-chains
  144 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4560 MET
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4586 SER
Chi-restraints excluded: chain B residue 4634 GLN
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4666 CYS
Chi-restraints excluded: chain B residue 4811 LEU
Chi-restraints excluded: chain D residue   33 LYS
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  844 MET
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  939 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 69 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0060
   chunk 120 optimal weight:    6.9990
   chunk 135 optimal weight:   20.0000
   chunk 35 optimal weight:   30.0000
   chunk 128 optimal weight:    0.6980
   overall best weight:    1.4998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B4634 GLN
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B4758 HIS
A 290 GLN
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 HIS
A 759 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.232251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.182709 restraints weight = 11546.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 2.45
r_work: 0.3580 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3547 r_free = 0.3547    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11658  Z= 0.122
  Angle     :  0.509   7.857  15787  Z= 0.260
  Chirality :  0.041   0.137   1779
  Planarity :  0.004   0.049   2039
  Dihedral  :  4.454  32.106   1530
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  8.65 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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: -0.26 (0.22), residues: 1426
  helix:  0.54 (0.21), residues: 593
  sheet: -0.96 (0.32), residues: 232
  loop : -0.41 (0.27), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1004 
 TYR   0.017   0.001   TYR A1045 
 PHE   0.013   0.001   PHE A 711 
 TRP   0.008   0.001   TRP A  99 
 HIS   0.005   0.001   HIS A 326 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 (11658)
  covalent geometry    : angle       0.50928 /  0.26 (15787)
  hydrogen bonds       : bond        0.03276 /  2.20 (  483)
  hydrogen bonds       : angle       4.92372 /  3.32 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4565 ASN cc_start: 0.7771 (m-40) cc_final: 0.7493 (m-40)
REVERT: B 4580 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8046 (mt0)
REVERT: B 4668 SER cc_start: 0.8482 (p) cc_final: 0.8230 (t)
REVERT: D   54 ARG cc_start: 0.6382 (mmm-85) cc_final: 0.6064 (mtt180)
REVERT: A  214 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8285 (mtmt)
REVERT: A  253 MET cc_start: 0.5072 (tpp) cc_final: 0.4445 (tpt)
REVERT: A  415 GLN cc_start: 0.7436 (mt0) cc_final: 0.6288 (mt0)
REVERT: A  628 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8197 (ttpp)
REVERT: A  867 ASN cc_start: 0.7688 (m-40) cc_final: 0.6875 (m110)
  outliers start: 36
  outliers final: 24
  residues processed: 152
  average time/residue: 0.0778
  time to fit residues: 18.0525
Evaluate side-chains
  145 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4723 SER
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  939 THR
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 131 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 102 optimal weight:    0.1980
   chunk 114 optimal weight:    0.0050
   chunk 138 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 129 optimal weight:    1.9990
   overall best weight:    1.2398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.233860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.182461 restraints weight = 11394.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 2.47
r_work: 0.3594 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11658  Z= 0.112
  Angle     :  0.498   7.113  15787  Z= 0.254
  Chirality :  0.041   0.136   1779
  Planarity :  0.004   0.056   2039
  Dihedral  :  4.378  43.171   1530
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.12 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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: -0.06 (0.23), residues: 1426
  helix:  0.75 (0.22), residues: 599
  sheet: -0.83 (0.33), residues: 219
  loop : -0.38 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B4574 
 TYR   0.023   0.001   TYR B4705 
 PHE   0.034   0.001   PHE B4537 
 TRP   0.008   0.001   TRP A 378 
 HIS   0.004   0.001   HIS A 326 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 (11658)
  covalent geometry    : angle       0.49787 /  0.25 (15787)
  hydrogen bonds       : bond        0.03083 /  2.08 (  483)
  hydrogen bonds       : angle       4.77373 /  3.23 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4541 GLU cc_start: 0.6898 (tt0) cc_final: 0.6014 (mp0)
REVERT: B 4565 ASN cc_start: 0.7758 (m-40) cc_final: 0.7484 (m-40)
REVERT: B 4580 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8112 (mt0)
REVERT: B 4668 SER cc_start: 0.8339 (p) cc_final: 0.8107 (t)
REVERT: D   54 ARG cc_start: 0.6362 (mmm-85) cc_final: 0.6096 (mtt180)
REVERT: A  214 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8278 (mtmt)
