Starting phenix.real_space_refine
on Sun Sep 13 00:54:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dbv_7851/09_2026/6dbv_7851_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dbv_7851/09_2026/6dbv_7851.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dbv_7851/09_2026/6dbv_7851_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dbv_7851/09_2026/6dbv_7851_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dbv_7851/09_2026/6dbv_7851.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dbv_7851/09_2026/6dbv_7851.map"
  }
  resolution = 4.29
  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=   0.009
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: 7
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     Zn      2      6.06       5
     P     222      5.49       5
     S     112      5.16       5
     C   11837      2.51       5
     N    3567      2.21       5
     O    4214      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 19958
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 4974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 4974
          Classifications: {'peptide': 616}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 591}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2714
          Classifications: {'peptide': 351}
          Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317}
    Chain: "C"
      Number of atoms: 4999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 4999
          Classifications: {'peptide': 621}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 596}
    Chain: "D"
      Number of atoms: 2714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2714
          Classifications: {'peptide': 351}
          Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317}
    Chain: "E"
      Number of atoms: 1023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1023
          Classifications: {'DNA': 50}
          Link IDs: {'rna3p': 49}
    Chain: "F"
      Number of atoms: 1027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1027
          Classifications: {'DNA': 50}
          Link IDs: {'rna3p': 49}
    Chain: "G"
      Number of atoms: 1245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1245
          Classifications: {'DNA': 61}
          Link IDs: {'rna3p': 60}
    Chain: "H"
      Number of atoms: 1256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1256
          Classifications: {'DNA': 61}
          Link IDs: {'rna3p': 60}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2646  SG  CYS A 749      63.182  58.280 104.600  1.00 45.82           S

  Residues with excluded nonbonded symmetry interactions: 28
    residue:
      pdb=" P    DA E  39 " occ=0.57
      ... (19 atoms not shown)
      pdb=" C4   DA E  39 " occ=0.57
    residue:
      pdb=" P    DA E  40 " occ=0.81
      ... (19 atoms not shown)
      pdb=" C4   DA E  40 " occ=0.81
    residue:
      pdb=" P    DA E  41 " occ=0.63
      ... (19 atoms not shown)
      pdb=" C4   DA E  41 " occ=0.63
    residue:
      pdb=" P    DA E  42 " occ=0.59
      ... (19 atoms not shown)
      pdb=" C4   DA E  42 " occ=0.59
    residue:
      pdb=" P    DC E  44 " occ=0.30
      ... (17 atoms not shown)
      pdb=" C6   DC E  44 " occ=0.30
    residue:
      pdb=" P    DG F   7 " occ=0.51
      ... (20 atoms not shown)
      pdb=" C4   DG F   7 " occ=0.51
    residue:
      pdb=" P    DG F   8 " occ=0.47
      ... (20 atoms not shown)
      pdb=" C4   DG F   8 " occ=0.47
    residue:
      pdb=" P    DT F   9 " occ=0.49
      ... (18 atoms not shown)
      pdb=" C6   DT F   9 " occ=0.49
    residue:
      pdb=" P    DT F  10 " occ=0.56
      ... (18 atoms not shown)
      pdb=" C6   DT F  10 " occ=0.56
    residue:
      pdb=" P    DT F  11 " occ=0.63
      ... (18 atoms not shown)
      pdb=" C6   DT F  11 " occ=0.63
    residue:
      pdb=" P    DT F  12 " occ=0.74
      ... (18 atoms not shown)
      pdb=" C6   DT F  12 " occ=0.74
    residue:
      pdb=" P    DT F  13 " occ=0.78
      ... (18 atoms not shown)
      pdb=" C6   DT F  13 " occ=0.78
    ... (remaining 16 not shown)
  Time building chain proxies: 4.70, per 1000 atoms: 0.24
  Number of scatterers: 19958
  At special positions: 0
  Unit cell: (158.464, 146.084, 123.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     Ca      4     19.99
     S     112     16.00
     P     222     15.00
     O    4214      8.00
     N    3567      7.00
     C   11837      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 705.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" NE2 HIS A 959 "
        pdb="ZN    ZN A1101 " - pdb=" NE2 HIS A 964 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 749 "


