Starting phenix.real_space_refine
on Tue Aug 26 11:14:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3jbw_6489/08_2025/3jbw_6489_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3jbw_6489/08_2025/3jbw_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_6489/08_2025/3jbw_6489_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3jbw_6489/08_2025/3jbw_6489_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/3jbw_6489/08_2025/3jbw_6489.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3jbw_6489/08_2025/3jbw_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-2.0-5787/lib/python3.9/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: 4.77, per 1000 atoms: 0.24
  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: 1.75
  Conformation dependent library (CDL) restraints added in 828.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 2.76
  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: 4.97

  Time building geometry restraints manager: 2.33 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=" O3'  DA H   2 "
       pdb=" P    DC H   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.767 -0.160 1.50e-02 4.44e+03 1.14e+02
  bond pdb=" P    DT G  42 "
       pdb=" O5'  DT G  42 "
    ideal  model  delta    sigma   weight residual
    1.600  1.395  0.205 2.00e-02 2.50e+03 1.05e+02
  bond pdb=" O3'  DC G  41 "
       pdb=" P    DT G  42 "
    ideal  model  delta    sigma   weight residual
    1.607  1.742 -0.135 1.50e-02 4.44e+03 8.08e+01
  bond pdb=" C3'  DA H   2 "
       pdb=" O3'  DA H   2 "
    ideal  model  delta    sigma   weight residual
    1.422  1.684 -0.262 3.00e-02 1.11e+03 7.64e+01
  bond pdb=" C3'  DG G  45 "
       pdb=" O3'  DG G  45 "
    ideal  model  delta    sigma   weight residual
    1.422  1.659 -0.237 3.00e-02 1.11e+03 6.24e+01
  ... (remaining 20875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.86: 28812
        5.86 -    11.73: 315
       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=" 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
  angle pdb=" N   ARG A 426 "
        pdb=" CA  ARG A 426 "
        pdb=" C   ARG A 426 "
      ideal   model   delta    sigma   weight residual
     111.69  124.20  -12.51 1.23e+00 6.61e-01 1.03e+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: 3042
       0.152 -    0.304: 131
       0.304 -    0.456: 12
       0.456 -    0.608: 5
       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       2.35   -3.00   -0.66 2.00e-01 2.50e+01 1.08e+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:                  0.010
  Normalize map: mean=0, sd=1:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.880
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
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= 0.676
  Angle     :  1.698  29.321  29159  Z= 1.029
  Chirality :  0.076   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 aren 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
  covalent geometry    : bond        0.01306 (20880)
  covalent geometry    : angle       1.69803 (29159)
  hydrogen bonds       : bond        0.16922 (  810)
  hydrogen bonds       : angle      10.70707 ( 2266)
  metal coordination   : bond        0.22079 (    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  : 0.677 
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: A  412 ARG cc_start: 0.4529 (ptt-90) cc_final: 0.3231 (tpm170)
REVERT: A  425 HIS cc_start: 0.8275 (t-90) cc_final: 0.7510 (m170)
REVERT: A  430 LEU cc_start: 0.8658 (mt) cc_final: 0.8179 (mt)
REVERT: A  432 ASN cc_start: 0.9136 (t0) cc_final: 0.8661 (t0)
REVERT: A  456 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.5831 (tt)
REVERT: A  524 ASN cc_start: 0.8994 (t0) cc_final: 0.8502 (t0)
REVERT: A  527 LYS cc_start: 0.9006 (mttm) cc_final: 0.7966 (tptt)
REVERT: A  572 ILE cc_start: 0.9567 (mt) cc_final: 0.9094 (tt)
REVERT: A  599 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7588 (tp30)
REVERT: A  664 GLN cc_start: 0.8135 (tt0) cc_final: 0.7834 (tp40)
REVERT: A  671 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7733 (pm20)
REVERT: A  672 LEU cc_start: 0.9190 (mt) cc_final: 0.8828 (mt)
REVERT: A  690 LEU cc_start: 0.9605 (tp) cc_final: 0.9269 (tp)
REVERT: A  704 MET cc_start: 0.9277 (ttm) cc_final: 0.8919 (mtp)
REVERT: A  801 VAL cc_start: 0.8965 (t) cc_final: 0.8652 (t)
REVERT: A  820 ILE cc_start: 0.9336 (mt) cc_final: 0.9098 (pt)
REVERT: A  905 MET cc_start: 0.8292 (tpp) cc_final: 0.7931 (tmm)
REVERT: A  911 MET cc_start: 0.9619 (ptm) cc_final: 0.8662 (mtm)
REVERT: A  947 LYS cc_start: 0.8857 (tttt) cc_final: 0.8481 (tppt)
REVERT: A  956 ASN cc_start: 0.9269 (m-40) cc_final: 0.8434 (m-40)
REVERT: A  960 LYS cc_start: 0.9231 (mttt) cc_final: 0.8340 (mmtm)
REVERT: A 1005 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8271 (pp20)
REVERT: A 1023 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8682 (tmtt)
REVERT: B   19 PHE cc_start: 0.9178 (p90) cc_final: 0.8865 (p90)
REVERT: B   64 ASN cc_start: 0.9280 (m-40) cc_final: 0.8971 (m-40)
REVERT: B  109 LEU cc_start: 0.9210 (tt) cc_final: 0.8921 (mm)
REVERT: B  146 ASN cc_start: 0.7170 (m-40) cc_final: 0.6838 (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: 0.8527 (t0)
