Starting phenix.real_space_refine
on Tue Sep 15 05:38:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3jbw_6489/09_2026/3jbw_6489_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3jbw_6489/09_2026/3jbw_6489.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/3jbw_6489/09_2026/3jbw_6489_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3jbw_6489/09_2026/3jbw_6489_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/3jbw_6489/09_2026/3jbw_6489.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3jbw_6489/09_2026/3jbw_6489.map"
  }
  resolution = 4.6
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 19997 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     222      5.49       5
     S     112      5.16       5
     C   11864      2.51       5
     N    3575      2.21       5
     O    4222      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 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: 19997
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 5008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 5008
          Classifications: {'peptide': 622}
          Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 593}
    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: 5008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 5008
          Classifications: {'peptide': 622}
          Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 593}
    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: 697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 697
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
    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: 1256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1256
          Classifications: {'DNA': 61}
          Link IDs: {'rna3p': 60}
    Chain: "H"
      Number of atoms: 919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 919
          Classifications: {'DNA': 45}
          Link IDs: {'rna3p': 44}
    Chain: "I"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 326
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "J"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 326
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2680  SG  CYS A 749      81.650  59.752 105.359  1.00130.76           S
  ATOM  10402  SG  CYS C 749      23.075  92.261 100.786  1.00110.57           S

  Residues with excluded nonbonded symmetry interactions: 29
    residue:
      pdb=" P    DA E  22 " occ=0.96
      ... (19 atoms not shown)
      pdb=" C4   DA E  22 " occ=0.96
    residue:
      pdb=" P    DA E  23 " occ=0.75
      ... (19 atoms not shown)
      pdb=" C4   DA E  23 " occ=0.75
    residue:
      pdb=" P    DA E  24 " occ=0.71
      ... (19 atoms not shown)
      pdb=" C4   DA E  24 " occ=0.71
    residue:
      pdb=" P    DA E  25 " occ=0.93
      ... (19 atoms not shown)
      pdb=" C4   DA E  25 " occ=0.93
    residue:
      pdb=" P    DA E  26 " occ=0.90
      ... (19 atoms not shown)
      pdb=" C4   DA E  26 " occ=0.90
    residue:
      pdb=" P    DC E  28 " occ=0.84
      ... (17 atoms not shown)
      pdb=" C6   DC E  28 " occ=0.84
    residue:
      pdb=" P    DG F   7 " occ=0.69
      ... (20 atoms not shown)
      pdb=" C4   DG F   7 " occ=0.69
    residue:
      pdb=" P    DG F   8 " occ=0.61
      ... (20 atoms not shown)
      pdb=" C4   DG F   8 " occ=0.61
    residue:
      pdb=" P    DT F   9 " occ=0.71
      ... (18 atoms not shown)
      pdb=" C6   DT F   9 " occ=0.71
    residue:
      pdb=" P    DT F  10 " occ=0.72
      ... (18 atoms not shown)
      pdb=" C6   DT F  10 " occ=0.72
    residue:
      pdb=" P    DT F  11 " occ=0.80
      ... (18 atoms not shown)
      pdb=" C6   DT F  11 " occ=0.80
    residue:
      pdb=" P    DT F  12 " occ=0.75
      ... (18 atoms not shown)
      pdb=" C6   DT F  12 " occ=0.75
    ... (remaining 17 not shown)
  Time building chain proxies: 3.75, per 1000 atoms: 0.19
  Number of scatterers: 19997
  At special positions: 0
  Unit cell: (108.24, 153.75, 161.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S     112     16.00
     P     222     15.00
     O    4222      8.00
     N    3575      7.00
     C   11864      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 701.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 749 "
        pdb="ZN    ZN A1101 " - pdb=" NE2 HIS A 964 "
        pdb="ZN    ZN A1101 " - pdb=" NE2 HIS A 959 "
      pdb="  ZN C1101 "
        pdb="ZN    ZN C1101 " - pdb=" NE2 HIS C 964 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 749 "
        pdb="ZN    ZN C1101 " - pdb=" NE2 HIS C 959 "


  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3612

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 19 sheets defined
      37.0% alpha, 21.5% beta
      59 base pairs and 164 stacking pairs defined.
    Time for finding SS restraints: 2.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 414 through 418
    Processing helix  chain 'A' and resid 420 through 426
      removed outlier: 4.253A  pdb=" N   HIS A 425 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 442
      removed outlier: 3.924A  pdb=" N   GLU A 439 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LYS A 440 " --> pdb=" O   THR A 436 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU A 441 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 459
      removed outlier: 4.565A  pdb=" N   VAL A 449 " --> pdb=" O   ASP A 445 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   CYS A 450 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU A 456 " --> pdb=" O   THR A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 473
      removed outlier: 4.173A  pdb=" N   GLU A 469 " --> pdb=" O   LYS A 465 " (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 524
    Processing helix  chain 'A' and resid 577 through 588
    Processing helix  chain 'A' and resid 589 through 600
    Processing helix  chain 'A' and resid 686 through 707
      removed outlier: 3.948A  pdb=" N   LEU A 690 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
      Proline residue:  A 696  - end of helix
      removed outlier: 4.594A  pdb=" N   GLU A 706 " --> pdb=" O   LYS A 702 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   SER A 707 " --> pdb=" O   ALA A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 738
    Processing helix  chain 'A' and resid 755 through 762
    Processing helix  chain 'A' and resid 771 through 785
    Processing helix  chain 'A' and resid 790 through 799
      removed outlier: 3.778A  pdb=" N   ASP A 796 " --> pdb=" O   ASP A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 835
      removed outlier: 4.163A  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 880
      removed outlier: 3.712A  pdb=" N   MET A 880 " --> pdb=" O   ALA A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 889
    Processing helix  chain 'A' and resid 894 through 917
      removed outlier: 3.798A  pdb=" N   GLU A 899 " --> pdb=" O   GLU A 895 " (cutoff:3.500A)
      Proline residue:  A 913  - end of helix
    Processing helix  chain 'A' and resid 919 through 924
    Processing helix  chain 'A' and resid 924 through 930
    Processing helix  chain 'A' and resid 930 through 946
    Processing helix  chain 'A' and resid 946 through 951
      removed outlier: 3.785A  pdb=" N   TYR A 950 " --> pdb=" O   PHE A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 964
    Processing helix  chain 'A' and resid 964 through 972
    Processing helix  chain 'A' and resid 975 through 979
    Processing helix  chain 'A' and resid 980 through 985
    Processing helix  chain 'A' and resid 986 through 996
    Processing helix  chain 'A' and resid 1004 through 1017
      removed outlier: 3.560A  pdb=" N   ASP A1008 " --> pdb=" O   PHE A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1023
      removed outlier: 3.826A  pdb=" N   GLN A1022 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 314
    Processing helix  chain 'C' and resid 419 through 443
      removed outlier: 4.334A  pdb=" N   GLN C 423 " --> pdb=" O   THR C 419 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   HIS C 425 " --> pdb=" O   ARG C 421 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   ASP C 429 " --> pdb=" O   HIS C 425 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   LEU C 430 " --> pdb=" O   ARG C 426 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLY C 443 " --> pdb=" O   GLU C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 460
      removed outlier: 3.609A  pdb=" N   THR C 452 " --> pdb=" O   SER C 448 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   PHE C 454 " --> pdb=" O   CYS C 450 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   LEU C 455 " --> pdb=" O   LEU C 451 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   LEU C 456 " --> pdb=" O   THR C 452 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ALA C 457 " --> pdb=" O   LEU C 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 464 through 473
      removed outlier: 4.161A  pdb=" N   MET C 473 " --> pdb=" O   GLU C 469 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 482 through 494
    Processing helix  chain 'C' and resid 496 through 510
    Processing helix  chain 'C' and resid 518 through 524
      removed outlier: 3.529A  pdb=" N   LEU C 522 " --> pdb=" O   PRO C 518 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 577 through 589
    Processing helix  chain 'C' and resid 589 through 601
    Processing helix  chain 'C' and resid 686 through 705
      removed outlier: 3.821A  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 738
    Processing helix  chain 'C' and resid 757 through 762
    Processing helix  chain 'C' and resid 771 through 785
    Processing helix  chain 'C' and resid 790 through 798
    Processing helix  chain 'C' and resid 814 through 835
      removed outlier: 3.684A  pdb=" N   CYS C 818 " --> pdb=" O   ASP C 814 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLY C 835 " --> pdb=" O   GLN C 831 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 844 through 862
    Processing helix  chain 'C' and resid 872 through 881
      removed outlier: 3.960A  pdb=" N   THR C 881 " --> pdb=" O   ARG C 877 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 881 through 890
      removed outlier: 3.737A  pdb=" N   ALA C 887 " --> pdb=" O   GLU C 883 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL C 888 " --> pdb=" O   ALA C 884 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 917
      removed outlier: 3.668A  pdb=" N   LEU C 902 " --> pdb=" O   ARG C 898 " (cutoff:3.500A)
      Proline residue:  C 913  - end of helix
    Processing helix  chain 'C' and resid 919 through 924
    Processing helix  chain 'C' and resid 924 through 930
      removed outlier: 3.571A  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 946 through 951
      removed outlier: 3.684A  pdb=" N   TYR C 950 " --> pdb=" O   PHE C 946 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 955 through 964
    Processing helix  chain 'C' and resid 964 through 973
    Processing helix  chain 'C' and resid 980 through 985
    Processing helix  chain 'C' and resid 986 through 993
    Processing helix  chain 'C' and resid 1001 through 1018
      removed outlier: 4.729A  pdb=" N   LEU C1006 " --> pdb=" O   LYS C1002 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   GLU C1007 " --> pdb=" O   THR C1003 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1018 through 1027
      removed outlier: 3.786A  pdb=" N   GLN C1022 " --> pdb=" O   SER C1018 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE C1024 " --> pdb=" O   TYR C1020 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ALA C1027 " --> pdb=" O   LYS C1023 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 314
    Processing sheet with id=A, first strand: chain 'A' and resid 536 through 539
      removed outlier: 6.657A  pdb=" N   THR A 612 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ILE A 649 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A 614 " --> pdb=" O   MET A 647 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL A 640 " --> pdb=" O   LEU A 679 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU A 679 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   PHE A 642 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 536 through 539
      removed outlier: 6.657A  pdb=" N   THR A 612 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ILE A 649 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A 614 " --> pdb=" O   MET A 647 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   MET A 647 " --> pdb=" O   GLN A 664 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLN A 664 " --> pdb=" O   MET A 647 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ILE A 649 " --> pdb=" O   ILE A 662 " (cutoff:3.500A)
    Processing sheet with id=C, first strand: chain 'B' and resid 2 through 6
      removed outlier: 3.739A  pdb=" N   PHE B 345 " --> pdb=" O   LEU B   6 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   THR B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'B' and resid 20 through 23
      removed outlier: 4.471A  pdb=" N   VAL B  28 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=E, first strand: chain 'B' and resid 61 through 62
      removed outlier: 6.742A  pdb=" N   SER B  61 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 8.506A  pdb=" N   CYS B 124 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   THR B 121 " --> pdb=" O   ASP B 112 " (cutoff:3.500A)
    Processing sheet with id=F, first strand: chain 'B' and resid 141 through 147
    Processing sheet with id=G, first strand: chain 'B' and resid 159 through 161
    Processing sheet with id=H, first strand: chain 'B' and resid 209 through 212
    Processing sheet with id=I, first strand: chain 'B' and resid 263 through 265
    Processing sheet with id=J, first strand: chain 'C' and resid 536 through 539
      removed outlier: 6.494A  pdb=" N   THR C 612 " --> pdb=" O   ILE C 649 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ILE C 649 " --> pdb=" O   THR C 612 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL C 614 " --> pdb=" O   MET C 647 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   VAL C 640 " --> pdb=" O   LEU C 679 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   LEU C 679 " --> pdb=" O   VAL C 640 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE C 642 " --> pdb=" O   LEU C 677 " (cutoff:3.500A)
    Processing sheet with id=K, first strand: chain 'C' and resid 536 through 539
      removed outlier: 6.494A  pdb=" N   THR C 612 " --> pdb=" O   ILE C 649 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ILE C 649 " --> pdb=" O   THR C 612 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL C 614 " --> pdb=" O   MET C 647 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   MET C 647 " --> pdb=" O   GLN C 664 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLN C 664 " --> pdb=" O   MET C 647 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ILE C 649 " --> pdb=" O   ILE C 662 " (cutoff:3.500A)
    Processing sheet with id=L, first strand: chain 'D' and resid 2 through 6
      removed outlier: 3.770A  pdb=" N   PHE D 345 " --> pdb=" O   LEU D   6 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   THR D 326 " --> pdb=" O   LEU D 322 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE D 318 " --> pdb=" O   ALA D 330 " (cutoff:3.500A)
    Processing sheet with id=M, first strand: chain 'D' and resid 20 through 23
      removed outlier: 4.559A  pdb=" N   VAL D  28 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=N, first strand: chain 'D' and resid 76 through 80
      removed outlier: 4.480A  pdb=" N   LEU D 106 " --> pdb=" O   LYS D 127 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   THR D 121 " --> pdb=" O   ASP D 112 " (cutoff:3.500A)
    Processing sheet with id=O, first strand: chain 'D' and resid 96 through 97
      removed outlier: 3.669A  pdb=" N   GLU D 101 " --> pdb=" O   THR D  97 " (cutoff:3.500A)
    Processing sheet with id=P, first strand: chain 'D' and resid 141 through 147
    Processing sheet with id=Q, first strand: chain 'D' and resid 159 through 161
    Processing sheet with id=R, first strand: chain 'D' and resid 209 through 212
      removed outlier: 3.628A  pdb=" N   LEU D 233 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
    Processing sheet with id=S, first strand: chain 'D' and resid 263 through 265
      removed outlier: 4.195A  pdb=" N   CYS D 287 " --> pdb=" O   ARG D 302 " (cutoff:3.500A)