  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3602

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 18 sheets defined
      37.2% alpha, 20.7% beta
      89 base pairs and 168 stacking pairs defined.
    Time for finding SS restraints: 2.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 419 through 442
      removed outlier: 5.614A  pdb=" N   ASP A 429 " --> pdb=" O   HIS A 425 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   LEU A 430 " --> pdb=" O   ARG A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 460
    Processing helix  chain 'A' and resid 463 through 474
      removed outlier: 3.630A  pdb=" N   ALA A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 492
    Processing helix  chain 'A' and resid 496 through 510
    Processing helix  chain 'A' and resid 518 through 523
      removed outlier: 4.085A  pdb=" N   LEU A 522 " --> pdb=" O   PRO A 518 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG A 523 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 518 through 523'
    Processing helix  chain 'A' and resid 577 through 600
      removed outlier: 5.218A  pdb=" N   GLU A 591 " --> pdb=" O   LYS A 587 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   ASP A 592 " --> pdb=" O   ASP A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 674
    Processing helix  chain 'A' and resid 686 through 705
      Proline residue:  A 696  - end of helix
      removed outlier: 3.611A  pdb=" N   MET A 705 " --> pdb=" O   ARG A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 739
    Processing helix  chain 'A' and resid 757 through 762
      removed outlier: 4.084A  pdb=" N   GLN A 761 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 785
    Processing helix  chain 'A' and resid 790 through 798
    Processing helix  chain 'A' and resid 815 through 835
      removed outlier: 3.618A  pdb=" N   ASP A 819 " --> pdb=" O   ALA A 815 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLY A 835 " --> pdb=" O   GLN A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 844 through 862
    Processing helix  chain 'A' and resid 872 through 879
    Processing helix  chain 'A' and resid 881 through 890
    Processing helix  chain 'A' and resid 894 through 912
    Processing helix  chain 'A' and resid 912 through 917
      removed outlier: 3.593A  pdb=" N   ARG A 916 " --> pdb=" O   LYS A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 924
    Processing helix  chain 'A' and resid 924 through 930
      removed outlier: 3.888A  pdb=" N   LEU A 928 " --> pdb=" O   CYS A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 947
    Processing helix  chain 'A' and resid 955 through 964
    Processing helix  chain 'A' and resid 964 through 972
      removed outlier: 3.601A  pdb=" N   ILE A 968 " --> pdb=" O   HIS A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 987
      removed outlier: 3.671A  pdb=" N   GLU A 984 " --> pdb=" O   SER A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 997
      removed outlier: 3.537A  pdb=" N   ARG A 994 " --> pdb=" O   PHE A 990 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS A 995 " --> pdb=" O   ARG A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1001 through 1018
      removed outlier: 4.163A  pdb=" N   LEU A1006 " --> pdb=" O   LYS A1002 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   GLU A1007 " --> pdb=" O   THR A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1027
      removed outlier: 3.736A  pdb=" N   GLN A1022 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 167
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'C' and resid 419 through 441
      removed outlier: 5.755A  pdb=" N   ASP C 429 " --> pdb=" O   HIS C 425 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   LEU C 430 " --> pdb=" O   ARG C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 459
      removed outlier: 3.935A  pdb=" N   VAL C 449 " --> pdb=" O   ASP C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 460 through 462
      No H-bonds generated for 'chain 'C' and resid 460 through 462'
    Processing helix  chain 'C' and resid 463 through 473
    Processing helix  chain 'C' and resid 482 through 492
    Processing helix  chain 'C' and resid 496 through 511
    Processing helix  chain 'C' and resid 518 through 527
    Processing helix  chain 'C' and resid 577 through 600
      removed outlier: 4.992A  pdb=" N   GLU C 591 " --> pdb=" O   LYS C 587 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   ASP C 592 " --> pdb=" O   ASP C 588 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 670 through 674
    Processing helix  chain 'C' and resid 686 through 703
      removed outlier: 3.921A  pdb=" N   LEU C 690 " --> pdb=" O   ASP C 686 " (cutoff:3.500A)
      Proline residue:  C 696  - end of helix
    Processing helix  chain 'C' and resid 730 through 737
    Processing helix  chain 'C' and resid 755 through 762
    Processing helix  chain 'C' and resid 771 through 785
    Processing helix  chain 'C' and resid 790 through 799
    Processing helix  chain 'C' and resid 819 through 835
      removed outlier: 3.516A  pdb=" N   GLY C 835 " --> pdb=" O   GLN C 831 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 844 through 863
      removed outlier: 3.618A  pdb=" N   ARG C 848 " --> pdb=" O   SER C 844 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 872 through 880
      removed outlier: 3.710A  pdb=" N   ALA C 876 " --> pdb=" O   ASN C 872 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 881 through 889
    Processing helix  chain 'C' and resid 894 through 917
      Proline residue:  C 913  - end of helix
    Processing helix  chain 'C' and resid 924 through 930
      removed outlier: 4.066A  pdb=" N   LEU C 928 " --> pdb=" O   CYS C 924 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 930 through 946
    Processing helix  chain 'C' and resid 955 through 972
      removed outlier: 3.704A  pdb=" N   HIS C 959 " --> pdb=" O   THR C 955 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   HIS C 964 " --> pdb=" O   LYS C 960 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   VAL C 965 " --> pdb=" O   THR C 961 " (cutoff:3.500A)
      Proline residue:  C 966  - end of helix
    Processing helix  chain 'C' and resid 975 through 979
      removed outlier: 3.599A  pdb=" N   ALA C 979 " --> pdb=" O   GLY C 976 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 980 through 998
      removed outlier: 4.510A  pdb=" N   LYS C 988 " --> pdb=" O   GLU C 984 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LEU C 989 " --> pdb=" O   SER C 985 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA C 998 " --> pdb=" O   ARG C 994 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1001 through 1017
      removed outlier: 4.158A  pdb=" N   LEU C1006 " --> pdb=" O   LYS C1002 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   GLU C1007 " --> pdb=" O   THR C1003 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1018 through 1024
    Processing helix  chain 'D' and resid 308 through 314
      removed outlier: 3.759A  pdb=" N   SER D 314 " --> pdb=" O   GLU D 310 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539
      removed outlier: 6.784A  pdb=" N   PHE A 611 " --> pdb=" O   PHE A 720 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   PHE A 722 " --> pdb=" O   PHE A 611 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL A 613 " --> pdb=" O   PHE A 722 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   PHE A 724 " --> pdb=" O   VAL A 613 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   VAL A 615 " --> pdb=" O   PHE A 724 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLY A 726 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   GLU A 617 " --> pdb=" O   GLY A 726 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLY A 728 " --> pdb=" O   GLU A 617 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   THR A 612 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ILE A 649 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL A 614 " --> pdb=" O   MET A 647 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL A 640 " --> pdb=" O   LEU A 679 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   LEU A 679 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   PHE A 642 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539
      removed outlier: 6.784A  pdb=" N   PHE A 611 " --> pdb=" O   PHE A 720 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   PHE A 722 " --> pdb=" O   PHE A 611 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL A 613 " --> pdb=" O   PHE A 722 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   PHE A 724 " --> pdb=" O   VAL A 613 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   VAL A 615 " --> pdb=" O   PHE A 724 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLY A 726 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   GLU A 617 " --> pdb=" O   GLY A 726 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLY A 728 " --> pdb=" O   GLU A 617 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   THR A 612 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ILE A 649 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL A 614 " --> pdb=" O   MET A 647 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   MET A 647 " --> pdb=" O   GLN A 664 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   GLN A 664 " --> pdb=" O   MET A 647 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ILE A 649 " --> pdb=" O   ILE A 662 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5
      removed outlier: 6.132A  pdb=" N   THR B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE B 318 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8
      removed outlier: 7.543A  pdb=" N   THR B   7 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 9.247A  pdb=" N   LEU B  57 " --> pdb=" O   THR B   7 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   VAL B  28 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78
    Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 97
      removed outlier: 3.614A  pdb=" N   GLU B 101 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147
    Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160
    Processing sheet with id=AA9, first strand: chain 'B' and resid 209 through 212
    Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265
    Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539
      removed outlier: 6.325A  pdb=" N   PHE C 611 " --> pdb=" O   ARG C 721 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE C 723 " --> pdb=" O   PHE C 611 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL C 613 " --> pdb=" O   PHE C 723 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR C 612 " --> pdb=" O   ILE C 649 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ILE C 649 " --> pdb=" O   THR C 612 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL C 614 " --> pdb=" O   MET C 647 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP C 620 " --> pdb=" O   ARG C 641 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   PHE C 644 " --> pdb=" O   PRO C 676 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 537 through 539
      removed outlier: 6.325A  pdb=" N   PHE C 611 " --> pdb=" O   ARG C 721 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE C 723 " --> pdb=" O   PHE C 611 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL C 613 " --> pdb=" O   PHE C 723 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR C 612 " --> pdb=" O   ILE C 649 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ILE C 649 " --> pdb=" O   THR C 612 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL C 614 " --> pdb=" O   MET C 647 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP C 620 " --> pdb=" O   ARG C 641 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 23
      removed outlier: 4.454A  pdb=" N   VAL D  28 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 8.508A  pdb=" N   LEU D  55 " --> pdb=" O   PRO D   5 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   THR D   7 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 8.977A  pdb=" N   LEU D  57 " --> pdb=" O   THR D   7 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   PHE D 345 " --> pdb=" O   LEU D   6 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ALA D   8 " --> pdb=" O   TYR D 343 " (cutoff:3.500A)
      removed outlier: 9.584A  pdb=" N   TYR D 343 " --> pdb=" O   ALA D   8 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   THR D 326 " --> pdb=" O   LEU D 322 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU D 322 " --> pdb=" O   THR D 326 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 80
      removed outlier: 3.664A  pdb=" N   HIS D  93 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   CYS D  89 " --> pdb=" O   PHE D  80 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LEU D 106 " --> pdb=" O   LYS D 127 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   THR D 121 " --> pdb=" O   ASP D 112 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147
    Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 160
    Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212
    Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265

    707 hydrogen bonds defined for protein.
    1953 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      222 hydrogen bonds
      436 hydrogen bond angles
      0 basepair planarities
      89 basepair parallelities
      168 stacking parallelities
  Total time for adding SS restraints: 5.38