REVERT: B  199 GLU cc_start: 0.8795 (mm-30) cc_final: 0.7553 (tt0)
REVERT: B  213 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7827 (pp30)
REVERT: B  214 ASP cc_start: 0.7607 (p0) cc_final: 0.6463 (p0)
REVERT: B  266 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5410 (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: 0.7762 (t80)
REVERT: B  317 TRP cc_start: 0.7954 (p-90) cc_final: 0.7651 (p-90)
REVERT: B  334 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7681 (tp30)
REVERT: B  347 GLN cc_start: 0.8390 (tt0) cc_final: 0.8139 (tm-30)
REVERT: C  421 ARG cc_start: 0.3170 (OUTLIER) cc_final: 0.1670 (tmm-80)
REVERT: C  455 LEU cc_start: 0.7973 (mp) cc_final: 0.7466 (tp)
REVERT: C  464 HIS cc_start: 0.6222 (OUTLIER) cc_final: 0.5991 (p-80)
REVERT: C  489 ILE cc_start: 0.9018 (mt) cc_final: 0.8788 (mm)
REVERT: C  543 LYS cc_start: 0.8785 (mttt) cc_final: 0.8532 (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: 0.8014 (mtp)
REVERT: C  620 ASP cc_start: 0.9059 (t0) cc_final: 0.8056 (p0)
REVERT: C  622 MET cc_start: 0.7819 (ttp) cc_final: 0.7451 (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: 0.7985 (m-40)
REVERT: C  677 LEU cc_start: 0.9420 (tt) cc_final: 0.9127 (tp)
REVERT: C  679 LEU cc_start: 0.9318 (mp) cc_final: 0.8881 (mp)
REVERT: C  686 ASP cc_start: 0.8338 (p0) cc_final: 0.7672 (p0)
REVERT: C  698 VAL cc_start: 0.9260 (t) cc_final: 0.8940 (p)
REVERT: C  712 SER cc_start: 0.8996 (p) cc_final: 0.8758 (m)
REVERT: C  730 ASP cc_start: 0.8992 (p0) cc_final: 0.8272 (m-30)
REVERT: C  732 LYS cc_start: 0.9008 (tttt) cc_final: 0.8675 (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: 0.8063 (m)
REVERT: C  871 MET cc_start: 0.8124 (ttp) cc_final: 0.7737 (ttp)
REVERT: C  896 GLU cc_start: 0.8473 (mp0) cc_final: 0.7933 (pm20)
REVERT: C  905 MET cc_start: 0.8214 (tpp) cc_final: 0.7788 (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: 0.7849 (p-90)
REVERT: C  926 ASP cc_start: 0.9123 (p0) cc_final: 0.8860 (p0)
REVERT: C  983 ASN cc_start: 0.8914 (t0) cc_final: 0.8570 (t0)
REVERT: C  985 SER cc_start: 0.9500 (m) cc_final: 0.9205 (p)
REVERT: C  989 LEU cc_start: 0.9329 (mt) cc_final: 0.9062 (mt)
REVERT: C  995 LYS cc_start: 0.9442 (mtmm) cc_final: 0.9126 (mmtm)
REVERT: C 1005 GLU cc_start: 0.8769 (tt0) cc_final: 0.8471 (mt-10)
REVERT: C 1006 LEU cc_start: 0.8596 (mt) cc_final: 0.8206 (mp)
REVERT: C 1020 TYR cc_start: 0.8976 (t80) cc_final: 0.8763 (t80)
REVERT: D    1 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8177 (mtt)
REVERT: D   16 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7777 (pt0)
REVERT: D   29 TYR cc_start: 0.8493 (m-80) cc_final: 0.8216 (m-80)
REVERT: D   39 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7405 (tpt-90)
REVERT: D   55 LEU cc_start: 0.9151 (tp) cc_final: 0.8914 (tt)
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: 0.7771 (mt)
REVERT: D  117 ASN cc_start: 0.7866 (t0) cc_final: 0.7043 (p0)
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: 0.8554 (tpp)
REVERT: D  188 GLU cc_start: 0.7841 (tp30) cc_final: 0.7586 (mm-30)
REVERT: D  217 TYR cc_start: 0.8478 (m-80) cc_final: 0.8222 (m-10)
REVERT: D  293 ASP cc_start: 0.9193 (t0) cc_final: 0.8916 (t70)
REVERT: D  303 GLU cc_start: 0.8551 (tt0) cc_final: 0.8300 (tm-30)
REVERT: D  310 GLU cc_start: 0.8474 (tt0) cc_final: 0.8224 (tp30)
  outliers start: 83
  outliers final: 11
  residues processed: 679
  average time/residue: 0.1876
  time to fit residues: 183.6439
Evaluate side-chains
  360 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 336
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 194 optimal weight:    6.9990
   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:    0.9990
   chunk 212 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 629 HIS
A 766 HIS
A 822 ASN
** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1000 GLN
B 171 ASN
B 173 ASN
B 278 GLN
C 423 GLN
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 937 GLN
** 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: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.089538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.073242 restraints weight = 89955.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.075237 restraints weight = 49622.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.076578 restraints weight = 31560.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.077436 restraints weight = 22435.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.077998 restraints weight = 17613.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    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 = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  20886  Z= 0.220
  Angle     :  0.850  11.796  29159  Z= 0.468
  Chirality :  0.046   0.202   3192
  Planarity :  0.007   0.082   2994
  Dihedral  : 24.830 177.861   4568
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 19.56
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.72 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.41 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 1.62 %
    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 aren not related in a simple way.