REVERT: A  245 LEU cc_start: 0.7770 (mt) cc_final: 0.7442 (tp)
REVERT: A  415 GLN cc_start: 0.7417 (mt0) cc_final: 0.6290 (mt0)
REVERT: A  628 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8156 (ttpp)
REVERT: A  867 ASN cc_start: 0.7640 (m-40) cc_final: 0.6796 (m110)
  outliers start: 32
  outliers final: 25
  residues processed: 147
  average time/residue: 0.0852
  time to fit residues: 18.4780
Evaluate side-chains
  148 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4586 SER
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4666 CYS
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 119 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9990
   chunk 131 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 118 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0370
   overall best weight:    1.4066

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.232822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.182728 restraints weight = 11389.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 2.53
r_work: 0.3603 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11658  Z= 0.117
  Angle     :  0.493   7.068  15787  Z= 0.253
  Chirality :  0.041   0.137   1779
  Planarity :  0.004   0.048   2039
  Dihedral  :  4.308  43.930   1530
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.43 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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:  0.13 (0.23), residues: 1426
  helix:  0.92 (0.22), residues: 595
  sheet: -0.66 (0.33), residues: 219
  loop : -0.33 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B4574 
 TYR   0.022   0.001   TYR B4705 
 PHE   0.017   0.001   PHE A 711 
 TRP   0.007   0.001   TRP A  99 
 HIS   0.007   0.001   HIS A 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 (11658)
  covalent geometry    : angle       0.49317 /  0.25 (15787)
  hydrogen bonds       : bond        0.03049 /  2.06 (  483)
  hydrogen bonds       : angle       4.74612 /  3.21 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4541 GLU cc_start: 0.6899 (tt0) cc_final: 0.5964 (mp0)
REVERT: B 4565 ASN cc_start: 0.7750 (m-40) cc_final: 0.7474 (m-40)
REVERT: B 4580 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8079 (mt0)
REVERT: B 4668 SER cc_start: 0.8445 (p) cc_final: 0.8206 (t)
REVERT: B 4790 MET cc_start: 0.4692 (ptm) cc_final: 0.4143 (ppp)
REVERT: A  214 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8282 (mtmt)
REVERT: A  245 LEU cc_start: 0.7801 (mt) cc_final: 0.7484 (tp)
REVERT: A  628 LYS cc_start: 0.8300 (ttmt) cc_final: 0.8026 (ttpp)
REVERT: A  867 ASN cc_start: 0.7583 (m-40) cc_final: 0.6772 (m110)
REVERT: A  926 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8039 (pp)
  outliers start: 32
  outliers final: 28
  residues processed: 150
  average time/residue: 0.0791
  time to fit residues: 17.7844
Evaluate side-chains
  150 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 121
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4586 SER
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4666 CYS
Chi-restraints excluded: chain B residue 4723 SER
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  939 THR
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 25 optimal weight:   20.0000
   chunk 127 optimal weight:    3.9990
   chunk 128 optimal weight:    0.0670
   chunk 109 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 114 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.3922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.234199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.184691 restraints weight = 11267.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.55
r_work: 0.3593 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11658  Z= 0.117
  Angle     :  0.498   6.301  15787  Z= 0.255
  Chirality :  0.041   0.139   1779
  Planarity :  0.004   0.047   2039
  Dihedral  :  4.290  43.619   1530
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.98 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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:  0.21 (0.23), residues: 1426
  helix:  1.01 (0.22), residues: 596
  sheet: -0.50 (0.34), residues: 219
  loop : -0.36 (0.26), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 175 
 TYR   0.023   0.001   TYR B4705 
 PHE   0.050   0.002   PHE A 557 
 TRP   0.007   0.001   TRP A  99 
 HIS   0.006   0.001   HIS A 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 (11658)
  covalent geometry    : angle       0.49827 /  0.26 (15787)
  hydrogen bonds       : bond        0.03036 /  2.05 (  483)
  hydrogen bonds       : angle       4.69971 /  3.19 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4541 GLU cc_start: 0.6847 (tt0) cc_final: 0.6002 (mp0)
REVERT: B 4565 ASN cc_start: 0.7730 (m-40) cc_final: 0.7473 (m-40)
REVERT: B 4580 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8162 (mt0)
REVERT: B 4668 SER cc_start: 0.8398 (p) cc_final: 0.8167 (t)
REVERT: A  214 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8339 (mtmt)
REVERT: A  245 LEU cc_start: 0.7862 (mt) cc_final: 0.7596 (tp)
REVERT: A  320 GLU cc_start: 0.8220 (pt0) cc_final: 0.7616 (pp20)