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4525
        1.33 -     1.46: 5954
        1.46 -     1.58: 9749
        1.58 -     1.71: 440
        1.71 -     1.83: 168
  Bond restraints: 20836
  Sorted by residual:
  bond pdb=" C1'  DT H  60 "
       pdb=" N1   DT H  60 "
    ideal  model  delta    sigma   weight residual
    1.468  1.531 -0.063 1.40e-02 5.10e+03 2.01e+01
  bond pdb=" C1'  DC F  18 "
       pdb=" N1   DC F  18 "
    ideal  model  delta    sigma   weight residual
    1.468  1.529 -0.061 1.40e-02 5.10e+03 1.91e+01
  bond pdb=" C1'  DC F  28 "
       pdb=" N1   DC F  28 "
    ideal  model  delta    sigma   weight residual
    1.468  1.528 -0.060 1.40e-02 5.10e+03 1.86e+01
  bond pdb=" C1'  DT H  46 "
       pdb=" N1   DT H  46 "
    ideal  model  delta    sigma   weight residual
    1.468  1.526 -0.058 1.40e-02 5.10e+03 1.69e+01
  bond pdb=" C3'  DG H  30 "
       pdb=" C2'  DG H  30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.51e+01
  ... (remaining 20831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 28888
        3.28 -     6.56: 200
        6.56 -     9.85: 8
        9.85 -    13.13: 4
       13.13 -    16.41: 4
  Bond angle restraints: 29104
  Sorted by residual:
  angle pdb=" O4'  DG F  34 "
        pdb=" C1'  DG F  34 "
        pdb=" N9   DG F  34 "
      ideal   model   delta    sigma   weight residual
     108.00  115.95   -7.95 7.00e-01 2.04e+00 1.29e+02
  angle pdb=" C   PRO D 339 "
        pdb=" N   PRO D 340 "
        pdb=" CA  PRO D 340 "
      ideal   model   delta    sigma   weight residual
     127.00  140.55  -13.55 2.40e+00 1.74e-01 3.19e+01
  angle pdb=" C4'  DG F  34 "
        pdb=" O4'  DG F  34 "
        pdb=" C1'  DG F  34 "
      ideal   model   delta    sigma   weight residual
     110.10  104.72    5.38 1.00e+00 1.00e+00 2.89e+01
  angle pdb=" O4'  DG H  32 "
        pdb=" C1'  DG H  32 "
        pdb=" N9   DG H  32 "
      ideal   model   delta    sigma   weight residual
     108.00  111.71   -3.71 7.00e-01 2.04e+00 2.81e+01
  angle pdb=" O4'  DA H  59 "
        pdb=" C1'  DA H  59 "
        pdb=" N9   DA H  59 "
      ideal   model   delta    sigma   weight residual
     108.00  111.62   -3.62 7.00e-01 2.04e+00 2.68e+01
  ... (remaining 29099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.45: 10840
       35.45 -    70.89: 1103
       70.89 -   106.34: 28
      106.34 -   141.78: 3
      141.78 -   177.23: 5
  Dihedral angle restraints: 11979
    sinusoidal: 6381
      harmonic: 5598
  Sorted by residual:
  dihedral pdb=" CA  GLY A 512 "
           pdb=" C   GLY A 512 "
           pdb=" N   ARG A 513 "
           pdb=" CA  ARG A 513 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.74   38.26     0      5.00e+00 4.00e-02 5.86e+01
  dihedral pdb=" CA  SER C 511 "
           pdb=" C   SER C 511 "
           pdb=" N   GLY C 512 "
           pdb=" CA  GLY C 512 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.87   28.13     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  PHE A 576 "
           pdb=" C   PHE A 576 "
           pdb=" N   ARG A 577 "
           pdb=" CA  ARG A 577 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.68   25.32     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 11976 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 2704
       0.074 -    0.148: 462
       0.148 -    0.222: 18
       0.222 -    0.297: 1
       0.297 -    0.371: 2
  Chirality restraints: 3187
  Sorted by residual:
  chirality pdb=" CA  GLN C1000 "
            pdb=" N   GLN C1000 "
            pdb=" C   GLN C1000 "
            pdb=" CB  GLN C1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" C1'  DG F  34 "
            pdb=" O4'  DG F  34 "
            pdb=" C2'  DG F  34 "
            pdb=" N9   DG F  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.12    0.31 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CB  ILE B 311 "
            pdb=" CA  ILE B 311 "
            pdb=" CG1 ILE B 311 "
            pdb=" CG2 ILE B 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.99e+00
  ... (remaining 3184 not shown)

  Planarity restraints: 2985
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG F  34 "   -0.047 2.00e-02 2.50e+03   2.08e-02 1.30e+01
        pdb=" N9   DG F  34 "    0.052 2.00e-02 2.50e+03
        pdb=" C8   DG F  34 "    0.006 2.00e-02 2.50e+03
        pdb=" N7   DG F  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DG F  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG F  34 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6   DG F  34 "   -0.011 2.00e-02 2.50e+03
        pdb=" N1   DG F  34 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2   DG F  34 "    0.003 2.00e-02 2.50e+03
        pdb=" N2   DG F  34 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG F  34 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DG F  34 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 338 "    0.044 5.00e-02 4.00e+02   6.59e-02 6.95e+00
        pdb=" N   PRO D 339 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO D 339 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D 339 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  28 "    0.030 2.00e-02 2.50e+03   1.63e-02 5.98e+00
        pdb=" N1   DC F  28 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2   DC F  28 "   -0.022 2.00e-02 2.50e+03
        pdb=" O2   DC F  28 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DC F  28 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DC F  28 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC F  28 "    0.017 2.00e-02 2.50e+03
        pdb=" C5   DC F  28 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6   DC F  28 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2982 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 106
        2.35 -     2.99: 10558
        2.99 -     3.62: 32345
        3.62 -     4.26: 47227
        4.26 -     4.90: 70905
  Nonbonded interactions: 161141
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C 505 "
            pdb=" OP2  DT F  25 "
     model   vdw
     1.709 3.120
  nonbonded pdb=" NH1 ARG A 523 "
            pdb=" OP2  DG G  24 "
     model   vdw
     1.808 3.120
  nonbonded pdb=" OE2 GLU C 789 "
            pdb=" NH1 ARG C 797 "
     model   vdw
     1.894 3.120
  nonbonded pdb=" OD2 ASP A 814 "
            pdb=" ND1 HIS A 817 "
     model   vdw
     1.924 3.120
  nonbonded pdb=" OE2 GLU C 738 "
            pdb=" ND2 ASN C 775 "
     model   vdw
     1.934 3.120
  ... (remaining 161136 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 408 through 464 or resid 466 through 1028 or resid 1101 th \ 
rough 1103))
  selection = (chain 'C' and (resid 408 through 464 or resid 466 through 628 or resid 635 thro \ 
ugh 1103))
}
ncs_group {
  reference = chain 'B'
  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=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.780
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
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      :  0.007   0.137  20840  Z= 0.504
  Angle     :  0.912  16.412  29104  Z= 0.646
  Chirality :  0.052   0.371   3187
  Planarity :  0.005   0.066   2985
  Dihedral  : 22.585 177.231   8377
  Min Nonbonded Distance : 1.709