  whole: -1.60 (0.17), residues: 1938
  helix: -0.79 (0.19), residues: 610
  sheet: -0.17 (0.26), residues: 315
  loop : -1.50 (0.17), residues: 1013

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG C 421 
 TYR   0.018   0.002   TYR C 908 
 PHE   0.028   0.002   PHE B 189 
 TRP   0.022   0.002   TRP A 560 
 HIS   0.010   0.002   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (20880)
  covalent geometry    : angle       0.84955 (29159)
  hydrogen bonds       : bond        0.06309 (  810)
  hydrogen bonds       : angle       6.01033 ( 2266)
  metal coordination   : bond        0.01333 (    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
  441 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 436
  time to evaluate  : 0.696 
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: A  412 ARG cc_start: 0.4077 (ptt-90) cc_final: 0.3338 (tpm170)
REVERT: A  418 LEU cc_start: 0.6989 (mm) cc_final: 0.6518 (mm)
REVERT: A  430 LEU cc_start: 0.8436 (mt) cc_final: 0.8113 (mt)
REVERT: A  527 LYS cc_start: 0.8257 (mttm) cc_final: 0.7807 (tptt)
REVERT: A  572 ILE cc_start: 0.9659 (mt) cc_final: 0.9126 (tt)
REVERT: A  599 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7161 (tp30)
REVERT: A  622 MET cc_start: 0.8300 (ttp) cc_final: 0.8047 (tpp)
REVERT: A  704 MET cc_start: 0.8316 (ttm) cc_final: 0.7977 (ttm)
REVERT: A  705 MET cc_start: 0.8167 (mmm) cc_final: 0.7288 (mmm)
REVERT: A  851 TRP cc_start: 0.8461 (m-10) cc_final: 0.7908 (m-10)
REVERT: A  880 MET cc_start: 0.7934 (ppp) cc_final: 0.7432 (ppp)
REVERT: A  911 MET cc_start: 0.9019 (ptm) cc_final: 0.8707 (ptt)
REVERT: A  955 THR cc_start: 0.7949 (t) cc_final: 0.7299 (m)
REVERT: A  957 TYR cc_start: 0.9158 (m-80) cc_final: 0.8732 (m-80)
REVERT: A  960 LYS cc_start: 0.9237 (mttt) cc_final: 0.8476 (tttt)
REVERT: B   19 PHE cc_start: 0.9191 (p90) cc_final: 0.8663 (p90)
REVERT: B   21 LEU cc_start: 0.8253 (mm) cc_final: 0.8049 (mm)
REVERT: B   46 PHE cc_start: 0.8073 (m-80) cc_final: 0.7814 (m-80)
REVERT: B   64 ASN cc_start: 0.9225 (m-40) cc_final: 0.8830 (m-40)
REVERT: B   92 ILE cc_start: 0.8674 (mp) cc_final: 0.8405 (mp)
REVERT: B  119 LYS cc_start: 0.7744 (ttmt) cc_final: 0.6906 (mmmt)
REVERT: B  124 CYS cc_start: 0.7757 (t) cc_final: 0.7465 (t)
REVERT: B  198 PRO cc_start: 0.8663 (Cg_exo) cc_final: 0.8416 (Cg_endo)
REVERT: B  199 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7584 (tt0)
REVERT: B  317 TRP cc_start: 0.7772 (p-90) cc_final: 0.7516 (p-90)
REVERT: C  424 LYS cc_start: 0.7941 (mttt) cc_final: 0.7573 (pttt)
REVERT: C  455 LEU cc_start: 0.7969 (mp) cc_final: 0.7520 (tp)
REVERT: C  620 ASP cc_start: 0.7936 (t0) cc_final: 0.7264 (t0)
REVERT: C  688 GLU cc_start: 0.8630 (pm20) cc_final: 0.8389 (pm20)
REVERT: C  896 GLU cc_start: 0.8269 (mp0) cc_final: 0.7620 (pm20)
REVERT: C  903 LYS cc_start: 0.8876 (tptt) cc_final: 0.8558 (tptt)
REVERT: C  915 TRP cc_start: 0.8969 (p-90) cc_final: 0.7945 (p-90)
REVERT: C  916 ARG cc_start: 0.8463 (tpt170) cc_final: 0.8234 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8252 (p0) cc_final: 0.7944 (p0)
REVERT: C  938 PHE cc_start: 0.8944 (t80) cc_final: 0.8345 (t80)
REVERT: C  978 TRP cc_start: 0.7547 (m100) cc_final: 0.6533 (m100)
REVERT: C  983 ASN cc_start: 0.8225 (t0) cc_final: 0.7661 (t0)
REVERT: C  989 LEU cc_start: 0.8996 (mt) cc_final: 0.8684 (mt)
REVERT: C 1007 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7874 (mt-10)
REVERT: D   55 LEU cc_start: 0.9347 (tp) cc_final: 0.8973 (pp)
REVERT: D   60 ILE cc_start: 0.9199 (mm) cc_final: 0.8885 (mt)
REVERT: D  117 ASN cc_start: 0.8111 (t0) cc_final: 0.7407 (p0)
REVERT: D  317 TRP cc_start: 0.7757 (p-90) cc_final: 0.7313 (p-90)
  outliers start: 5
  outliers final: 0
  residues processed: 441
  average time/residue: 0.1723
  time to fit residues: 112.8487
Evaluate side-chains
  280 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 174 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 160 optimal weight:    0.9990
   chunk 147 optimal weight:    8.9990
   chunk 82 optimal weight:   20.0000
   chunk 73 optimal weight:   20.0000