    721 hydrogen bonds defined for protein.
    2004 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      141 hydrogen bonds
      262 hydrogen bond angles
      0 basepair planarities
      59 basepair parallelities
      164 stacking parallelities
  Total time for adding SS restraints: 4.41

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2914
        1.32 -     1.45: 6824
        1.45 -     1.58: 10519
        1.58 -     1.71: 452
        1.71 -     1.84: 171
  Bond restraints: 20880
  Sorted by residual:
  bond pdb=" P    DT G  42 "
       pdb=" O5'  DT G  42 "
    ideal  model  delta    sigma   weight residual
    1.593  1.395  0.198 1.00e-02 1.00e+04 3.90e+02
  bond pdb=" C3'  DA H   2 "
       pdb=" O3'  DA H   2 "
    ideal  model  delta    sigma   weight residual
    1.435  1.684 -0.249 1.30e-02 5.92e+03 3.68e+02
  bond pdb=" C3'  DG G  45 "
       pdb=" O3'  DG G  45 "
    ideal  model  delta    sigma   weight residual
    1.435  1.659 -0.224 1.30e-02 5.92e+03 2.97e+02
  bond pdb=" C3'  DG H   5 "
       pdb=" O3'  DG H   5 "
    ideal  model  delta    sigma   weight residual
    1.435  1.659 -0.224 1.30e-02 5.92e+03 2.96e+02
  bond pdb=" N3   DC H   3 "
       pdb=" C4   DC H   3 "
    ideal  model  delta    sigma   weight residual
    1.335  1.444 -0.109 7.00e-03 2.04e+04 2.44e+02
  ... (remaining 20875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.86: 28808
        5.86 -    11.73: 319
       11.73 -    17.59: 26
       17.59 -    23.46: 5
       23.46 -    29.32: 1
  Bond angle restraints: 29159
  Sorted by residual:
  angle pdb=" N   ARG C 420 "
        pdb=" CA  ARG C 420 "
        pdb=" C   ARG C 420 "
      ideal   model   delta    sigma   weight residual
     111.33  131.50  -20.17 1.21e+00 6.83e-01 2.78e+02
  angle pdb=" N   ALA C 422 "
        pdb=" CA  ALA C 422 "
        pdb=" C   ALA C 422 "
      ideal   model   delta    sigma   weight residual
     113.43   92.89   20.54 1.26e+00 6.30e-01 2.66e+02
  angle pdb=" O4'  DC H   3 "
        pdb=" C1'  DC H   3 "
        pdb=" N1   DC H   3 "
      ideal   model   delta    sigma   weight residual
     108.00  116.86   -8.86 7.00e-01 2.04e+00 1.60e+02
  angle pdb=" N   ARG C 999 "
        pdb=" CA  ARG C 999 "
        pdb=" C   ARG C 999 "
      ideal   model   delta    sigma   weight residual
     111.07  124.38  -13.31 1.07e+00 8.73e-01 1.55e+02
  angle pdb=" N   ASP C 468 "
        pdb=" CA  ASP C 468 "
        pdb=" C   ASP C 468 "
      ideal   model   delta    sigma   weight residual
     111.14  123.22  -12.08 1.08e+00 8.57e-01 1.25e+02
  ... (remaining 29154 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.99: 10922
       35.99 -    71.98: 1038
       71.98 -   107.96: 33
      107.96 -   143.95: 3
      143.95 -   179.94: 4
  Dihedral angle restraints: 12000
    sinusoidal: 6384
      harmonic: 5616
  Sorted by residual:
  dihedral pdb=" CA  ASN A 462 "
           pdb=" C   ASN A 462 "
           pdb=" N   GLU A 463 "
           pdb=" CA  GLU A 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.75   40.25     0      5.00e+00 4.00e-02 6.48e+01
  dihedral pdb=" CA  ARG C 477 "
           pdb=" C   ARG C 477 "
           pdb=" N   GLY C 478 "
           pdb=" CA  GLY C 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.07  -33.93     0      5.00e+00 4.00e-02 4.60e+01
  dihedral pdb=" C   ARG C 421 "
           pdb=" N   ARG C 421 "
           pdb=" CA  ARG C 421 "
           pdb=" CB  ARG C 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.36   15.76     0      2.50e+00 1.60e-01 3.98e+01
  ... (remaining 11997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.152: 3008
       0.152 -    0.304: 165
       0.304 -    0.456: 13
       0.456 -    0.608: 4
       0.608 -    0.760: 2
  Chirality restraints: 3192
  Sorted by residual:
  chirality pdb=" CA  ARG C 421 "
            pdb=" N   ARG C 421 "
            pdb=" C   ARG C 421 "
            pdb=" CB  ARG C 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.75    0.76 2.00e-01 2.50e+01 1.44e+01
  chirality pdb=" P    DC H   3 "
            pdb=" OP1  DC H   3 "
            pdb=" OP2  DC H   3 "
            pdb=" O5'  DC H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -3.00   -0.67 2.00e-01 2.50e+01 1.11e+01
  chirality pdb=" CG  LEU A 451 "
            pdb=" CB  LEU A 451 "
            pdb=" CD1 LEU A 451 "
            pdb=" CD2 LEU A 451 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.16    0.57 2.00e-01 2.50e+01 8.19e+00
  ... (remaining 3189 not shown)