Molprobity Statistics.
  All-atom Clashscore : 23.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 10.78 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  : 24.73 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -4.29 (0.15), residues: 1929
  helix: -2.87 (0.15), residues: 645
  sheet: -1.48 (0.26), residues: 335
  loop : -3.38 (0.16), residues: 949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 513 
 TYR   0.028   0.003   TYR B 343 
 PHE   0.022   0.003   PHE A 724 
 TRP   0.018   0.002   TRP C1014 
 HIS   0.011   0.002   HIS A 959 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00664 /  0.49 (20836)
  covalent geometry    : angle       0.91167 /  0.65 (29104)
  hydrogen bonds       : bond        0.12226 /  8.41 (  891)
  hydrogen bonds       : angle       6.69017 /  4.73 ( 2389)
  metal coordination   : bond        0.11273 /  6.11 (    3)
  Misc. bond           : bond        0.13703 /  8.56 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 381
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 GLN cc_start: 0.8131 (mt0) cc_final: 0.7807 (tp40)
REVERT: A  517 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8638 (mp10)
REVERT: A  670 SER cc_start: 0.8365 (m) cc_final: 0.7390 (m)
REVERT: A  704 MET cc_start: 0.6820 (tpp) cc_final: 0.6616 (tpp)
REVERT: A  740 LEU cc_start: 0.8376 (mt) cc_final: 0.8031 (mt)
REVERT: A  806 PHE cc_start: 0.8551 (p90) cc_final: 0.8299 (p90)
REVERT: C  429 ASP cc_start: 0.7901 (m-30) cc_final: 0.7342 (p0)
REVERT: C  479 PHE cc_start: 0.7864 (t80) cc_final: 0.7020 (m-80)
REVERT: C  604 ASP cc_start: 0.6865 (m-30) cc_final: 0.6542 (p0)
REVERT: C  680 MET cc_start: 0.7856 (mtm) cc_final: 0.7595 (mtm)
REVERT: C  731 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8395 (tm-30)
REVERT: C  869 MET cc_start: 0.8080 (pp-130) cc_final: 0.7740 (ppp)
REVERT: C  951 ASP cc_start: 0.7999 (p0) cc_final: 0.7255 (p0)
REVERT: D  129 LEU cc_start: 0.7924 (mt) cc_final: 0.7702 (pt)
  outliers start: 1
  outliers final: 1
  residues processed: 381
  average time/residue: 0.1741
  time to fit residues: 97.0602
Evaluate side-chains
  198 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 194 optimal weight:   40.0000
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 200 optimal weight:   40.0000
   chunk 212 optimal weight:   30.0000
   chunk 77 optimal weight:    6.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 687 HIS
A 874 ASN
** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
B 269 HIS
B 344 HIS
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 464 HIS
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 936 GLN
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1028 HIS
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 222 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.083560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.060211 restraints weight = 95788.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.061780 restraints weight = 54913.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.062761 restraints weight = 38474.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.063375 restraints weight = 30653.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.063739 restraints weight = 26790.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       76 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  20840  Z= 0.197
  Angle     :  0.824  12.094  29104  Z= 0.450
  Chirality :  0.051   0.338   3187
  Planarity :  0.007   0.070   2985
  Dihedral  : 25.988 179.637   4567
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.31 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  4.30 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -3.11 (0.17), residues: 1929
  helix: -1.45 (0.18), residues: 649
  sheet: -1.26 (0.27), residues: 343
  loop : -2.86 (0.17), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 922 
 TYR   0.017   0.002   TYR A 578 
 PHE   0.028   0.002   PHE C 681 
 TRP   0.024   0.003   TRP A 782 
 HIS   0.018   0.002   HIS B 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.20 (20836)
  covalent geometry    : angle       0.82382 /  0.45 (29104)
  hydrogen bonds       : bond        0.05998 /  3.97 (  891)
  hydrogen bonds       : angle       5.33661 /  3.78 ( 2389)
  metal coordination   : bond        0.00972 /  0.56 (    3)
  Misc. bond           : bond        0.00742 /  0.46 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 297
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  504 TYR cc_start: 0.8006 (t80) cc_final: 0.7708 (t80)
REVERT: A  594 MET cc_start: 0.8620 (mmt) cc_final: 0.8297 (mmt)
REVERT: A  617 GLU cc_start: 0.7833 (pm20) cc_final: 0.7488 (pm20)
REVERT: A  806 PHE cc_start: 0.9204 (p90) cc_final: 0.8402 (p90)
REVERT: A  863 MET cc_start: 0.7746 (mmm) cc_final: 0.6860 (mmp)
REVERT: A  883 GLU cc_start: 0.8835 (pm20) cc_final: 0.8580 (pp20)
REVERT: C  429 ASP cc_start: 0.7961 (m-30) cc_final: 0.7531 (p0)
REVERT: C  473 MET cc_start: 0.8803 (ttp) cc_final: 0.7384 (ttt)
REVERT: C  474 MET cc_start: 0.6867 (mmt) cc_final: 0.6008 (mmm)
REVERT: C  479 PHE cc_start: 0.7411 (t80) cc_final: 0.6811 (m-80)
REVERT: C  495 LEU cc_start: 0.9265 (tp) cc_final: 0.8991 (mt)
REVERT: C  594 MET cc_start: 0.8985 (mmm) cc_final: 0.8417 (mmt)
REVERT: C  622 MET cc_start: 0.6877 (tpt) cc_final: 0.6265 (tpp)
REVERT: C  677 LEU cc_start: 0.9287 (tp) cc_final: 0.8511 (tp)
REVERT: C  850 ARG cc_start: 0.8947 (mtm110) cc_final: 0.8656 (ptt90)
REVERT: C  877 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8247 (ttp-110)
REVERT: C  951 ASP cc_start: 0.7753 (p0) cc_final: 0.7375 (p0)
REVERT: D  129 LEU cc_start: 0.8189 (mt) cc_final: 0.7869 (pt)
REVERT: D  155 LEU cc_start: 0.8924 (tt) cc_final: 0.8057 (mm)
REVERT: D  227 ASP cc_start: 0.8485 (m-30) cc_final: 0.8228 (m-30)
REVERT: D  241 LEU cc_start: 0.7960 (mm) cc_final: 0.7427 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1501
  time to fit residues: 67.3448
Evaluate side-chains
  180 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   chunk 10 optimal weight:    0.4980
   chunk 145 optimal weight:    4.9990
   chunk 191 optimal weight:    4.9990
   chunk 102 optimal weight:    7.9990
   chunk 168 optimal weight:    9.9990
   chunk 188 optimal weight:    2.9990
   chunk 176 optimal weight:   10.0000
   chunk 96 optimal weight:   40.0000
   overall best weight:    3.8988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 983 ASN
** B  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 ASN
B 253 HIS
** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 423 GLN
C 534 HIS
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 983 ASN
C1012 HIS
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 173 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.081992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.058223 restraints weight = 96005.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.059717 restraints weight = 55220.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.060648 restraints weight = 38770.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.061226 restraints weight = 31052.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.061560 restraints weight = 27088.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       76 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.116  20840  Z= 0.205
  Angle     :  0.763  12.116  29104  Z= 0.420
  Chirality :  0.048   0.329   3187
  Planarity :  0.005   0.054   2985
  Dihedral  : 25.973 179.823   4567
  Min Nonbonded Distance : 1.665