REVERT: A  726 ILE cc_start: 0.5653 (OUTLIER) cc_final: 0.5334 (mt)
REVERT: A  867 ASN cc_start: 0.7666 (m-40) cc_final: 0.6869 (m110)
  outliers start: 30
  outliers final: 26
  residues processed: 148
  average time/residue: 0.0875
  time to fit residues: 19.6357
Evaluate side-chains
  154 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4586 SER
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  939 THR
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 118 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 132 optimal weight:    7.9990
   chunk 104 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 133 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B4644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.224752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.176632 restraints weight = 11531.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.98
r_work: 0.3453 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.5053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  11658  Z= 0.242
  Angle     :  0.664   9.977  15787  Z= 0.337
  Chirality :  0.046   0.156   1779
  Planarity :  0.005   0.114   2039
  Dihedral  :  4.889  47.411   1530
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  9.91 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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: -0.34 (0.22), residues: 1426
  helix:  0.45 (0.21), residues: 599
  sheet: -0.70 (0.32), residues: 228
  loop : -0.57 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B4574 
 TYR   0.022   0.002   TYR B4705 
 PHE   0.060   0.002   PHE A 557 
 TRP   0.012   0.002   TRP A 660 
 HIS   0.007   0.001   HIS A 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00598 /  0.24 (11658)
  covalent geometry    : angle       0.66388 /  0.34 (15787)
  hydrogen bonds       : bond        0.04187 /  2.78 (  483)
  hydrogen bonds       : angle       5.27908 /  3.58 ( 1371)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 4565 ASN cc_start: 0.8028 (m-40) cc_final: 0.7751 (m-40)
REVERT: B 4590 PRO cc_start: 0.8535 (Cg_exo) cc_final: 0.8302 (Cg_endo)
REVERT: B 4591 LEU cc_start: 0.7203 (tp) cc_final: 0.6796 (tp)
REVERT: B 4668 SER cc_start: 0.8440 (p) cc_final: 0.8176 (t)
REVERT: B 4712 GLU cc_start: 0.5946 (pm20) cc_final: 0.5147 (tp30)
REVERT: A  214 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8357 (mtmt)
REVERT: A  851 LYS cc_start: 0.6479 (pttm) cc_final: 0.6109 (pttp)
REVERT: A  867 ASN cc_start: 0.7943 (m-40) cc_final: 0.7123 (m-40)
REVERT: A  926 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8143 (pp)
  outliers start: 33
  outliers final: 27
  residues processed: 153
  average time/residue: 0.0814
  time to fit residues: 19.1247
Evaluate side-chains
  152 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4583 VAL
Chi-restraints excluded: chain B residue 4586 SER
Chi-restraints excluded: chain B residue 4643 VAL
Chi-restraints excluded: chain B residue 4723 SER
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  449 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  536 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  926 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  938 THR
Chi-restraints excluded: chain A residue  939 THR
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  981 ILE
Chi-restraints excluded: chain A residue  984 THR
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1025 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 90 optimal weight:    0.0470
   chunk 70 optimal weight:    0.0670
   chunk 108 optimal weight:   30.0000
   chunk 35 optimal weight:   20.0000
   overall best weight:    0.7818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B4558 HIS
B4696 GLN
** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.232209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.183034 restraints weight = 11390.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.61
r_work: 0.3590 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.5108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11658  Z= 0.106
  Angle     :  0.526   9.350  15787  Z= 0.270
  Chirality :  0.041   0.149   1779
  Planarity :  0.004   0.050   2039
  Dihedral  :  4.497  44.509   1530
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.16 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.07 %
    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:  0.14 (0.22), residues: 1426
  helix:  0.97 (0.22), residues: 596
  sheet: -0.33 (0.34), residues: 211
  loop : -0.52 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 175 
 TYR   0.017   0.001   TYR B4705 
 PHE   0.039   0.001   PHE A 557 
 TRP   0.010   0.001   TRP A 378 
 HIS   0.006   0.001   HIS A 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 (11658)
  covalent geometry    : angle       0.52571 /  0.27 (15787)
  hydrogen bonds       : bond        0.03071 /  2.08 (  483)
  hydrogen bonds       : angle       4.79714 /  3.25 ( 1371)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2429.44 seconds
wall clock time: 42 minutes 23.63 seconds (2543.63 seconds total)