  Planarity restraints: 2994
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA H   2 "   -0.069 2.00e-02 2.50e+03   3.17e-02 2.77e+01
        pdb=" N9   DA H   2 "   -0.004 2.00e-02 2.50e+03
        pdb=" C8   DA H   2 "    0.049 2.00e-02 2.50e+03
        pdb=" N7   DA H   2 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA H   2 "    0.018 2.00e-02 2.50e+03
        pdb=" C6   DA H   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA H   2 "   -0.037 2.00e-02 2.50e+03
        pdb=" N1   DA H   2 "   -0.018 2.00e-02 2.50e+03
        pdb=" C2   DA H   2 "    0.008 2.00e-02 2.50e+03
        pdb=" N3   DA H   2 "    0.030 2.00e-02 2.50e+03
        pdb=" C4   DA H   2 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 450 "   -0.026 2.00e-02 2.50e+03   5.25e-02 2.76e+01
        pdb=" C   CYS A 450 "    0.091 2.00e-02 2.50e+03
        pdb=" O   CYS A 450 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   LEU A 451 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 480 "    0.024 2.00e-02 2.50e+03   4.68e-02 2.19e+01
        pdb=" C   GLY A 480 "   -0.081 2.00e-02 2.50e+03
        pdb=" O   GLY A 480 "    0.030 2.00e-02 2.50e+03
        pdb=" N   LEU A 481 "    0.027 2.00e-02 2.50e+03
  ... (remaining 2991 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 221
        2.56 -     3.15: 16056
        3.15 -     3.73: 32711
        3.73 -     4.32: 45489
        4.32 -     4.90: 70294
  Nonbonded interactions: 164771
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 119 "
            pdb=" OP1  DG J   6 "
     model   vdw
     1.977 3.120
  nonbonded pdb=" C3'  DT G  12 "
            pdb=" OP2  DT G  13 "
     model   vdw
     2.058 2.776
  nonbonded pdb=" OP1  DT G  42 "
            pdb=" C5'  DT G  42 "
     model   vdw
     2.060 2.752
  nonbonded pdb=" O2   DC E  15 "
            pdb=" N2   DG F  20 "
     model   vdw
     2.066 2.496
  nonbonded pdb=" NE2 GLN A 858 "
            pdb=" O   ALA A 887 "
     model   vdw
     2.101 3.120
  ... (remaining 164766 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'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

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=0.07 max=1.00 mean=0.99
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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     22.420
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
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      :  0.014   0.321  20886  Z= 1.106
  Angle     :  1.730  29.321  29159  Z= 1.169
  Chirality :  0.080   0.760   3192
  Planarity :  0.007   0.053   2994
  Dihedral  : 21.901 179.939   8388
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 22.64
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  5.57 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 12.04 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.57 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.37 (0.14), residues: 1938
  helix: -2.83 (0.15), residues: 613
  sheet: -0.91 (0.25), residues: 326
  loop : -2.29 (0.14), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.068   0.002   ARG C 459 
 TYR   0.025   0.003   TYR A 908 
 PHE   0.042   0.004   PHE C 454 
 TRP   0.026   0.003   TRP C 978 
 HIS   0.022   0.003   HIS A 414 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01356 /  1.10 (20880)
  covalent geometry    : angle       1.72996 /  1.17 (29159)
  hydrogen bonds       : bond        0.16922 / 11.38 (  810)
  hydrogen bonds       : angle      10.70707 /  7.47 ( 2266)
  metal coordination   : bond        0.22079 / 15.46 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  712 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 629
  time to evaluate  : 0.746 
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: 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  412 ARG cc_start: 0.4529 (ptt-90) cc_final: 0.3230 (tpm170)
REVERT: A  425 HIS cc_start: 0.8275 (t-90) cc_final: 0.7511 (m170)
REVERT: A  430 LEU cc_start: 0.8658 (mt) cc_final: 0.8177 (mt)
REVERT: A  432 ASN cc_start: 0.9136 (t0) cc_final: 0.8660 (t0)
REVERT: A  456 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.5833 (tt)
REVERT: A  524 ASN cc_start: 0.8994 (t0) cc_final: 0.8500 (t0)
REVERT: A  527 LYS cc_start: 0.9006 (mttm) cc_final: 0.7968 (tptt)
REVERT: A  572 ILE cc_start: 0.9567 (mt) cc_final: 0.9097 (tt)
REVERT: A  599 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7589 (tp30)
REVERT: A  664 GLN cc_start: 0.8135 (tt0) cc_final: 0.7835 (tp40)
REVERT: A  671 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8209 (mp0)
REVERT: A  690 LEU cc_start: 0.9605 (tp) cc_final: 0.9268 (tp)
REVERT: A  704 MET cc_start: 0.9277 (ttm) cc_final: 0.8918 (mtp)
REVERT: A  731 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7667 (mp0)
REVERT: A  801 VAL cc_start: 0.8965 (t) cc_final: 0.8649 (t)
REVERT: A  820 ILE cc_start: 0.9336 (mt) cc_final: 0.9101 (pt)
REVERT: A  863 MET cc_start: 0.8509 (mmp) cc_final: 0.8305 (mmm)
REVERT: A  905 MET cc_start: 0.8292 (tpp) cc_final: 0.7932 (tmm)
REVERT: A  911 MET cc_start: 0.9619 (ptm) cc_final: 0.8665 (mtm)
REVERT: A  947 LYS cc_start: 0.8857 (tttt) cc_final: 0.8483 (tppt)
REVERT: A  956 ASN cc_start: 0.9269 (m-40) cc_final: 0.8502 (m110)
REVERT: A  960 LYS cc_start: 0.9231 (mttt) cc_final: 0.8519 (mmtm)
REVERT: A 1005 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8265 (pp20)
REVERT: A 1023 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8681 (tmtt)
REVERT: B   19 PHE cc_start: 0.9178 (p90) cc_final: 0.8866 (p90)
REVERT: B   64 ASN cc_start: 0.9280 (m-40) cc_final: 0.8962 (m-40)
REVERT: B  109 LEU cc_start: 0.9210 (tt) cc_final: 0.8918 (mm)
REVERT: B  146 ASN cc_start: 0.7170 (m-40) cc_final: 0.6837 (t0)
REVERT: B  162 MET cc_start: 0.8905 (mtt) cc_final: 0.8527 (ptp)
REVERT: B  173 ASN cc_start: 0.8850 (t0) cc_final: 0.8528 (t0)
REVERT: B  199 GLU cc_start: 0.8795 (mm-30) cc_final: 0.7553 (tt0)
REVERT: B  213 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7826 (pp30)
REVERT: B  214 ASP cc_start: 0.7607 (p0) cc_final: 0.6461 (p0)
REVERT: B  266 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.5403 (mt)
REVERT: B  273 ILE cc_start: 0.8697 (mm) cc_final: 0.8273 (tp)
REVERT: B  289 TYR cc_start: 0.7972 (t80) cc_final: 0.7766 (t80)
REVERT: B  317 TRP cc_start: 0.7954 (p-90) cc_final: 0.7652 (p-90)
REVERT: B  334 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7680 (tp30)
REVERT: B  347 GLN cc_start: 0.8390 (tt0) cc_final: 0.8135 (tm-30)
REVERT: C  421 ARG cc_start: 0.3170 (OUTLIER) cc_final: 0.1613 (tmm-80)
REVERT: C  455 LEU cc_start: 0.7973 (mp) cc_final: 0.7465 (tp)
REVERT: C  489 ILE cc_start: 0.9018 (mt) cc_final: 0.8785 (mm)
REVERT: C  543 LYS cc_start: 0.8785 (mttt) cc_final: 0.8531 (mmmm)
REVERT: C  545 VAL cc_start: 0.9249 (t) cc_final: 0.8785 (t)
REVERT: C  578 TYR cc_start: 0.8483 (t80) cc_final: 0.8056 (t80)
REVERT: C  594 MET cc_start: 0.8643 (mmm) cc_final: 0.8016 (mtp)
REVERT: C  620 ASP cc_start: 0.9059 (t0) cc_final: 0.8072 (p0)
REVERT: C  622 MET cc_start: 0.7819 (ttp) cc_final: 0.7445 (ttm)
REVERT: C  649 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9078 (tt)
REVERT: C  669 ASN cc_start: 0.8759 (m-40) cc_final: 0.7768 (m-40)
REVERT: C  672 LEU cc_start: 0.9180 (mt) cc_final: 0.8976 (mm)
REVERT: C  677 LEU cc_start: 0.9420 (tt) cc_final: 0.9134 (tp)
REVERT: C  679 LEU cc_start: 0.9318 (mp) cc_final: 0.8875 (mp)
REVERT: C  686 ASP cc_start: 0.8338 (p0) cc_final: 0.7679 (p0)
REVERT: C  698 VAL cc_start: 0.9260 (t) cc_final: 0.8943 (p)
REVERT: C  712 SER cc_start: 0.8996 (p) cc_final: 0.8755 (m)
REVERT: C  730 ASP cc_start: 0.8992 (p0) cc_final: 0.8270 (m-30)
REVERT: C  732 LYS cc_start: 0.9008 (tttt) cc_final: 0.8665 (ttmm)
REVERT: C  831 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8704 (tp40)
REVERT: C  868 VAL cc_start: 0.8399 (m) cc_final: 0.8060 (m)
REVERT: C  871 MET cc_start: 0.8124 (ttp) cc_final: 0.7732 (ttp)
REVERT: C  896 GLU cc_start: 0.8473 (mp0) cc_final: 0.7927 (pm20)
REVERT: C  905 MET cc_start: 0.8214 (tpp) cc_final: 0.7789 (tmm)
REVERT: C  909 LEU cc_start: 0.8684 (mt) cc_final: 0.8333 (mt)
REVERT: C  915 TRP cc_start: 0.9156 (p-90) cc_final: 0.7851 (p-90)
REVERT: C  926 ASP cc_start: 0.9123 (p0) cc_final: 0.8861 (p0)
REVERT: C  983 ASN cc_start: 0.8914 (t0) cc_final: 0.8568 (t0)
REVERT: C  985 SER cc_start: 0.9500 (m) cc_final: 0.9211 (p)
REVERT: C  989 LEU cc_start: 0.9329 (mt) cc_final: 0.9058 (mt)
REVERT: C  995 LYS cc_start: 0.9442 (mtmm) cc_final: 0.9132 (mmtm)
REVERT: C 1005 GLU cc_start: 0.8769 (tt0) cc_final: 0.8472 (mt-10)
REVERT: C 1006 LEU cc_start: 0.8596 (mt) cc_final: 0.8214 (mp)
REVERT: C 1020 TYR cc_start: 0.8976 (t80) cc_final: 0.8766 (t80)
REVERT: D    1 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8177 (mtt)
REVERT: D   16 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7759 (pt0)
REVERT: D   29 TYR cc_start: 0.8493 (m-80) cc_final: 0.8219 (m-80)
REVERT: D   60 ILE cc_start: 0.9276 (mm) cc_final: 0.8934 (mt)
REVERT: D   69 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7772 (mt)
REVERT: D  148 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7322 (ptt90)
REVERT: D  162 MET cc_start: 0.8847 (tpt) cc_final: 0.8556 (tpp)
REVERT: D  188 GLU cc_start: 0.7841 (tp30) cc_final: 0.7585 (mm-30)
REVERT: D  217 TYR cc_start: 0.8477 (m-80) cc_final: 0.8221 (m-10)
REVERT: D  293 ASP cc_start: 0.9193 (t0) cc_final: 0.8912 (t70)
REVERT: D  303 GLU cc_start: 0.8551 (tt0) cc_final: 0.8299 (tm-30)
REVERT: D  310 GLU cc_start: 0.8474 (tt0) cc_final: 0.8227 (tp30)
  outliers start: 83
  outliers final: 11
  residues processed: 679
  average time/residue: 0.1616
  time to fit residues: 160.5350
Evaluate side-chains
  361 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 338
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 200 optimal weight:    5.9990
   chunk 212 optimal weight:    9.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    3.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 766 HIS
A 822 ASN
** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 ASN
B 173 ASN
B 278 GLN
C 423 GLN
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 170 GLN
D 278 GLN
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.089249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073114 restraints weight = 90070.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.075124 restraints weight = 49589.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.076455 restraints weight = 31477.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.077277 restraints weight = 22338.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.077882 restraints weight = 17569.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       67 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 22 (27 function evaluations)
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  20886  Z= 0.237
  Angle     :  0.947  12.933  29159  Z= 0.524
  Chirality :  0.052   0.408   3192
  Planarity :  0.007   0.083   2994
  Dihedral  : 24.821 179.690   4568
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 21.47
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.72 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.76 %
    Favored  : 95.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -1.77 (0.16), residues: 1938
  helix: -1.05 (0.18), residues: 615
  sheet: -0.23 (0.25), residues: 337
  loop : -1.57 (0.17), residues: 986