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.78 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.30 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.18), residues: 1929
  helix: -0.82 (0.19), residues: 655
  sheet: -1.03 (0.27), residues: 344
  loop : -2.53 (0.18), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 999 
 TYR   0.034   0.002   TYR A 578 
 PHE   0.020   0.002   PHE A 494 
 TRP   0.025   0.003   TRP C1014 
 HIS   0.010   0.002   HIS B 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.20 (20836)
  covalent geometry    : angle       0.76336 /  0.42 (29104)
  hydrogen bonds       : bond        0.05406 /  3.61 (  891)
  hydrogen bonds       : angle       4.96748 /  3.50 ( 2389)
  metal coordination   : bond        0.00620 /  0.36 (    3)
  Misc. bond           : bond        0.00755 /  0.47 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 242
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8411 (mm-40)
REVERT: A  590 GLU cc_start: 0.8506 (tt0) cc_final: 0.8214 (tt0)
REVERT: A  617 GLU cc_start: 0.7964 (pm20) cc_final: 0.7678 (pm20)
REVERT: B   14 LEU cc_start: 0.9180 (mp) cc_final: 0.8976 (mp)
REVERT: C  429 ASP cc_start: 0.8015 (m-30) cc_final: 0.7625 (p0)
REVERT: C  473 MET cc_start: 0.8828 (ttp) cc_final: 0.8065 (ttt)
REVERT: C  474 MET cc_start: 0.6897 (mmt) cc_final: 0.6589 (mpp)
REVERT: C  479 PHE cc_start: 0.7394 (t80) cc_final: 0.6499 (m-80)
REVERT: C  495 LEU cc_start: 0.9333 (tp) cc_final: 0.9029 (mt)
REVERT: C  677 LEU cc_start: 0.9340 (tp) cc_final: 0.8536 (tp)
REVERT: C  737 MET cc_start: 0.6918 (ttm) cc_final: 0.5751 (ttm)
REVERT: C  871 MET cc_start: 0.8566 (mmt) cc_final: 0.8310 (mmm)
REVERT: C  951 ASP cc_start: 0.7749 (p0) cc_final: 0.7370 (p0)
REVERT: C 1007 GLU cc_start: 0.8790 (mt-10) cc_final: 0.7856 (mp0)
REVERT: D  129 LEU cc_start: 0.8060 (mt) cc_final: 0.7815 (pt)
REVERT: D  218 PHE cc_start: 0.8161 (m-80) cc_final: 0.7955 (m-10)
REVERT: D  227 ASP cc_start: 0.8526 (m-30) cc_final: 0.8293 (m-30)
REVERT: D  241 LEU cc_start: 0.7993 (mm) cc_final: 0.7486 (tt)
REVERT: D  272 ILE cc_start: 0.9085 (mm) cc_final: 0.8848 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1544
  time to fit residues: 56.7187
Evaluate side-chains
  160 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 144 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0870
   chunk 4 optimal weight:    8.9990
   chunk 152 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 175 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 213 optimal weight:   30.0000
   chunk 214 optimal weight:   50.0000
   overall best weight:    2.2164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 499 GLN
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 HIS
** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.083003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.059630 restraints weight = 92614.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.061150 restraints weight = 53408.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.062101 restraints weight = 37424.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.062710 restraints weight = 29845.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.063034 restraints weight = 25796.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  20840  Z= 0.159
  Angle     :  0.724   9.400  29104  Z= 0.399
  Chirality :  0.046   0.331   3187
  Planarity :  0.005   0.063   2985
  Dihedral  : 25.865 179.126   4567
  Min Nonbonded Distance : 1.768

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.48 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.18), residues: 1929
  helix: -0.35 (0.19), residues: 655
  sheet: -0.89 (0.27), residues: 348
  loop : -2.27 (0.19), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 477 
 TYR   0.024   0.002   TYR A 578 
 PHE   0.023   0.002   PHE C 681 
 TRP   0.019   0.002   TRP C 915 
 HIS   0.009   0.001   HIS B 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.16 (20836)
  covalent geometry    : angle       0.72397 /  0.40 (29104)
  hydrogen bonds       : bond        0.04951 /  3.30 (  891)
  hydrogen bonds       : angle       4.75805 /  3.38 ( 2389)
  metal coordination   : bond        0.00357 /  0.20 (    3)
  Misc. bond           : bond        0.00965 /  0.60 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8441 (mm-40)
REVERT: A  606 MET cc_start: 0.7476 (ppp) cc_final: 0.6916 (ppp)
REVERT: A  617 GLU cc_start: 0.8073 (pm20) cc_final: 0.7700 (pm20)
REVERT: A  675 ARG cc_start: 0.8950 (mmm-85) cc_final: 0.8449 (mmm-85)
REVERT: A  698 VAL cc_start: 0.9149 (t) cc_final: 0.8821 (p)
REVERT: A  740 LEU cc_start: 0.8756 (mt) cc_final: 0.8387 (mt)
REVERT: C  429 ASP cc_start: 0.8056 (m-30) cc_final: 0.7699 (p0)
REVERT: C  473 MET cc_start: 0.8827 (ttp) cc_final: 0.7665 (ttt)
REVERT: C  474 MET cc_start: 0.6935 (mmt) cc_final: 0.6126 (mmm)
REVERT: C  479 PHE cc_start: 0.7408 (t80) cc_final: 0.6533 (m-80)
REVERT: C  677 LEU cc_start: 0.9315 (tp) cc_final: 0.9101 (tp)
REVERT: C  704 MET cc_start: 0.8767 (tpp) cc_final: 0.8551 (tpp)
REVERT: C  951 ASP cc_start: 0.7607 (p0) cc_final: 0.7203 (p0)
REVERT: C  996 MET cc_start: 0.8683 (mtt) cc_final: 0.7612 (mtt)
REVERT: D  129 LEU cc_start: 0.8014 (mt) cc_final: 0.7764 (pt)
REVERT: D  218 PHE cc_start: 0.8152 (m-80) cc_final: 0.7952 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1440
  time to fit residues: 53.6219
Evaluate side-chains
  166 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 167 optimal weight:   10.0000
   chunk 3 optimal weight:   50.0000
   chunk 155 optimal weight:   10.0000
   chunk 132 optimal weight:   10.0000
   chunk 186 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9990
   chunk 144 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 126 optimal weight:    9.9990
   chunk 135 optimal weight:    2.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 ASN
** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 517 GLN
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 822 ASN
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.081371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.057949 restraints weight = 92758.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.059434 restraints weight = 53935.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.060350 restraints weight = 38066.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.060942 restraints weight = 30558.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.061301 restraints weight = 26532.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120  20840  Z= 0.200
  Angle     :  0.741  11.204  29104  Z= 0.405
  Chirality :  0.047   0.337   3187
  Planarity :  0.005   0.057   2985
  Dihedral  : 25.816 176.055   4567
  Min Nonbonded Distance : 1.678