   chunk 77 optimal weight:   40.0000
   chunk 177 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 822 ASN
A 831 GLN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
B 195 HIS
C 831 GLN
C 858 GLN
** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 937 GLN
D 237 HIS
** 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 = 0.3684 r_free = 0.3684 target = 0.085890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.069379 restraints weight = 90598.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.071390 restraints weight = 49507.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.072746 restraints weight = 31404.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.073651 restraints weight = 22222.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.074248 restraints weight = 17223.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       58 |
|-----------------------------------------------------------------------------|
r_final: 0.3420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.5012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  20886  Z= 0.212
  Angle     :  0.782  10.202  29159  Z= 0.429
  Chirality :  0.043   0.205   3192
  Planarity :  0.006   0.076   2994
  Dihedral  : 24.749 174.317   4568
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.23 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  4.41 %
    Favored  : 95.53 %
  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 aren not related in a simple way.
  whole: -1.09 (0.17), residues: 1938
  helix: -0.31 (0.20), residues: 615
  sheet:  0.30 (0.28), residues: 295
  loop : -1.29 (0.18), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG C 421 
 TYR   0.024   0.002   TYR D  29 
 PHE   0.020   0.002   PHE A 681 
 TRP   0.023   0.002   TRP C1014 
 HIS   0.009   0.002   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (20880)
  covalent geometry    : angle       0.78236 (29159)
  hydrogen bonds       : bond        0.05590 (  810)
  hydrogen bonds       : angle       5.55062 ( 2266)
  metal coordination   : bond        0.00748 (    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
  364 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 363
  time to evaluate  : 0.811 
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: 0.7167 (mm) cc_final: 0.6952 (mm)
REVERT: A  430 LEU cc_start: 0.8436 (mt) cc_final: 0.8149 (mt)
REVERT: A  431 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7992 (tppt)
REVERT: A  565 ASP cc_start: 0.8212 (p0) cc_final: 0.8012 (p0)
REVERT: A  572 ILE cc_start: 0.9698 (mt) cc_final: 0.9200 (tt)
REVERT: A  688 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7638 (mm-30)
REVERT: A  911 MET cc_start: 0.9008 (ptm) cc_final: 0.8781 (ptt)
REVERT: A  960 LYS cc_start: 0.9311 (mttt) cc_final: 0.8378 (tttm)
REVERT: A  987 ASN cc_start: 0.9075 (m-40) cc_final: 0.7947 (p0)
REVERT: A 1005 GLU cc_start: 0.8601 (pt0) cc_final: 0.8215 (pt0)
REVERT: B   46 PHE cc_start: 0.8105 (m-80) cc_final: 0.7781 (m-80)
REVERT: B   64 ASN cc_start: 0.9294 (m-40) cc_final: 0.8839 (m-40)
REVERT: B   92 ILE cc_start: 0.8801 (mp) cc_final: 0.8563 (mp)
REVERT: B  129 LEU cc_start: 0.8404 (mp) cc_final: 0.8063 (mp)
REVERT: B  222 HIS cc_start: 0.8183 (t-90) cc_final: 0.7832 (t-90)
REVERT: B  317 TRP cc_start: 0.7911 (p-90) cc_final: 0.7656 (p-90)
REVERT: C  455 LEU cc_start: 0.8042 (mp) cc_final: 0.7572 (pp)
REVERT: C  495 LEU cc_start: 0.8810 (mt) cc_final: 0.8391 (mt)
REVERT: C  555 ASP cc_start: 0.8087 (m-30) cc_final: 0.7816 (m-30)
REVERT: C  589 LEU cc_start: 0.9164 (mm) cc_final: 0.8854 (tp)
REVERT: C  620 ASP cc_start: 0.8004 (t0) cc_final: 0.7572 (t70)
REVERT: C  672 LEU cc_start: 0.8810 (mm) cc_final: 0.8559 (mm)
REVERT: C  688 GLU cc_start: 0.8623 (pm20) cc_final: 0.8346 (pm20)
REVERT: C  905 MET cc_start: 0.8193 (tmm) cc_final: 0.7733 (tmm)
REVERT: C  915 TRP cc_start: 0.8926 (p-90) cc_final: 0.8430 (p-90)
REVERT: C  916 ARG cc_start: 0.8493 (tpt170) cc_final: 0.8161 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8400 (p0) cc_final: 0.8130 (p0)
REVERT: C  938 PHE cc_start: 0.8894 (t80) cc_final: 0.8369 (t80)