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.037   0.001   ARG C 421 
 TYR   0.019   0.002   TYR C 908 
 PHE   0.025   0.002   PHE A 830 
 TRP   0.015   0.002   TRP B 172 
 HIS   0.010   0.002   HIS A 414 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.24 (20880)
  covalent geometry    : angle       0.94720 /  0.52 (29159)
  hydrogen bonds       : bond        0.06905 /  4.63 (  810)
  hydrogen bonds       : angle       6.33509 /  4.44 ( 2266)
  metal coordination   : bond        0.01097 /  0.75 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  439 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 436
  time to evaluate  : 0.580 
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: symmetry clash
REVERT: A  412 ARG cc_start: 0.4117 (ptt-90) cc_final: 0.3351 (tpm170)
REVERT: A  418 LEU cc_start: 0.6823 (mm) cc_final: 0.6485 (mm)
REVERT: A  430 LEU cc_start: 0.8432 (mt) cc_final: 0.8132 (mt)
REVERT: A  572 ILE cc_start: 0.9622 (mt) cc_final: 0.9021 (tt)
REVERT: A  599 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7167 (tp30)
REVERT: A  672 LEU cc_start: 0.9088 (mt) cc_final: 0.8495 (mt)
REVERT: A  688 GLU cc_start: 0.8002 (mm-30) cc_final: 0.6503 (mt-10)
REVERT: A  704 MET cc_start: 0.8387 (ttm) cc_final: 0.8032 (ttm)
REVERT: A  705 MET cc_start: 0.8157 (mmm) cc_final: 0.7228 (mmt)
REVERT: A  826 PHE cc_start: 0.9060 (m-10) cc_final: 0.8673 (m-10)
REVERT: A  911 MET cc_start: 0.9119 (ptm) cc_final: 0.8765 (ptt)
REVERT: A  955 THR cc_start: 0.7942 (t) cc_final: 0.7727 (t)
REVERT: A  960 LYS cc_start: 0.9279 (mttt) cc_final: 0.8937 (tttt)
REVERT: A 1005 GLU cc_start: 0.8481 (pt0) cc_final: 0.7775 (pp20)
REVERT: A 1006 LEU cc_start: 0.8886 (tp) cc_final: 0.8533 (tp)
REVERT: B   19 PHE cc_start: 0.9245 (p90) cc_final: 0.8694 (p90)
REVERT: B   46 PHE cc_start: 0.8285 (m-80) cc_final: 0.7918 (m-80)
REVERT: B   64 ASN cc_start: 0.9273 (m-40) cc_final: 0.8875 (m-40)
REVERT: B   92 ILE cc_start: 0.8750 (mp) cc_final: 0.8497 (mp)
REVERT: B  124 CYS cc_start: 0.7701 (t) cc_final: 0.7403 (t)
REVERT: B  198 PRO cc_start: 0.8673 (Cg_exo) cc_final: 0.8354 (Cg_endo)
REVERT: B  199 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7515 (tt0)
REVERT: B  317 TRP cc_start: 0.7714 (p-90) cc_final: 0.7448 (p-90)
REVERT: B  344 HIS cc_start: 0.6785 (m-70) cc_final: 0.6494 (m-70)
REVERT: C  424 LYS cc_start: 0.7728 (mttt) cc_final: 0.6918 (ptmt)
REVERT: C  455 LEU cc_start: 0.7827 (mp) cc_final: 0.7383 (tp)
REVERT: C  594 MET cc_start: 0.8422 (mmm) cc_final: 0.8129 (mtp)
REVERT: C  620 ASP cc_start: 0.7967 (t0) cc_final: 0.7348 (t0)
REVERT: C  649 ILE cc_start: 0.9148 (tt) cc_final: 0.8850 (tp)
REVERT: C  672 LEU cc_start: 0.9049 (mt) cc_final: 0.8840 (mm)
REVERT: C  677 LEU cc_start: 0.8906 (tt) cc_final: 0.8544 (tp)
REVERT: C  688 GLU cc_start: 0.8561 (pm20) cc_final: 0.8287 (pm20)
REVERT: C  753 ASP cc_start: 0.8799 (m-30) cc_final: 0.8092 (m-30)
REVERT: C  812 THR cc_start: 0.8623 (t) cc_final: 0.8411 (t)
REVERT: C  896 GLU cc_start: 0.8233 (mp0) cc_final: 0.7701 (pm20)
REVERT: C  909 LEU cc_start: 0.8328 (mt) cc_final: 0.7913 (mt)
REVERT: C  915 TRP cc_start: 0.9003 (p-90) cc_final: 0.7987 (p-90)
REVERT: C  926 ASP cc_start: 0.8330 (p0) cc_final: 0.7987 (p0)
REVERT: C  938 PHE cc_start: 0.8980 (t80) cc_final: 0.8245 (t80)
REVERT: C  983 ASN cc_start: 0.8075 (t0) cc_final: 0.7505 (t0)
REVERT: C  989 LEU cc_start: 0.8900 (mt) cc_final: 0.8571 (mt)
REVERT: C  995 LYS cc_start: 0.9096 (mttp) cc_final: 0.8829 (mmtm)
REVERT: C 1007 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7889 (mt-10)
REVERT: D   55 LEU cc_start: 0.9307 (tt) cc_final: 0.9001 (pp)
REVERT: D   60 ILE cc_start: 0.9243 (mm) cc_final: 0.8911 (mt)
REVERT: D  317 TRP cc_start: 0.7673 (p-90) cc_final: 0.7463 (p-90)
  outliers start: 3
  outliers final: 2
  residues processed: 439
  average time/residue: 0.1543
  time to fit residues: 102.2472
Evaluate side-chains
  285 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 283
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 174 optimal weight:    6.9990
   chunk 113 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 160 optimal weight:    3.9990
   chunk 147 optimal weight:    6.9990
   chunk 82 optimal weight:   40.0000
   chunk 73 optimal weight:    0.7980
   chunk 77 optimal weight:   10.0000
   chunk 177 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 629 HIS
A 817 HIS
A 831 GLN
** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1000 GLN
B 117 ASN
B 204 GLN
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 910 GLN
C 959 HIS
D 237 HIS
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.087855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.071315 restraints weight = 91827.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.073335 restraints weight = 50266.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.074684 restraints weight = 31977.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.075551 restraints weight = 22679.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.076053 restraints weight = 17727.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       67 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (14 function evaluations)
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.900  20886  Z= 0.288
  Angle     :  0.834  10.753  29159  Z= 0.463
  Chirality :  0.048   0.341   3192
  Planarity :  0.007   0.090   2994
  Dihedral  : 24.819 179.103   4568
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.18 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.82 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.34 (0.17), residues: 1938
  helix: -0.65 (0.19), residues: 616
  sheet:  0.04 (0.26), residues: 329
  loop : -1.34 (0.18), residues: 993