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.36 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  3.42 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.91 (0.18), residues: 1929
  helix: -0.34 (0.20), residues: 658
  sheet: -0.80 (0.27), residues: 348
  loop : -2.17 (0.19), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 992 
 TYR   0.026   0.002   TYR A 729 
 PHE   0.041   0.002   PHE C 806 
 TRP   0.019   0.002   TRP C 782 
 HIS   0.012   0.001   HIS B  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.20 (20836)
  covalent geometry    : angle       0.74091 /  0.41 (29104)
  hydrogen bonds       : bond        0.05219 /  3.48 (  891)
  hydrogen bonds       : angle       4.77447 /  3.38 ( 2389)
  metal coordination   : bond        0.00541 /  0.33 (    3)
  Misc. bond           : bond        0.00169 /  0.11 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8365 (mm-40)
REVERT: A  590 GLU cc_start: 0.8681 (tt0) cc_final: 0.8441 (tt0)
REVERT: A  606 MET cc_start: 0.7481 (ppp) cc_final: 0.6885 (ppp)
REVERT: A  617 GLU cc_start: 0.8257 (pm20) cc_final: 0.8045 (pm20)
REVERT: A  740 LEU cc_start: 0.8961 (mt) cc_final: 0.8638 (mm)
REVERT: A  863 MET cc_start: 0.7777 (mmm) cc_final: 0.7567 (mmm)
REVERT: A 1007 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8328 (mt-10)
REVERT: C  429 ASP cc_start: 0.8087 (m-30) cc_final: 0.7760 (p0)
REVERT: C  473 MET cc_start: 0.8880 (ttp) cc_final: 0.7594 (ttt)
REVERT: C  474 MET cc_start: 0.6933 (mmt) cc_final: 0.5973 (mmm)
REVERT: C  479 PHE cc_start: 0.7444 (t80) cc_final: 0.6509 (m-80)
REVERT: C  495 LEU cc_start: 0.9335 (mt) cc_final: 0.9012 (mt)
REVERT: C  704 MET cc_start: 0.8987 (tpp) cc_final: 0.8634 (tpp)
REVERT: C  733 MET cc_start: 0.9044 (tpp) cc_final: 0.8733 (tpp)
REVERT: C  951 ASP cc_start: 0.7555 (p0) cc_final: 0.7180 (p0)
REVERT: D  129 LEU cc_start: 0.8148 (mt) cc_final: 0.7782 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1384
  time to fit residues: 46.6105
Evaluate side-chains
  159 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 126 optimal weight:    8.9990
   chunk 202 optimal weight:   50.0000
   chunk 213 optimal weight:   30.0000
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 115 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   chunk 192 optimal weight:    5.9990
   chunk 117 optimal weight:    0.9980
   chunk 198 optimal weight:   50.0000
   chunk 156 optimal weight:    5.9990
   overall best weight:    1.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 539 GLN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 GLN
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 810 GLN
C 822 ASN
C 959 HIS
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.082548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.059164 restraints weight = 91517.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.060687 restraints weight = 53099.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.061649 restraints weight = 37347.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.062255 restraints weight = 29864.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.062584 restraints weight = 25914.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  20840  Z= 0.152
  Angle     :  0.704   8.610  29104  Z= 0.386
  Chirality :  0.046   0.336   3187
  Planarity :  0.005   0.087   2985
  Dihedral  : 25.738 179.601   4567
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.48 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.77 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.64 (0.18), residues: 1929
  helix: -0.07 (0.20), residues: 661
  sheet: -0.70 (0.28), residues: 348
  loop : -2.02 (0.19), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 992 
 TYR   0.021   0.002   TYR A 504 
 PHE   0.024   0.002   PHE D 350 
 TRP   0.013   0.002   TRP C 915 
 HIS   0.008   0.001   HIS B 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.15 (20836)
  covalent geometry    : angle       0.70436 /  0.39 (29104)
  hydrogen bonds       : bond        0.04873 /  3.29 (  891)
  hydrogen bonds       : angle       4.57697 /  3.26 ( 2389)
  metal coordination   : bond        0.00284 /  0.17 (    3)
  Misc. bond           : bond        0.00012 /  0.01 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8377 (mm-40)
REVERT: A  539 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8674 (mp10)
REVERT: A  606 MET cc_start: 0.7499 (ppp) cc_final: 0.6856 (ppp)
REVERT: A  617 GLU cc_start: 0.8270 (pm20) cc_final: 0.7994 (pm20)
REVERT: A  737 MET cc_start: 0.8628 (tpp) cc_final: 0.8374 (tpp)
REVERT: A  740 LEU cc_start: 0.8954 (mt) cc_final: 0.8104 (mt)
REVERT: C  429 ASP cc_start: 0.8081 (m-30) cc_final: 0.7798 (p0)
REVERT: C  473 MET cc_start: 0.8809 (ttp) cc_final: 0.8389 (ttt)
REVERT: C  474 MET cc_start: 0.6822 (mmt) cc_final: 0.6244 (mmm)
REVERT: C  503 MET cc_start: 0.9035 (ppp) cc_final: 0.8792 (tmm)
REVERT: C  705 MET cc_start: 0.9133 (mmm) cc_final: 0.8844 (mpp)
REVERT: C  733 MET cc_start: 0.8999 (tpp) cc_final: 0.8659 (tpp)
REVERT: C  951 ASP cc_start: 0.7533 (p0) cc_final: 0.7142 (p0)
REVERT: D  129 LEU cc_start: 0.8107 (mt) cc_final: 0.7763 (pt)
REVERT: D  155 LEU cc_start: 0.8962 (tt) cc_final: 0.8161 (mm)
REVERT: D  218 PHE cc_start: 0.7974 (m-80) cc_final: 0.7724 (m-80)
REVERT: D  241 LEU cc_start: 0.8228 (mm) cc_final: 0.7760 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1342
  time to fit residues: 46.7788
Evaluate side-chains
  158 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 198 optimal weight:   50.0000
   chunk 150 optimal weight:    8.9990
   chunk 110 optimal weight:    9.9990
   chunk 131 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0570
   chunk 77 optimal weight:    0.8980
   chunk 178 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    3.3904

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 822 ASN
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.081860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.057860 restraints weight = 93821.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.059365 restraints weight = 53831.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.060311 restraints weight = 37881.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.060881 restraints weight = 30409.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.061237 restraints weight = 26630.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  20840  Z= 0.178
  Angle     :  0.717   9.751  29104  Z= 0.392
  Chirality :  0.045   0.343   3187
  Planarity :  0.005   0.068   2985
  Dihedral  : 25.699 178.361   4567
  Min Nonbonded Distance : 1.711