REVERT: D    7 THR cc_start: 0.8912 (p) cc_final: 0.8536 (t)
REVERT: D   31 PHE cc_start: 0.8386 (t80) cc_final: 0.8176 (t80)
REVERT: D   45 ILE cc_start: 0.9343 (mm) cc_final: 0.9015 (mm)
REVERT: D   91 LEU cc_start: 0.8944 (mm) cc_final: 0.8637 (mm)
REVERT: D  108 MET cc_start: 0.7737 (tpt) cc_final: 0.7271 (tpt)
REVERT: D  117 ASN cc_start: 0.8216 (t0) cc_final: 0.7701 (p0)
REVERT: D  217 TYR cc_start: 0.6769 (m-10) cc_final: 0.6560 (m-10)
REVERT: D  318 PHE cc_start: 0.7819 (p90) cc_final: 0.7253 (p90)
REVERT: D  343 TYR cc_start: 0.8184 (m-80) cc_final: 0.7965 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 364
  average time/residue: 0.1587
  time to fit residues: 87.9476
Evaluate side-chains
  259 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 164 optimal weight:    9.9990
   chunk 147 optimal weight:    5.9990
   chunk 207 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 208 optimal weight:   10.0000
   chunk 157 optimal weight:    2.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 GLN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 910 GLN
** 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 = 0.3660 r_free = 0.3660 target = 0.084758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.068680 restraints weight = 90821.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.070561 restraints weight = 50633.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.071804 restraints weight = 32457.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.072663 restraints weight = 23342.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.073158 restraints weight = 18326.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       58 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
r_final: 0.3398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  20886  Z= 0.201
  Angle     :  0.751   9.958  29159  Z= 0.411
  Chirality :  0.042   0.198   3192
  Planarity :  0.006   0.081   2994
  Dihedral  : 24.777 178.902   4568
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.33 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  3.82 %
    Favored  : 96.12 %
  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 aren not related in a simple way.
  whole: -0.97 (0.18), residues: 1938
  helix: -0.15 (0.20), residues: 613
  sheet:  0.44 (0.29), residues: 302
  loop : -1.29 (0.18), residues: 1023

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 756 
 TYR   0.022   0.002   TYR A 827 
 PHE   0.021   0.002   PHE C 681 
 TRP   0.033   0.002   TRP C 782 
 HIS   0.009   0.002   HIS D 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (20880)
  covalent geometry    : angle       0.75077 (29159)
  hydrogen bonds       : bond        0.05275 (  810)
  hydrogen bonds       : angle       5.30247 ( 2266)
  metal coordination   : bond        0.01850 (    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
  335 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 334
  time to evaluate  : 0.719 
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: A  428 ARG cc_start: 0.9228 (ptt-90) cc_final: 0.8916 (ptt180)
REVERT: A  431 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7982 (tppt)
REVERT: A  466 GLN cc_start: 0.8575 (mp-120) cc_final: 0.8361 (mp10)
REVERT: A  527 LYS cc_start: 0.8680 (mttm) cc_final: 0.7480 (tptp)
REVERT: A  565 ASP cc_start: 0.8418 (p0) cc_final: 0.8208 (p0)
REVERT: A  572 ILE cc_start: 0.9686 (mt) cc_final: 0.9365 (tt)
REVERT: A  575 ARG cc_start: 0.8350 (ptt90) cc_final: 0.7778 (ptm-80)
REVERT: A  644 PHE cc_start: 0.9114 (p90) cc_final: 0.8850 (p90)
REVERT: A  672 LEU cc_start: 0.9146 (mt) cc_final: 0.8943 (mp)
REVERT: A  688 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8004 (mm-30)
REVERT: A  698 VAL cc_start: 0.9346 (t) cc_final: 0.8882 (t)
REVERT: A  731 GLU cc_start: 0.8369 (pt0) cc_final: 0.7431 (pp20)
REVERT: A  868 VAL cc_start: 0.9481 (m) cc_final: 0.9245 (m)
REVERT: A  872 ASN cc_start: 0.9109 (p0) cc_final: 0.8795 (p0)
REVERT: A  911 MET cc_start: 0.8988 (ptm) cc_final: 0.8780 (ptt)