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG C 421 
 TYR   0.030   0.002   TYR D  90 
 PHE   0.017   0.002   PHE A 830 
 TRP   0.022   0.002   TRP B 172 
 HIS   0.007   0.002   HIS A 534 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.20 (20880)
  covalent geometry    : angle       0.83415 /  0.46 (29159)
  hydrogen bonds       : bond        0.06129 /  4.05 (  810)
  hydrogen bonds       : angle       5.87868 /  4.13 ( 2266)
  metal coordination   : bond        0.36770 / 33.45 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 373
  time to evaluate  : 0.688 
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: A  412 ARG cc_start: 0.4250 (ptt-90) cc_final: 0.3334 (tpm170)
REVERT: A  418 LEU cc_start: 0.7010 (mm) cc_final: 0.6480 (mm)
REVERT: A  430 LEU cc_start: 0.8389 (mt) cc_final: 0.8128 (mt)
REVERT: A  527 LYS cc_start: 0.8564 (mttm) cc_final: 0.7730 (tptt)
REVERT: A  565 ASP cc_start: 0.8029 (p0) cc_final: 0.7607 (p0)
REVERT: A  572 ILE cc_start: 0.9663 (mt) cc_final: 0.9149 (tt)
REVERT: A  599 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7111 (tp30)
REVERT: A  818 CYS cc_start: 0.9401 (t) cc_final: 0.9044 (t)
REVERT: A  851 TRP cc_start: 0.8574 (m-10) cc_final: 0.8073 (m-10)
REVERT: A  911 MET cc_start: 0.8955 (ptm) cc_final: 0.8703 (ptt)
REVERT: A  955 THR cc_start: 0.8003 (t) cc_final: 0.7711 (t)
REVERT: A  957 TYR cc_start: 0.9239 (m-80) cc_final: 0.8651 (m-80)
REVERT: A  960 LYS cc_start: 0.9206 (mttt) cc_final: 0.8989 (tttt)
REVERT: A 1005 GLU cc_start: 0.8655 (pt0) cc_final: 0.8422 (pt0)
REVERT: B   19 PHE cc_start: 0.9194 (p90) cc_final: 0.8617 (p90)
REVERT: B   21 LEU cc_start: 0.8331 (mm) cc_final: 0.8119 (mm)
REVERT: B   46 PHE cc_start: 0.8020 (m-80) cc_final: 0.7771 (m-80)
REVERT: B   64 ASN cc_start: 0.9273 (m-40) cc_final: 0.8841 (m-40)
REVERT: B   92 ILE cc_start: 0.8742 (mp) cc_final: 0.8349 (mp)
REVERT: B  124 CYS cc_start: 0.7549 (t) cc_final: 0.7345 (t)
REVERT: B  150 LYS cc_start: 0.8358 (mppt) cc_final: 0.8087 (mppt)
REVERT: B  317 TRP cc_start: 0.7886 (p-90) cc_final: 0.7619 (p-90)
REVERT: C  424 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7626 (pttt)
REVERT: C  455 LEU cc_start: 0.7758 (mp) cc_final: 0.7296 (tp)
REVERT: C  495 LEU cc_start: 0.8760 (mt) cc_final: 0.8356 (mt)
REVERT: C  594 MET cc_start: 0.8237 (mmm) cc_final: 0.8010 (mtp)
REVERT: C  620 ASP cc_start: 0.8545 (t0) cc_final: 0.8098 (t0)
REVERT: C  649 ILE cc_start: 0.9041 (tt) cc_final: 0.8774 (tt)
REVERT: C  672 LEU cc_start: 0.9082 (mt) cc_final: 0.8761 (mt)
REVERT: C  677 LEU cc_start: 0.8928 (tt) cc_final: 0.8635 (tp)
REVERT: C  733 MET cc_start: 0.8505 (mmm) cc_final: 0.8066 (mmm)
REVERT: C  896 GLU cc_start: 0.8175 (mp0) cc_final: 0.7592 (pm20)
REVERT: C  915 TRP cc_start: 0.8958 (p-90) cc_final: 0.8015 (p-90)
REVERT: C  926 ASP cc_start: 0.8278 (p0) cc_final: 0.8002 (p0)
REVERT: C  938 PHE cc_start: 0.8811 (t80) cc_final: 0.8290 (t80)
REVERT: C  983 ASN cc_start: 0.8093 (t0) cc_final: 0.7651 (t0)
REVERT: D    7 THR cc_start: 0.8843 (p) cc_final: 0.8321 (t)
REVERT: D   55 LEU cc_start: 0.9322 (tt) cc_final: 0.9112 (pp)
REVERT: D   91 LEU cc_start: 0.8790 (mm) cc_final: 0.8580 (mm)
REVERT: D  108 MET cc_start: 0.7408 (tpt) cc_final: 0.7163 (tpt)
REVERT: D  289 TYR cc_start: 0.9036 (t80) cc_final: 0.8775 (t80)
REVERT: D  317 TRP cc_start: 0.7690 (p-90) cc_final: 0.7272 (p-90)
REVERT: D  318 PHE cc_start: 0.7608 (p90) cc_final: 0.7335 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 375
  average time/residue: 0.1505
  time to fit residues: 85.7997
Evaluate side-chains
  272 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 164 optimal weight:    3.9990
   chunk 147 optimal weight:    6.9990
   chunk 207 optimal weight:   50.0000
   chunk 47 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 208 optimal weight:   40.0000
   chunk 157 optimal weight:    7.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 414 HIS
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 HIS
B 222 HIS
C 423 GLN
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 831 GLN
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 344 HIS
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.086284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.069831 restraints weight = 90002.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.071825 restraints weight = 49617.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.073165 restraints weight = 31728.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.074071 restraints weight = 22535.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.074671 restraints weight = 17497.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3431
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  20886  Z= 0.212
  Angle     :  0.814  10.482  29159  Z= 0.454
  Chirality :  0.048   0.314   3192
  Planarity :  0.006   0.079   2994
  Dihedral  : 24.889 179.259   4568
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.59 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.23 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.23 (0.17), residues: 1938
  helix: -0.56 (0.19), residues: 620
  sheet:  0.38 (0.28), residues: 295
  loop : -1.33 (0.18), residues: 1023

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG A 675 
 TYR   0.027   0.002   TYR A 827 
 PHE   0.027   0.002   PHE A 946 
 TRP   0.041   0.002   TRP A1014 
 HIS   0.007   0.002   HIS C 959 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.21 (20880)
  covalent geometry    : angle       0.81386 /  0.45 (29159)
  hydrogen bonds       : bond        0.05745 /  3.78 (  810)
  hydrogen bonds       : angle       5.63535 /  3.96 ( 2266)
  metal coordination   : bond        0.01695 /  1.62 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 336
  time to evaluate  : 0.655 
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: A  418 LEU cc_start: 0.7107 (mm) cc_final: 0.6898 (mm)
REVERT: A  430 LEU cc_start: 0.8400 (mt) cc_final: 0.8092 (mt)
REVERT: A  431 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7960 (tppt)
REVERT: A  565 ASP cc_start: 0.8092 (p0) cc_final: 0.7726 (p0)
REVERT: A  572 ILE cc_start: 0.9664 (mt) cc_final: 0.9134 (tt)
REVERT: A  599 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7117 (tp30)
REVERT: A  818 CYS cc_start: 0.9499 (t) cc_final: 0.9117 (t)
REVERT: A  851 TRP cc_start: 0.8639 (m-10) cc_final: 0.7911 (m-10)
REVERT: A  872 ASN cc_start: 0.9015 (p0) cc_final: 0.8811 (p0)
REVERT: A  911 MET cc_start: 0.8996 (ptm) cc_final: 0.8762 (ptt)
REVERT: A  957 TYR cc_start: 0.9281 (m-80) cc_final: 0.8843 (m-80)
REVERT: A  960 LYS cc_start: 0.9364 (mttt) cc_final: 0.9087 (tttt)
REVERT: B   46 PHE cc_start: 0.8102 (m-80) cc_final: 0.7729 (m-80)
REVERT: B   64 ASN cc_start: 0.9303 (m-40) cc_final: 0.8874 (m-40)
REVERT: B   92 ILE cc_start: 0.8862 (mp) cc_final: 0.8617 (mp)
REVERT: B  173 ASN cc_start: 0.8340 (t0) cc_final: 0.7992 (t0)
REVERT: B  222 HIS cc_start: 0.8430 (t-90) cc_final: 0.8155 (t70)
REVERT: B  317 TRP cc_start: 0.7952 (p-90) cc_final: 0.7708 (p-90)
REVERT: C  421 ARG cc_start: 0.2275 (OUTLIER) cc_final: 0.1409 (ttm-80)
REVERT: C  455 LEU cc_start: 0.7783 (mp) cc_final: 0.7339 (tp)
REVERT: C  474 MET cc_start: 0.8381 (mmp) cc_final: 0.7369 (ppp)
REVERT: C  495 LEU cc_start: 0.8737 (mt) cc_final: 0.8506 (mt)
REVERT: C  555 ASP cc_start: 0.7870 (m-30) cc_final: 0.7558 (m-30)
REVERT: C  594 MET cc_start: 0.8353 (mmm) cc_final: 0.8131 (mtp)
REVERT: C  611 PHE cc_start: 0.8138 (m-80) cc_final: 0.7929 (m-80)
REVERT: C  620 ASP cc_start: 0.8337 (t0) cc_final: 0.7605 (t0)
REVERT: C  647 MET cc_start: 0.8585 (mtp) cc_final: 0.8029 (mtp)
REVERT: C  672 LEU cc_start: 0.9136 (mt) cc_final: 0.8881 (mt)
REVERT: C  677 LEU cc_start: 0.9015 (tt) cc_final: 0.8665 (tp)
REVERT: C  704 MET cc_start: 0.8231 (ptp) cc_final: 0.7799 (ptp)
REVERT: C  879 LEU cc_start: 0.9293 (tp) cc_final: 0.9091 (tp)
REVERT: C  915 TRP cc_start: 0.8898 (p-90) cc_final: 0.7974 (p-90)
REVERT: C  926 ASP cc_start: 0.8411 (p0) cc_final: 0.8141 (p0)
REVERT: C  938 PHE cc_start: 0.8889 (t80) cc_final: 0.8472 (t80)
REVERT: C  983 ASN cc_start: 0.8138 (t0) cc_final: 0.7791 (t0)
REVERT: D    1 MET cc_start: 0.7596 (mpp) cc_final: 0.7317 (mtt)
REVERT: D    7 THR cc_start: 0.8805 (p) cc_final: 0.8300 (t)
REVERT: D   55 LEU cc_start: 0.9405 (tt) cc_final: 0.9183 (pp)
REVERT: D  317 TRP cc_start: 0.7627 (p-90) cc_final: 0.7181 (p-90)
REVERT: D  318 PHE cc_start: 0.7695 (p90) cc_final: 0.7177 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 338
  average time/residue: 0.1400
  time to fit residues: 73.3970
Evaluate side-chains
  251 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 133 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 167 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 57 optimal weight:   20.0000
   chunk 212 optimal weight:   50.0000
   chunk 131 optimal weight:    0.4980
   chunk 115 optimal weight:    7.9990
   overall best weight:    5.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 GLN
A 822 ASN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 858 GLN
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.084639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.068178 restraints weight = 91056.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.070086 restraints weight = 50626.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.071323 restraints weight = 32464.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.072220 restraints weight = 23492.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.072817 restraints weight = 18428.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.5370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  20886  Z= 0.227
  Angle     :  0.815  10.703  29159  Z= 0.454
  Chirality :  0.047   0.291   3192
  Planarity :  0.006   0.074   2994
  Dihedral  : 24.933 178.426   4568
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 19.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.85 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.22 (0.18), residues: 1938
  helix: -0.54 (0.20), residues: 620
  sheet:  0.33 (0.29), residues: 305
  loop : -1.34 (0.18), residues: 1013