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.79 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.54 (0.18), residues: 1929
  helix:  0.04 (0.20), residues: 664
  sheet: -0.63 (0.28), residues: 338
  loop : -1.98 (0.19), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 992 
 TYR   0.020   0.002   TYR A 504 
 PHE   0.020   0.002   PHE B 274 
 TRP   0.010   0.001   TRP B 317 
 HIS   0.009   0.001   HIS B  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.18 (20836)
  covalent geometry    : angle       0.71742 /  0.39 (29104)
  hydrogen bonds       : bond        0.04950 /  3.33 (  891)
  hydrogen bonds       : angle       4.56461 /  3.24 ( 2389)
  metal coordination   : bond        0.00533 /  0.32 (    3)
  Misc. bond           : bond        0.00102 /  0.06 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  474 MET cc_start: 0.8043 (ppp) cc_final: 0.7838 (ppp)
REVERT: A  517 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8373 (mm-40)
REVERT: C  429 ASP cc_start: 0.7995 (m-30) cc_final: 0.7732 (p0)
REVERT: C  473 MET cc_start: 0.8696 (ttp) cc_final: 0.8414 (ttt)
REVERT: C  474 MET cc_start: 0.6860 (mmt) cc_final: 0.6282 (mmm)
REVERT: C  590 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: C  622 MET cc_start: 0.6695 (mtt) cc_final: 0.6490 (mtt)
REVERT: C  733 MET cc_start: 0.9040 (tpp) cc_final: 0.8545 (tpp)
REVERT: C  737 MET cc_start: 0.8087 (mmp) cc_final: 0.7554 (mmp)
REVERT: C  869 MET cc_start: 0.7843 (ppp) cc_final: 0.7453 (ppp)
REVERT: C  951 ASP cc_start: 0.7618 (p0) cc_final: 0.7165 (p0)
REVERT: D  129 LEU cc_start: 0.8163 (mt) cc_final: 0.7803 (pt)
REVERT: D  155 LEU cc_start: 0.9044 (tt) cc_final: 0.8220 (mm)
REVERT: D  218 PHE cc_start: 0.8007 (m-80) cc_final: 0.7612 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1299
  time to fit residues: 45.0707
Evaluate side-chains
  155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 140 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 170 optimal weight:    6.9990
   chunk 168 optimal weight:    5.9990
   chunk 185 optimal weight:   20.0000
   chunk 92 optimal weight:    6.9990
   chunk 148 optimal weight:    7.9990
   chunk 161 optimal weight:   20.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 858 GLN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 822 ASN
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 983 ASN
D  79 HIS
** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.079849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.055593 restraints weight = 95089.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.057042 restraints weight = 55124.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.057932 restraints weight = 39200.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.058483 restraints weight = 31739.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.058826 restraints weight = 27921.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       77 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.4715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.126  20840  Z= 0.242
  Angle     :  0.775  13.517  29104  Z= 0.419
  Chirality :  0.047   0.355   3187
  Planarity :  0.005   0.064   2985
  Dihedral  : 25.744 179.959   4567
  Min Nonbonded Distance : 1.712

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.67 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.57 (0.19), residues: 1929
  helix: -0.06 (0.20), residues: 662
  sheet: -0.67 (0.29), residues: 334
  loop : -1.92 (0.19), residues: 933

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 882 
 TYR   0.023   0.002   TYR D  90 
 PHE   0.022   0.002   PHE B 274 
 TRP   0.017   0.002   TRP D 317 
 HIS   0.012   0.002   HIS B  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00498 /  0.24 (20836)
  covalent geometry    : angle       0.77467 /  0.42 (29104)
  hydrogen bonds       : bond        0.05420 /  3.64 (  891)
  hydrogen bonds       : angle       4.70103 /  3.31 ( 2389)
  metal coordination   : bond        0.00767 /  0.45 (    3)
  Misc. bond           : bond        0.00116 /  0.07 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  474 MET cc_start: 0.8051 (ppp) cc_final: 0.7820 (ppp)
REVERT: A  517 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8256 (mm-40)
REVERT: A  606 MET cc_start: 0.7742 (ppp) cc_final: 0.7229 (ppp)
REVERT: A  675 ARG cc_start: 0.9153 (mmm-85) cc_final: 0.8448 (mmm-85)
REVERT: B  285 MET cc_start: 0.8589 (tpp) cc_final: 0.8317 (tpp)
REVERT: B  341 GLU cc_start: 0.8197 (mp0) cc_final: 0.7970 (mp0)
REVERT: C  429 ASP cc_start: 0.8110 (m-30) cc_final: 0.7757 (p0)
REVERT: C  473 MET cc_start: 0.8708 (ttp) cc_final: 0.8397 (ttt)
REVERT: C  474 MET cc_start: 0.6911 (mmt) cc_final: 0.6331 (mmm)
REVERT: C  503 MET cc_start: 0.8900 (ppp) cc_final: 0.8689 (tmm)
REVERT: C  622 MET cc_start: 0.7337 (mtt) cc_final: 0.7099 (mtt)
REVERT: C  647 MET cc_start: 0.8058 (mpp) cc_final: 0.7407 (mpp)
REVERT: C  737 MET cc_start: 0.7977 (mmp) cc_final: 0.7419 (mmp)
REVERT: C  807 MET cc_start: 0.7379 (mtp) cc_final: 0.6855 (mtp)
REVERT: C  869 MET cc_start: 0.7787 (ppp) cc_final: 0.7435 (ppp)
REVERT: C  951 ASP cc_start: 0.7868 (p0) cc_final: 0.7351 (p0)
REVERT: D   34 LYS cc_start: 0.9222 (ttmm) cc_final: 0.8897 (ttmm)
REVERT: D  129 LEU cc_start: 0.8376 (mt) cc_final: 0.7960 (pt)
REVERT: D  155 LEU cc_start: 0.9070 (tt) cc_final: 0.8251 (mm)
REVERT: D  218 PHE cc_start: 0.8095 (m-80) cc_final: 0.7667 (m-80)
REVERT: D  241 LEU cc_start: 0.8277 (mm) cc_final: 0.7825 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1398
  time to fit residues: 45.3315
Evaluate side-chains
  145 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 197 optimal weight:   50.0000
   chunk 174 optimal weight:    2.9990
   chunk 69 optimal weight:    0.4980
   chunk 99 optimal weight:   20.0000
   chunk 172 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0870
   chunk 208 optimal weight:   50.0000
   chunk 213 optimal weight:   30.0000
   chunk 21 optimal weight:    7.9990
   chunk 129 optimal weight:    7.9990
   overall best weight:    2.1162

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 822 ASN
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.081836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.057440 restraints weight = 92896.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.058911 restraints weight = 53972.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.059837 restraints weight = 38239.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.060441 restraints weight = 30842.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.060788 restraints weight = 26949.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  20840  Z= 0.152
  Angle     :  0.717   9.425  29104  Z= 0.391
  Chirality :  0.046   0.350   3187
  Planarity :  0.005   0.065   2985
  Dihedral  : 25.690 179.376   4567
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.38 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.39 (0.19), residues: 1929
  helix:  0.09 (0.20), residues: 662
  sheet: -0.63 (0.29), residues: 336
  loop : -1.79 (0.20), residues: 931