REVERT: A  960 LYS cc_start: 0.9241 (mttt) cc_final: 0.8437 (mmtp)
REVERT: A 1005 GLU cc_start: 0.8176 (pt0) cc_final: 0.7863 (pt0)
REVERT: B   46 PHE cc_start: 0.8154 (m-80) cc_final: 0.7828 (m-80)
REVERT: B   92 ILE cc_start: 0.8705 (mp) cc_final: 0.8475 (mp)
REVERT: B  128 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: B  173 ASN cc_start: 0.8257 (t0) cc_final: 0.7958 (t0)
REVERT: B  222 HIS cc_start: 0.8335 (t-90) cc_final: 0.8123 (t70)
REVERT: C  455 LEU cc_start: 0.8194 (mp) cc_final: 0.7820 (pp)
REVERT: C  474 MET cc_start: 0.8243 (mmp) cc_final: 0.7459 (ppp)
REVERT: C  495 LEU cc_start: 0.8772 (mt) cc_final: 0.8454 (mt)
REVERT: C  555 ASP cc_start: 0.8305 (m-30) cc_final: 0.7781 (m-30)
REVERT: C  589 LEU cc_start: 0.9114 (mm) cc_final: 0.8814 (tp)
REVERT: C  620 ASP cc_start: 0.7501 (t0) cc_final: 0.6656 (t0)
REVERT: C  640 VAL cc_start: 0.9173 (t) cc_final: 0.8940 (t)
REVERT: C  679 LEU cc_start: 0.9169 (mt) cc_final: 0.8898 (mt)
REVERT: C  704 MET cc_start: 0.8056 (ptp) cc_final: 0.7623 (ptp)
REVERT: C  915 TRP cc_start: 0.8894 (p-90) cc_final: 0.8447 (p-90)
REVERT: C  916 ARG cc_start: 0.8453 (tpt170) cc_final: 0.8118 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8322 (p0) cc_final: 0.7994 (p0)
REVERT: C  938 PHE cc_start: 0.8768 (t80) cc_final: 0.8417 (t80)
REVERT: C  983 ASN cc_start: 0.8265 (t0) cc_final: 0.8059 (t0)
REVERT: C  989 LEU cc_start: 0.8885 (mt) cc_final: 0.8619 (mt)
REVERT: D   91 LEU cc_start: 0.8970 (mm) cc_final: 0.8698 (mm)
REVERT: D  117 ASN cc_start: 0.8241 (t0) cc_final: 0.7886 (p0)
REVERT: D  343 TYR cc_start: 0.8308 (m-80) cc_final: 0.8074 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 334
  average time/residue: 0.1593
  time to fit residues: 81.0690
Evaluate side-chains
  250 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 76 optimal weight:   20.0000
   chunk 98 optimal weight:    9.9990
   chunk 11 optimal weight:    0.1980
   chunk 167 optimal weight:    0.0020
   chunk 69 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 212 optimal weight:   10.0000
   chunk 131 optimal weight:    0.5980
   chunk 115 optimal weight:   20.0000
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 GLN
B 173 ASN
C 464 HIS
** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3720 r_free = 0.3720 target = 0.087691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.071352 restraints weight = 89552.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.073322 restraints weight = 49402.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.074624 restraints weight = 31500.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.075480 restraints weight = 22557.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.076047 restraints weight = 17708.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.5984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20886  Z= 0.160
  Angle     :  0.720   9.534  29159  Z= 0.389
  Chirality :  0.041   0.203   3192
  Planarity :  0.005   0.072   2994
  Dihedral  : 24.692 175.816   4568
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.87 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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 aren not related in a simple way.
  whole: -0.77 (0.18), residues: 1938
  helix:  0.02 (0.20), residues: 615
  sheet:  0.76 (0.30), residues: 281
  loop : -1.21 (0.18), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG A 701 
 TYR   0.017   0.002   TYR A 933 
 PHE   0.020   0.002   PHE A 724 
 TRP   0.022   0.002   TRP A 538 
 HIS   0.005   0.001   HIS D 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (20880)
  covalent geometry    : angle       0.71961 (29159)
  hydrogen bonds       : bond        0.05060 (  810)
  hydrogen bonds       : angle       5.05215 ( 2266)
  metal coordination   : bond        0.00285 (    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
  341 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 341
  time to evaluate  : 0.713 
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  527 LYS cc_start: 0.8551 (mttm) cc_final: 0.7521 (tptp)
REVERT: A  572 ILE cc_start: 0.9679 (mt) cc_final: 0.9355 (tt)