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 735 
 TYR   0.026   0.002   TYR A 957 
 PHE   0.018   0.002   PHE A 479 
 TRP   0.044   0.003   TRP C 782 
 HIS   0.008   0.002   HIS A 687 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.23 (20880)
  covalent geometry    : angle       0.81529 /  0.45 (29159)
  hydrogen bonds       : bond        0.05651 /  3.74 (  810)
  hydrogen bonds       : angle       5.64833 /  4.00 ( 2266)
  metal coordination   : bond        0.00673 /  0.63 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.701 
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: A  418 LEU cc_start: 0.7179 (mm) cc_final: 0.6963 (mm)
REVERT: A  431 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8039 (tppt)
REVERT: A  572 ILE cc_start: 0.9655 (mt) cc_final: 0.9203 (tt)
REVERT: A  575 ARG cc_start: 0.8455 (ptt90) cc_final: 0.7685 (ptm-80)
REVERT: A  872 ASN cc_start: 0.9058 (p0) cc_final: 0.8786 (p0)
REVERT: A  910 GLN cc_start: 0.9117 (mm110) cc_final: 0.8605 (mm-40)
REVERT: A  911 MET cc_start: 0.9087 (ptm) cc_final: 0.8762 (ptt)
REVERT: B   46 PHE cc_start: 0.8227 (m-80) cc_final: 0.7816 (m-80)
REVERT: B   64 ASN cc_start: 0.9163 (m-40) cc_final: 0.8760 (m-40)
REVERT: B   92 ILE cc_start: 0.8810 (mp) cc_final: 0.8584 (mp)
REVERT: B  124 CYS cc_start: 0.8290 (t) cc_final: 0.7969 (t)
REVERT: B  128 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7452 (tm-30)
REVERT: B  150 LYS cc_start: 0.8392 (mppt) cc_final: 0.8143 (mppt)
REVERT: B  162 MET cc_start: 0.6799 (ptt) cc_final: 0.6512 (ptt)
REVERT: B  173 ASN cc_start: 0.8552 (t0) cc_final: 0.8131 (t0)
REVERT: C  455 LEU cc_start: 0.8092 (mp) cc_final: 0.7678 (pp)
REVERT: C  474 MET cc_start: 0.8362 (mmp) cc_final: 0.7863 (ppp)
REVERT: C  495 LEU cc_start: 0.8800 (mt) cc_final: 0.8549 (mt)
REVERT: C  503 MET cc_start: 0.8479 (ptm) cc_final: 0.7904 (tmm)
REVERT: C  555 ASP cc_start: 0.8201 (m-30) cc_final: 0.7764 (m-30)
REVERT: C  589 LEU cc_start: 0.9172 (mm) cc_final: 0.8891 (tp)
REVERT: C  620 ASP cc_start: 0.7707 (t0) cc_final: 0.7480 (t0)
REVERT: C  672 LEU cc_start: 0.9281 (mt) cc_final: 0.9054 (mt)
REVERT: C  679 LEU cc_start: 0.9137 (mt) cc_final: 0.8899 (mt)
REVERT: C  689 THR cc_start: 0.9026 (m) cc_final: 0.8582 (p)
REVERT: C  777 GLU cc_start: 0.9110 (pt0) cc_final: 0.8894 (mp0)
REVERT: C  865 LEU cc_start: 0.9014 (mt) cc_final: 0.8756 (mt)
REVERT: C  915 TRP cc_start: 0.8952 (p-90) cc_final: 0.8107 (p-90)
REVERT: C  926 ASP cc_start: 0.8452 (p0) cc_final: 0.8194 (p0)
REVERT: C  938 PHE cc_start: 0.8903 (t80) cc_final: 0.8264 (t80)
REVERT: C  983 ASN cc_start: 0.8135 (t0) cc_final: 0.7915 (t0)
REVERT: C 1007 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7585 (mp0)
REVERT: D    7 THR cc_start: 0.8933 (p) cc_final: 0.8589 (t)
REVERT: D   91 LEU cc_start: 0.9086 (mm) cc_final: 0.8720 (mm)
REVERT: D  107 TYR cc_start: 0.8287 (m-80) cc_final: 0.7815 (m-80)
REVERT: D  108 MET cc_start: 0.7932 (tpt) cc_final: 0.7659 (tpt)
REVERT: D  289 TYR cc_start: 0.8887 (t80) cc_final: 0.8597 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.1353
  time to fit residues: 66.1814
Evaluate side-chains
  226 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 203 optimal weight:   40.0000
   chunk 9 optimal weight:   10.0000
   chunk 161 optimal weight:    0.7980
   chunk 145 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 147 optimal weight:    2.9990
   chunk 92 optimal weight:   30.0000
   chunk 156 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 ASN
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 817 HIS
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.086083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.069571 restraints weight = 89624.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071541 restraints weight = 49378.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.072841 restraints weight = 31520.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.073691 restraints weight = 22531.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.074251 restraints weight = 17727.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3424
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.5673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  20886  Z= 0.171
  Angle     :  0.764  11.284  29159  Z= 0.424
  Chirality :  0.046   0.282   3192
  Planarity :  0.006   0.077   2994
  Dihedral  : 24.907 178.824   4568
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.39 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.53 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    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: -1.11 (0.18), residues: 1938
  helix: -0.37 (0.20), residues: 626
  sheet:  0.53 (0.29), residues: 283
  loop : -1.33 (0.17), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 420 
 TYR   0.030   0.002   TYR A 957 
 PHE   0.020   0.002   PHE A 479 
 TRP   0.020   0.002   TRP A 538 
 HIS   0.006   0.001   HIS C 464 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.17 (20880)
  covalent geometry    : angle       0.76374 /  0.42 (29159)
  hydrogen bonds       : bond        0.05348 /  3.56 (  810)
  hydrogen bonds       : angle       5.30899 /  3.76 ( 2266)
  metal coordination   : bond        0.00520 /  0.51 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 307
  time to evaluate  : 0.656 
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: A  431 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7982 (tppt)
REVERT: A  572 ILE cc_start: 0.9643 (mt) cc_final: 0.9240 (tt)
REVERT: A  575 ARG cc_start: 0.8423 (ptt90) cc_final: 0.7611 (ptm-80)
REVERT: A  704 MET cc_start: 0.8781 (mmp) cc_final: 0.8533 (mmp)
REVERT: A  851 TRP cc_start: 0.8341 (m-10) cc_final: 0.7953 (m-90)
REVERT: A  872 ASN cc_start: 0.8986 (p0) cc_final: 0.8753 (p0)
REVERT: A  911 MET cc_start: 0.8981 (ptm) cc_final: 0.8743 (ptt)
REVERT: A  960 LYS cc_start: 0.9238 (tttt) cc_final: 0.9014 (tttt)
REVERT: B   46 PHE cc_start: 0.8097 (m-80) cc_final: 0.7704 (m-80)
REVERT: B   64 ASN cc_start: 0.9183 (m-40) cc_final: 0.8771 (m-40)
REVERT: B   92 ILE cc_start: 0.8742 (mp) cc_final: 0.8529 (mp)
REVERT: B  124 CYS cc_start: 0.8305 (t) cc_final: 0.7941 (t)
REVERT: B  128 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: B  150 LYS cc_start: 0.8344 (mppt) cc_final: 0.8117 (mppt)
REVERT: C  455 LEU cc_start: 0.8027 (mp) cc_final: 0.7643 (pp)
REVERT: C  474 MET cc_start: 0.8466 (mmp) cc_final: 0.7910 (ppp)
REVERT: C  495 LEU cc_start: 0.8789 (mt) cc_final: 0.8528 (mt)
REVERT: C  503 MET cc_start: 0.8365 (ptm) cc_final: 0.7766 (tmm)
REVERT: C  555 ASP cc_start: 0.8277 (m-30) cc_final: 0.7768 (m-30)
REVERT: C  672 LEU cc_start: 0.9192 (mt) cc_final: 0.8840 (mm)
REVERT: C  679 LEU cc_start: 0.9157 (mt) cc_final: 0.8954 (mt)
REVERT: C  794 LEU cc_start: 0.9251 (tp) cc_final: 0.8868 (tp)
REVERT: C  915 TRP cc_start: 0.8983 (p-90) cc_final: 0.8093 (p-90)
REVERT: C  926 ASP cc_start: 0.8323 (p0) cc_final: 0.8009 (p0)
REVERT: C  938 PHE cc_start: 0.8866 (t80) cc_final: 0.8500 (t80)
REVERT: C  943 SER cc_start: 0.8636 (m) cc_final: 0.8282 (p)
REVERT: D   91 LEU cc_start: 0.9056 (mm) cc_final: 0.8799 (mm)
REVERT: D  108 MET cc_start: 0.8175 (tpt) cc_final: 0.7825 (tpt)
REVERT: D  289 TYR cc_start: 0.8811 (t80) cc_final: 0.8597 (t80)
REVERT: D  317 TRP cc_start: 0.7919 (p-90) cc_final: 0.7675 (p-90)
REVERT: D  324 LYS cc_start: 0.8664 (mttp) cc_final: 0.8296 (mmmt)
  outliers start: 1
  outliers final: 0
  residues processed: 307
  average time/residue: 0.1417
  time to fit residues: 67.4430
Evaluate side-chains
  227 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 104 optimal weight:    0.8980
   chunk 131 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:   30.0000
   chunk 72 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 155 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   overall best weight:    3.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 ASN
B 204 GLN
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 HIS
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.085440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.068898 restraints weight = 89115.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.070863 restraints weight = 48823.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.072160 restraints weight = 31094.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.072974 restraints weight = 22243.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.073595 restraints weight = 17629.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3406
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       70 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.5929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  20886  Z= 0.182
  Angle     :  0.759   9.543  29159  Z= 0.421
  Chirality :  0.046   0.288   3192
  Planarity :  0.005   0.073   2994
  Dihedral  : 24.918 178.704   4568
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.01 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    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: -1.07 (0.18), residues: 1938
  helix: -0.29 (0.20), residues: 623
  sheet:  0.50 (0.29), residues: 285
  loop : -1.33 (0.18), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 420 
 TYR   0.024   0.002   TYR A 957 
 PHE   0.020   0.002   PHE A 479 
 TRP   0.022   0.002   TRP A 782 
 HIS   0.010   0.002   HIS A 959 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.18 (20880)
  covalent geometry    : angle       0.75929 /  0.42 (29159)
  hydrogen bonds       : bond        0.05448 /  3.66 (  810)
  hydrogen bonds       : angle       5.29143 /  3.76 ( 2266)
  metal coordination   : bond        0.01899 /  1.03 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.549 
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: A  418 LEU cc_start: 0.7328 (mm) cc_final: 0.7112 (mm)
REVERT: A  431 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8075 (tppt)
REVERT: A  572 ILE cc_start: 0.9657 (mt) cc_final: 0.9342 (tt)
REVERT: A  647 MET cc_start: 0.6601 (mmm) cc_final: 0.6284 (mmm)
REVERT: A  704 MET cc_start: 0.8802 (mmp) cc_final: 0.8533 (mmp)
REVERT: A  851 TRP cc_start: 0.8343 (m-10) cc_final: 0.7938 (m-90)
REVERT: A  872 ASN cc_start: 0.9110 (p0) cc_final: 0.8826 (p0)
REVERT: A  910 GLN cc_start: 0.9139 (mm110) cc_final: 0.8573 (mm-40)
REVERT: A  911 MET cc_start: 0.9123 (ptm) cc_final: 0.8766 (ptt)
REVERT: A  960 LYS cc_start: 0.9161 (tttt) cc_final: 0.8923 (tttt)
REVERT: B   46 PHE cc_start: 0.8218 (m-80) cc_final: 0.7754 (m-80)
REVERT: B   64 ASN cc_start: 0.9177 (m-40) cc_final: 0.8734 (m-40)
REVERT: B   92 ILE cc_start: 0.8712 (mp) cc_final: 0.8491 (mp)
REVERT: B  124 CYS cc_start: 0.8370 (t) cc_final: 0.8030 (t)
REVERT: B  128 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: C  455 LEU cc_start: 0.8097 (mp) cc_final: 0.7647 (pp)
REVERT: C  495 LEU cc_start: 0.8776 (mt) cc_final: 0.8525 (mt)
REVERT: C  555 ASP cc_start: 0.8177 (m-30) cc_final: 0.7618 (m-30)
REVERT: C  589 LEU cc_start: 0.9069 (mm) cc_final: 0.8784 (tp)
REVERT: C  640 VAL cc_start: 0.9209 (t) cc_final: 0.8876 (t)
REVERT: C  672 LEU cc_start: 0.9189 (mt) cc_final: 0.8859 (mm)
REVERT: C  679 LEU cc_start: 0.9159 (mt) cc_final: 0.8831 (mt)
REVERT: C  680 MET cc_start: 0.8491 (pmm) cc_final: 0.8087 (pmm)