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 992 
 TYR   0.027   0.002   TYR A 504 
 PHE   0.017   0.002   PHE C 681 
 TRP   0.012   0.002   TRP C 915 
 HIS   0.009   0.001   HIS B  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.15 (20836)
  covalent geometry    : angle       0.71749 /  0.39 (29104)
  hydrogen bonds       : bond        0.04847 /  3.27 (  891)
  hydrogen bonds       : angle       4.54449 /  3.20 ( 2389)
  metal coordination   : bond        0.00385 /  0.23 (    3)
  Misc. bond           : bond        0.00048 /  0.03 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  474 MET cc_start: 0.8006 (ppp) cc_final: 0.7782 (ppp)
REVERT: A  517 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8269 (mm-40)
REVERT: A  606 MET cc_start: 0.7727 (ppp) cc_final: 0.7231 (ppp)
REVERT: A  691 THR cc_start: 0.9160 (p) cc_final: 0.8540 (t)
REVERT: A 1007 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: B  100 ASN cc_start: 0.8081 (p0) cc_final: 0.7804 (p0)
REVERT: C  429 ASP cc_start: 0.7995 (m-30) cc_final: 0.7735 (p0)
REVERT: C  473 MET cc_start: 0.8704 (ttp) cc_final: 0.8422 (ttt)
REVERT: C  474 MET cc_start: 0.6783 (mmt) cc_final: 0.6171 (mmm)
REVERT: C  622 MET cc_start: 0.6998 (mtt) cc_final: 0.6751 (mtt)
REVERT: C  647 MET cc_start: 0.8028 (mpp) cc_final: 0.7328 (mpp)
REVERT: C  705 MET cc_start: 0.8875 (mpp) cc_final: 0.8608 (mpp)
REVERT: C  733 MET cc_start: 0.9179 (tpp) cc_final: 0.8911 (tpp)
REVERT: C  737 MET cc_start: 0.8225 (mmp) cc_final: 0.7134 (mmp)
REVERT: C  869 MET cc_start: 0.7751 (ppp) cc_final: 0.7476 (ppp)
REVERT: C  945 MET cc_start: 0.8790 (mmm) cc_final: 0.8503 (mmm)
REVERT: C  951 ASP cc_start: 0.7829 (p0) cc_final: 0.7340 (p0)
REVERT: D  129 LEU cc_start: 0.8235 (mt) cc_final: 0.7873 (pt)
REVERT: D  155 LEU cc_start: 0.9011 (tt) cc_final: 0.8235 (mm)
REVERT: D  218 PHE cc_start: 0.8066 (m-80) cc_final: 0.7602 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1329
  time to fit residues: 46.1430
Evaluate side-chains
  155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 130 optimal weight:    0.0010
   chunk 76 optimal weight:    8.9990
   chunk 155 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 139 optimal weight:    1.9990
   chunk 109 optimal weight:    8.9990
   chunk 27 optimal weight:    0.5980
   chunk 213 optimal weight:   30.0000
   chunk 97 optimal weight:    8.9990
   chunk 104 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.6990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 GLN
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 822 ASN
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.082053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.058059 restraints weight = 91498.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.059632 restraints weight = 51659.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.060657 restraints weight = 35767.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.061295 restraints weight = 28298.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.061687 restraints weight = 24373.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
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      :  0.003   0.072  20840  Z= 0.153
  Angle     :  0.720   9.046  29104  Z= 0.393
  Chirality :  0.045   0.353   3187
  Planarity :  0.005   0.059   2985
  Dihedral  : 25.614 179.083   4567
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.29 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.31 (0.19), residues: 1929
  helix:  0.15 (0.20), residues: 662
  sheet: -0.57 (0.29), residues: 336
  loop : -1.75 (0.20), residues: 931

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 778 
 TYR   0.028   0.002   TYR A 504 
 PHE   0.017   0.002   PHE A 494 
 TRP   0.012   0.001   TRP C 915 
 HIS   0.008   0.001   HIS B  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.15 (20836)
  covalent geometry    : angle       0.71955 /  0.39 (29104)
  hydrogen bonds       : bond        0.04787 /  3.24 (  891)
  hydrogen bonds       : angle       4.55822 /  3.23 ( 2389)
  metal coordination   : bond        0.00264 /  0.16 (    3)
  Misc. bond           : bond        0.00049 /  0.03 (    1)

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

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

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3858 Ramachandran restraints generated.
    1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  474 MET cc_start: 0.8048 (ppp) cc_final: 0.7811 (ppp)
REVERT: A  517 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8244 (mm-40)
REVERT: A  606 MET cc_start: 0.7725 (ppp) cc_final: 0.7236 (ppp)
REVERT: A 1007 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: B  343 TYR cc_start: 0.8956 (m-80) cc_final: 0.8728 (m-80)
REVERT: C  429 ASP cc_start: 0.7976 (m-30) cc_final: 0.7716 (p0)
REVERT: C  473 MET cc_start: 0.8704 (ttp) cc_final: 0.8427 (ttt)
REVERT: C  474 MET cc_start: 0.6635 (mmt) cc_final: 0.6034 (mmm)
REVERT: C  503 MET cc_start: 0.8957 (ppp) cc_final: 0.8690 (tmm)
REVERT: C  647 MET cc_start: 0.8031 (mpp) cc_final: 0.7329 (mpp)
REVERT: C  705 MET cc_start: 0.8979 (mpp) cc_final: 0.8688 (mpp)
REVERT: C  733 MET cc_start: 0.9151 (tpp) cc_final: 0.8880 (tpp)
REVERT: C  737 MET cc_start: 0.8276 (mmp) cc_final: 0.7295 (mmp)
REVERT: C  869 MET cc_start: 0.7721 (ppp) cc_final: 0.7422 (ppp)
REVERT: C  945 MET cc_start: 0.8847 (mmm) cc_final: 0.8646 (mmm)
REVERT: C  951 ASP cc_start: 0.7730 (p0) cc_final: 0.7209 (p0)
REVERT: D  129 LEU cc_start: 0.8205 (mt) cc_final: 0.7843 (pt)
REVERT: D  155 LEU cc_start: 0.9015 (tt) cc_final: 0.8241 (mm)
REVERT: D  218 PHE cc_start: 0.8047 (m-80) cc_final: 0.7610 (m-80)
REVERT: D  241 LEU cc_start: 0.8262 (mm) cc_final: 0.7811 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1314
  time to fit residues: 44.6328
Evaluate side-chains
  157 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 183 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 153 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 126 optimal weight:    0.8980
   chunk 158 optimal weight:    6.9990
   chunk 209 optimal weight:   50.0000
   chunk 113 optimal weight:    0.9990
   chunk 87 optimal weight:    0.1980
   chunk 208 optimal weight:   50.0000
   chunk 176 optimal weight:    0.0770
   overall best weight:    1.0342

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 959 HIS
** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.083315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.059068 restraints weight = 93029.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.060577 restraints weight = 53750.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.061545 restraints weight = 37844.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.062141 restraints weight = 30318.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.062524 restraints weight = 26404.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       78 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  20840  Z= 0.140
  Angle     :  0.708  12.236  29104  Z= 0.384
  Chirality :  0.045   0.356   3187
  Planarity :  0.005   0.053   2985
  Dihedral  : 25.499 179.048   4567
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.59 %
    Cis-general     : 1.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.19), residues: 1929
  helix:  0.31 (0.20), residues: 658
  sheet: -0.51 (0.28), residues: 336
  loop : -1.66 (0.20), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 850 
 TYR   0.024   0.002   TYR A 504 
 PHE   0.016   0.001   PHE C 938 
 TRP   0.015   0.001   TRP C 915 
 HIS   0.006   0.001   HIS B  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.14 (20836)
  covalent geometry    : angle       0.70803 /  0.38 (29104)
  hydrogen bonds       : bond        0.04646 /  3.17 (  891)
  hydrogen bonds       : angle       4.45766 /  3.14 ( 2389)
  metal coordination   : bond        0.00153 /  0.09 (    3)
  Misc. bond           : bond        0.00003 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3521.61 seconds
wall clock time: 61 minutes 44.95 seconds (3704.95 seconds total)