REVERT: A  575 ARG cc_start: 0.8095 (ptt90) cc_final: 0.7599 (ptm-80)
REVERT: A  615 VAL cc_start: 0.8466 (t) cc_final: 0.8221 (t)
REVERT: A  644 PHE cc_start: 0.9091 (p90) cc_final: 0.8699 (p90)
REVERT: A  688 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7741 (mm-30)
REVERT: A  781 ILE cc_start: 0.9103 (mt) cc_final: 0.8812 (tp)
REVERT: A  801 VAL cc_start: 0.9245 (t) cc_final: 0.8987 (t)
REVERT: A  807 MET cc_start: 0.7734 (mpp) cc_final: 0.7389 (mpp)
REVERT: A  851 TRP cc_start: 0.8299 (m-10) cc_final: 0.7887 (m-90)
REVERT: A  872 ASN cc_start: 0.9088 (p0) cc_final: 0.8806 (p0)
REVERT: A  911 MET cc_start: 0.9004 (ptm) cc_final: 0.8743 (ptt)
REVERT: A  960 LYS cc_start: 0.9213 (mttt) cc_final: 0.8661 (mmtp)
REVERT: A  987 ASN cc_start: 0.8992 (m-40) cc_final: 0.7934 (p0)
REVERT: A 1005 GLU cc_start: 0.8489 (pt0) cc_final: 0.7868 (pt0)
REVERT: B  106 LEU cc_start: 0.9660 (tt) cc_final: 0.9353 (tt)
REVERT: B  150 LYS cc_start: 0.8417 (mppt) cc_final: 0.8211 (mppt)
REVERT: B  222 HIS cc_start: 0.8119 (t-90) cc_final: 0.7604 (t-90)
REVERT: C  455 LEU cc_start: 0.7884 (mp) cc_final: 0.7511 (pp)
REVERT: C  495 LEU cc_start: 0.8712 (mt) cc_final: 0.8419 (mt)
REVERT: C  555 ASP cc_start: 0.8335 (m-30) cc_final: 0.8031 (m-30)
REVERT: C  620 ASP cc_start: 0.7256 (t0) cc_final: 0.6922 (t0)
REVERT: C  640 VAL cc_start: 0.9146 (t) cc_final: 0.8793 (t)
REVERT: C  679 LEU cc_start: 0.9112 (mt) cc_final: 0.8908 (mm)
REVERT: C  680 MET cc_start: 0.8446 (pmm) cc_final: 0.8167 (pmm)
REVERT: C  818 CYS cc_start: 0.9143 (t) cc_final: 0.8652 (t)
REVERT: C  896 GLU cc_start: 0.8227 (mp0) cc_final: 0.7737 (pt0)
REVERT: C  904 LEU cc_start: 0.8582 (tt) cc_final: 0.7703 (pp)
REVERT: C  915 TRP cc_start: 0.8866 (p-90) cc_final: 0.7813 (p-90)
REVERT: C  916 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7859 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8341 (p0) cc_final: 0.8026 (p0)
REVERT: C  938 PHE cc_start: 0.8788 (t80) cc_final: 0.8221 (t80)
REVERT: C  983 ASN cc_start: 0.8250 (t0) cc_final: 0.8020 (t0)
REVERT: C  989 LEU cc_start: 0.8907 (mt) cc_final: 0.8659 (mt)
REVERT: D  108 MET cc_start: 0.8275 (tpt) cc_final: 0.7850 (tpt)
REVERT: D  117 ASN cc_start: 0.8215 (t0) cc_final: 0.7879 (p0)
REVERT: D  184 LEU cc_start: 0.7893 (tp) cc_final: 0.7641 (tp)
REVERT: D  313 HIS cc_start: 0.8472 (m90) cc_final: 0.8249 (m170)
REVERT: D  343 TYR cc_start: 0.8061 (m-80) cc_final: 0.7816 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 341
  average time/residue: 0.1575
  time to fit residues: 82.1271
Evaluate side-chains
  250 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 161 optimal weight:    3.9990
   chunk 145 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 147 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 156 optimal weight:    9.9990
   chunk 98 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 501 HIS
C 524 ASN
** 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 = 0.3688 r_free = 0.3688 target = 0.086023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.069544 restraints weight = 89477.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.071395 restraints weight = 50340.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.072699 restraints weight = 32696.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.073562 restraints weight = 23511.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.074130 restraints weight = 18405.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3417
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
r_final: 0.3417
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.6322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  20886  Z= 0.177
  Angle     :  0.703   9.768  29159  Z= 0.385
  Chirality :  0.041   0.202   3192
  Planarity :  0.005   0.074   2994
  Dihedral  : 24.682 174.563   4568
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.82 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.88 %
    Favored  : 97.06 %
  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 aren not related in a simple way.