REVERT: C  698 VAL cc_start: 0.9576 (p) cc_final: 0.9113 (p)
REVERT: C  915 TRP cc_start: 0.8983 (p-90) cc_final: 0.8136 (p-90)
REVERT: C  926 ASP cc_start: 0.8413 (p0) cc_final: 0.8116 (p0)
REVERT: C  938 PHE cc_start: 0.8892 (t80) cc_final: 0.8531 (t80)
REVERT: C  943 SER cc_start: 0.8617 (m) cc_final: 0.8284 (p)
REVERT: D   91 LEU cc_start: 0.9057 (mm) cc_final: 0.8774 (mm)
REVERT: D  108 MET cc_start: 0.8238 (tpt) cc_final: 0.7827 (tpt)
REVERT: D  184 LEU cc_start: 0.7849 (tp) cc_final: 0.7648 (tp)
REVERT: D  233 LEU cc_start: 0.8581 (mt) cc_final: 0.8350 (mt)
REVERT: D  324 LYS cc_start: 0.8691 (mttp) cc_final: 0.8289 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 300
  average time/residue: 0.1395
  time to fit residues: 65.6468
Evaluate side-chains
  216 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 169 optimal weight:   20.0000
   chunk 77 optimal weight:    6.9990
   chunk 82 optimal weight:    7.9990
   chunk 181 optimal weight:   30.0000
   chunk 30 optimal weight:    0.6980
   chunk 188 optimal weight:    9.9990
   chunk 54 optimal weight:    8.9990
   chunk 175 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   overall best weight:    5.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 ASN
** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.083832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.067401 restraints weight = 90454.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.069292 restraints weight = 50097.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.070577 restraints weight = 32004.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.071405 restraints weight = 22967.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.071954 restraints weight = 18162.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       70 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       70 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.6276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  20886  Z= 0.211
  Angle     :  0.780   9.081  29159  Z= 0.434
  Chirality :  0.046   0.316   3192
  Planarity :  0.006   0.078   2994
  Dihedral  : 24.973 177.559   4568
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.16 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.18), residues: 1938
  helix: -0.24 (0.20), residues: 621
  sheet:  0.37 (0.28), residues: 303
  loop : -1.35 (0.18), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 860 
 TYR   0.024   0.002   TYR A 957 
 PHE   0.019   0.002   PHE A 611 
 TRP   0.024   0.002   TRP A 538 
 HIS   0.009   0.002   HIS D 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.21 (20880)
  covalent geometry    : angle       0.77964 /  0.43 (29159)
  hydrogen bonds       : bond        0.05533 /  3.69 (  810)
  hydrogen bonds       : angle       5.34464 /  3.80 ( 2266)
  metal coordination   : bond        0.01383 /  0.84 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.665 
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: A  418 LEU cc_start: 0.7425 (mm) cc_final: 0.7178 (mm)
REVERT: A  527 LYS cc_start: 0.8683 (mttm) cc_final: 0.7695 (tptp)
REVERT: A  572 ILE cc_start: 0.9682 (mt) cc_final: 0.9398 (tt)
REVERT: A  688 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7897 (mm-30)
REVERT: A  704 MET cc_start: 0.8963 (mmp) cc_final: 0.8620 (mmp)
REVERT: A  872 ASN cc_start: 0.9095 (p0) cc_final: 0.8837 (p0)
REVERT: A  911 MET cc_start: 0.9111 (ptm) cc_final: 0.8812 (ptt)
REVERT: A  960 LYS cc_start: 0.9187 (tttt) cc_final: 0.8936 (tttt)
REVERT: B   46 PHE cc_start: 0.8250 (m-80) cc_final: 0.7871 (m-80)
REVERT: B   73 ARG cc_start: 0.6937 (mtm180) cc_final: 0.6470 (mtt180)
REVERT: B  124 CYS cc_start: 0.8109 (t) cc_final: 0.7860 (t)
REVERT: B  128 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7667 (tm-30)
REVERT: B  150 LYS cc_start: 0.8387 (mppt) cc_final: 0.8179 (mppt)
REVERT: B  222 HIS cc_start: 0.8374 (t-90) cc_final: 0.8074 (t70)
REVERT: C  428 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7253 (tpp80)
REVERT: C  455 LEU cc_start: 0.8070 (mp) cc_final: 0.7762 (pp)
REVERT: C  495 LEU cc_start: 0.8736 (mt) cc_final: 0.8494 (mt)
REVERT: C  555 ASP cc_start: 0.8277 (m-30) cc_final: 0.7714 (m-30)
REVERT: C  589 LEU cc_start: 0.9050 (mm) cc_final: 0.8794 (tp)
REVERT: C  611 PHE cc_start: 0.8689 (m-80) cc_final: 0.8422 (m-80)
REVERT: C  640 VAL cc_start: 0.9255 (t) cc_final: 0.8924 (t)
REVERT: C  672 LEU cc_start: 0.9276 (mt) cc_final: 0.8850 (mt)
REVERT: C  680 MET cc_start: 0.8798 (pmm) cc_final: 0.8413 (pmm)
REVERT: C  871 MET cc_start: 0.9025 (tmm) cc_final: 0.8142 (tmm)
REVERT: C  879 LEU cc_start: 0.9383 (tt) cc_final: 0.9165 (tp)
REVERT: C  915 TRP cc_start: 0.8994 (p-90) cc_final: 0.8216 (p-90)
REVERT: C  926 ASP cc_start: 0.8537 (p0) cc_final: 0.8161 (p0)
REVERT: C  938 PHE cc_start: 0.8920 (t80) cc_final: 0.8544 (t80)
REVERT: C  943 SER cc_start: 0.8501 (m) cc_final: 0.8262 (p)
REVERT: D   91 LEU cc_start: 0.9188 (mm) cc_final: 0.8788 (mm)
REVERT: D  108 MET cc_start: 0.8059 (tpt) cc_final: 0.7671 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1378
  time to fit residues: 62.4541
Evaluate side-chains
  201 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 160 optimal weight:    7.9990
   chunk 143 optimal weight:    0.8980
   chunk 141 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 125 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 169 optimal weight:    7.9990
   chunk 137 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 HIS
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.084950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.068466 restraints weight = 89345.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.070399 restraints weight = 49216.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071675 restraints weight = 31514.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.072553 restraints weight = 22598.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.072933 restraints weight = 17722.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       70 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.6449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  20886  Z= 0.178
  Angle     :  0.759  10.226  29159  Z= 0.421
  Chirality :  0.046   0.292   3192
  Planarity :  0.005   0.073   2994
  Dihedral  : 24.983 178.294   4568
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.16 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.18), residues: 1938
  helix: -0.14 (0.20), residues: 615
  sheet:  0.57 (0.30), residues: 283
  loop : -1.33 (0.18), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 232 
 TYR   0.021   0.002   TYR A 957 
 PHE   0.019   0.002   PHE D  62 
 TRP   0.053   0.002   TRP C 782 
 HIS   0.006   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.18 (20880)
  covalent geometry    : angle       0.75937 /  0.42 (29159)
  hydrogen bonds       : bond        0.05330 /  3.57 (  810)
  hydrogen bonds       : angle       5.22944 /  3.72 ( 2266)
  metal coordination   : bond        0.00432 /  0.42 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.722 
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: A  418 LEU cc_start: 0.7329 (mm) cc_final: 0.7044 (mm)
REVERT: A  466 GLN cc_start: 0.8912 (mp10) cc_final: 0.8567 (mp10)
REVERT: A  527 LYS cc_start: 0.8576 (mttm) cc_final: 0.7943 (tptp)
REVERT: A  565 ASP cc_start: 0.8339 (p0) cc_final: 0.8078 (p0)
REVERT: A  572 ILE cc_start: 0.9686 (mt) cc_final: 0.9446 (tt)
REVERT: A  704 MET cc_start: 0.8878 (mmp) cc_final: 0.8511 (mmp)
REVERT: A  851 TRP cc_start: 0.8263 (m-10) cc_final: 0.7964 (m-90)
REVERT: A  872 ASN cc_start: 0.9082 (p0) cc_final: 0.8870 (p0)
REVERT: A  911 MET cc_start: 0.9072 (ptm) cc_final: 0.8772 (ptt)
REVERT: A  960 LYS cc_start: 0.9189 (tttt) cc_final: 0.8947 (tttt)
REVERT: B   46 PHE cc_start: 0.8386 (m-80) cc_final: 0.7924 (m-80)
REVERT: B   64 ASN cc_start: 0.9101 (m-40) cc_final: 0.8834 (m-40)
REVERT: B   73 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6831 (mtm180)
REVERT: B  124 CYS cc_start: 0.8142 (t) cc_final: 0.7905 (t)
REVERT: B  128 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7594 (tm-30)
REVERT: B  222 HIS cc_start: 0.8425 (t-90) cc_final: 0.8095 (t70)
REVERT: C  428 ARG cc_start: 0.7627 (mmt90) cc_final: 0.7104 (tpp80)
REVERT: C  455 LEU cc_start: 0.8161 (mp) cc_final: 0.7852 (pp)
REVERT: C  495 LEU cc_start: 0.8742 (mt) cc_final: 0.8478 (mt)
REVERT: C  555 ASP cc_start: 0.8322 (m-30) cc_final: 0.7732 (m-30)
REVERT: C  589 LEU cc_start: 0.9089 (mm) cc_final: 0.8805 (tp)
REVERT: C  640 VAL cc_start: 0.9226 (t) cc_final: 0.8869 (t)
REVERT: C  672 LEU cc_start: 0.9237 (mt) cc_final: 0.8796 (mt)
REVERT: C  680 MET cc_start: 0.8837 (pmm) cc_final: 0.8455 (pmm)
REVERT: C  807 MET cc_start: 0.8032 (tpp) cc_final: 0.7527 (tpp)
REVERT: C  871 MET cc_start: 0.8997 (tmm) cc_final: 0.8281 (tmm)
REVERT: C  915 TRP cc_start: 0.9003 (p-90) cc_final: 0.8168 (p-90)
REVERT: C  926 ASP cc_start: 0.8421 (p0) cc_final: 0.8054 (p0)
REVERT: C  938 PHE cc_start: 0.8887 (t80) cc_final: 0.8515 (t80)
REVERT: C  996 MET cc_start: 0.8897 (mmm) cc_final: 0.8356 (mmp)
REVERT: D   91 LEU cc_start: 0.9214 (mm) cc_final: 0.8904 (mm)
REVERT: D  108 MET cc_start: 0.8224 (tpt) cc_final: 0.7844 (tpt)
REVERT: D  184 LEU cc_start: 0.8055 (tp) cc_final: 0.7726 (tp)
REVERT: D  185 ILE cc_start: 0.9051 (tt) cc_final: 0.8757 (mm)
REVERT: D  233 LEU cc_start: 0.8590 (mt) cc_final: 0.8305 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 287
  average time/residue: 0.1541
  time to fit residues: 68.5491
Evaluate side-chains
  218 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 121 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 193 optimal weight:    7.9990
   chunk 143 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 102 optimal weight:   10.0000
   chunk 182 optimal weight:    0.9980
   chunk 179 optimal weight:    6.9990
   chunk 173 optimal weight:    7.9990
   overall best weight:    4.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 HIS
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 HIS
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.084009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.067757 restraints weight = 90324.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.069612 restraints weight = 51044.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.070833 restraints weight = 33016.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071674 restraints weight = 23899.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.072235 restraints weight = 18809.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       71 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       72 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.6673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  20886  Z= 0.198
  Angle     :  0.779  11.738  29159  Z= 0.429
  Chirality :  0.046   0.296   3192
  Planarity :  0.006   0.078   2994
  Dihedral  : 24.996 177.588   4568
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 20.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.57 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.18), residues: 1938
  helix: -0.12 (0.21), residues: 619
  sheet:  0.46 (0.29), residues: 300
  loop : -1.34 (0.18), residues: 1019

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 701 
 TYR   0.021   0.002   TYR A 957 
 PHE   0.037   0.002   PHE A 806 
 TRP   0.036   0.002   TRP C 782 
 HIS   0.011   0.002   HIS B  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.20 (20880)
  covalent geometry    : angle       0.77880 /  0.43 (29159)
  hydrogen bonds       : bond        0.05475 /  3.67 (  810)
  hydrogen bonds       : angle       5.28854 /  3.78 ( 2266)
  metal coordination   : bond        0.00498 /  0.39 (    6)

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

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

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3876 Ramachandran restraints generated.
    1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 0.640 
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: A  418 LEU cc_start: 0.7394 (mm) cc_final: 0.7128 (mm)
REVERT: A  428 ARG cc_start: 0.8891 (mmp80) cc_final: 0.8554 (mmp80)
REVERT: A  527 LYS cc_start: 0.8719 (mttm) cc_final: 0.7812 (tptp)
REVERT: A  572 ILE cc_start: 0.9685 (mt) cc_final: 0.9472 (tt)
REVERT: A  615 VAL cc_start: 0.8293 (t) cc_final: 0.8092 (t)
REVERT: A  863 MET cc_start: 0.7481 (mmt) cc_final: 0.7268 (mmp)
REVERT: A  911 MET cc_start: 0.9093 (ptm) cc_final: 0.8794 (ptt)
REVERT: A  960 LYS cc_start: 0.9202 (tttt) cc_final: 0.8898 (tttt)
REVERT: B   46 PHE cc_start: 0.8382 (m-80) cc_final: 0.7928 (m-80)
REVERT: B   64 ASN cc_start: 0.9130 (m-40) cc_final: 0.8278 (p0)
REVERT: B  124 CYS cc_start: 0.8129 (t) cc_final: 0.7862 (t)
REVERT: B  128 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7619 (tm-30)
REVERT: B  280 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7944 (tp30)
REVERT: C  428 ARG cc_start: 0.7445 (mmt90) cc_final: 0.7097 (tpp80)
REVERT: C  455 LEU cc_start: 0.8100 (mp) cc_final: 0.7569 (pp)
REVERT: C  495 LEU cc_start: 0.8780 (mt) cc_final: 0.8540 (mt)
REVERT: C  555 ASP cc_start: 0.8359 (m-30) cc_final: 0.7756 (m-30)
REVERT: C  589 LEU cc_start: 0.9063 (mm) cc_final: 0.8804 (tp)
REVERT: C  640 VAL cc_start: 0.9219 (t) cc_final: 0.8885 (t)
REVERT: C  672 LEU cc_start: 0.9272 (mt) cc_final: 0.8819 (mt)
REVERT: C  680 MET cc_start: 0.8939 (pmm) cc_final: 0.8537 (pmm)
REVERT: C  871 MET cc_start: 0.8976 (tmm) cc_final: 0.8372 (tmm)
REVERT: C  908 TYR cc_start: 0.8467 (t80) cc_final: 0.8267 (t80)
REVERT: C  915 TRP cc_start: 0.9007 (p-90) cc_final: 0.8275 (p-90)
REVERT: C  926 ASP cc_start: 0.8527 (p0) cc_final: 0.8102 (p0)
REVERT: C  938 PHE cc_start: 0.8904 (t80) cc_final: 0.8569 (t80)
REVERT: D  108 MET cc_start: 0.8116 (tpt) cc_final: 0.7783 (tpt)
REVERT: D  109 LEU cc_start: 0.9122 (tt) cc_final: 0.8920 (tt)
REVERT: D  184 LEU cc_start: 0.8096 (tp) cc_final: 0.7864 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.1565
  time to fit residues: 67.7994
Evaluate side-chains
  213 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 184 optimal weight:    9.9990
   chunk 133 optimal weight:    0.0060
   chunk 10 optimal weight:    6.9990
   chunk 200 optimal weight:   40.0000
   chunk 158 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 178 optimal weight:    9.9990
   chunk 76 optimal weight:   40.0000
   chunk 63 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    4.0004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
A 687 HIS
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 HIS
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 237 HIS
** D 347 GLN ** 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 = 0.3648 r_free = 0.3648 target = 0.084308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.067863 restraints weight = 91293.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.069805 restraints weight = 50860.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.071093 restraints weight = 32533.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.071964 restraints weight = 23329.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.072532 restraints weight = 18262.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3379
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       72 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       72 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3379
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.6807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  20886  Z= 0.184
  Angle     :  0.771  13.141  29159  Z= 0.424
  Chirality :  0.045   0.291   3192
  Planarity :  0.005   0.074   2994
  Dihedral  : 25.008 177.736   4568
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.47 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.18), residues: 1938
  helix: -0.09 (0.21), residues: 619
  sheet:  0.50 (0.29), residues: 300
  loop : -1.36 (0.18), residues: 1019

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 675 
 TYR   0.019   0.002   TYR A 957 
 PHE   0.031   0.002   PHE A 806 
 TRP   0.035   0.002   TRP C 782 
 HIS   0.006   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.18 (20880)
  covalent geometry    : angle       0.77076 /  0.42 (29159)
  hydrogen bonds       : bond        0.05363 /  3.58 (  810)
  hydrogen bonds       : angle       5.25100 /  3.75 ( 2266)
  metal coordination   : bond        0.00490 /  0.44 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3120.12 seconds
wall clock time: 54 minutes 58.90 seconds (3298.90 seconds total)