  whole: -0.73 (0.18), residues: 1938
  helix:  0.09 (0.20), residues: 617
  sheet:  0.78 (0.30), residues: 283
  loop : -1.22 (0.18), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 756 
 TYR   0.017   0.002   TYR A 957 
 PHE   0.026   0.002   PHE C 454 
 TRP   0.024   0.002   TRP A 538 
 HIS   0.007   0.001   HIS B  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (20880)
  covalent geometry    : angle       0.70295 (29159)
  hydrogen bonds       : bond        0.05009 (  810)
  hydrogen bonds       : angle       4.99894 ( 2266)
  metal coordination   : bond        0.00209 (    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
  315 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 314
  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: A  527 LYS cc_start: 0.8833 (mttm) cc_final: 0.7593 (tptp)
REVERT: A  565 ASP cc_start: 0.8474 (p0) cc_final: 0.8245 (p0)
REVERT: A  572 ILE cc_start: 0.9681 (mt) cc_final: 0.9440 (tt)
REVERT: A  644 PHE cc_start: 0.9067 (p90) cc_final: 0.8654 (p90)
REVERT: A  688 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7913 (mm-30)
REVERT: A  781 ILE cc_start: 0.9137 (mt) cc_final: 0.8879 (tp)
REVERT: A  851 TRP cc_start: 0.8288 (m-10) cc_final: 0.7890 (m-90)
REVERT: A  872 ASN cc_start: 0.9172 (p0) cc_final: 0.8820 (p0)
REVERT: A  911 MET cc_start: 0.9068 (ptm) cc_final: 0.8838 (ptt)
REVERT: A 1005 GLU cc_start: 0.8550 (pt0) cc_final: 0.8066 (pt0)
REVERT: B   46 PHE cc_start: 0.8203 (m-80) cc_final: 0.7925 (m-80)
REVERT: B   64 ASN cc_start: 0.8569 (m-40) cc_final: 0.8224 (p0)
REVERT: B  128 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: B  150 LYS cc_start: 0.8407 (mppt) cc_final: 0.8200 (mppt)
REVERT: B  162 MET cc_start: 0.7567 (ptt) cc_final: 0.7336 (ptt)
REVERT: B  222 HIS cc_start: 0.8101 (t-90) cc_final: 0.7687 (t-90)
REVERT: B  233 LEU cc_start: 0.9408 (tp) cc_final: 0.9183 (tt)
REVERT: C  455 LEU cc_start: 0.7899 (mp) cc_final: 0.7377 (pp)
REVERT: C  495 LEU cc_start: 0.8737 (mt) cc_final: 0.8506 (mt)
REVERT: C  555 ASP cc_start: 0.8486 (m-30) cc_final: 0.8019 (m-30)
REVERT: C  589 LEU cc_start: 0.9143 (mm) cc_final: 0.8870 (tp)
REVERT: C  598 ARG cc_start: 0.8566 (ptp-110) cc_final: 0.8177 (ptt-90)
REVERT: C  640 VAL cc_start: 0.9203 (t) cc_final: 0.8891 (t)
REVERT: C  647 MET cc_start: 0.7923 (mtp) cc_final: 0.7579 (mtp)
REVERT: C  672 LEU cc_start: 0.9223 (mt) cc_final: 0.8788 (mt)
REVERT: C  704 MET cc_start: 0.8124 (ptp) cc_final: 0.7678 (ptp)
REVERT: C  871 MET cc_start: 0.9055 (tmm) cc_final: 0.8160 (tmm)
REVERT: C  904 LEU cc_start: 0.8634 (tt) cc_final: 0.7728 (pp)
REVERT: C  915 TRP cc_start: 0.8892 (p-90) cc_final: 0.7856 (p-90)
REVERT: C  916 ARG cc_start: 0.8324 (tpt170) cc_final: 0.7911 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8393 (p0) cc_final: 0.8042 (p0)
REVERT: C  938 PHE cc_start: 0.8868 (t80) cc_final: 0.8204 (t80)
REVERT: C  989 LEU cc_start: 0.8852 (mt) cc_final: 0.8589 (mt)
REVERT: D   31 PHE cc_start: 0.8402 (t80) cc_final: 0.8110 (t80)
REVERT: D   45 ILE cc_start: 0.9278 (mm) cc_final: 0.8949 (mm)
REVERT: D   91 LEU cc_start: 0.9253 (mm) cc_final: 0.8903 (mm)
REVERT: D  108 MET cc_start: 0.8173 (tpt) cc_final: 0.7795 (tpt)
REVERT: D  117 ASN cc_start: 0.8293 (t0) cc_final: 0.7980 (p0)
REVERT: D  184 LEU cc_start: 0.7912 (tp) cc_final: 0.7661 (tp)
REVERT: D  218 PHE cc_start: 0.7890 (m-80) cc_final: 0.7197 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 315
  average time/residue: 0.1523
  time to fit residues: 74.0739
Evaluate side-chains
  238 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 131 optimal weight:   20.0000
   chunk 37 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 155 optimal weight:    0.9980
   chunk 67 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 ASN
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 501 HIS
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 930 GLN
** 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 = 0.3646 r_free = 0.3646 target = 0.084094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.067436 restraints weight = 93147.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.069272 restraints weight = 51796.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.070555 restraints weight = 33336.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.071383 restraints weight = 23916.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.071889 restraints weight = 18924.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.6718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  20886  Z= 0.216
  Angle     :  0.733   9.418  29159  Z= 0.402
  Chirality :  0.042   0.273   3192
  Planarity :  0.005   0.074   2994
  Dihedral  : 24.811 177.479   4568
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 19.55
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.80 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  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 aren not related in a simple way.
  whole: -0.85 (0.18), residues: 1938
  helix:  0.00 (0.20), residues: 615
  sheet:  0.70 (0.29), residues: 291
  loop : -1.30 (0.18), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 783 
 TYR   0.020   0.002   TYR A 957 
 PHE   0.021   0.002   PHE D  62 
 TRP   0.050   0.003   TRP C 782 
 HIS   0.014   0.002   HIS C 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (20880)
  covalent geometry    : angle       0.73264 (29159)
  hydrogen bonds       : bond        0.05125 (  810)
  hydrogen bonds       : angle       5.14043 ( 2266)
  metal coordination   : bond        0.00280 (    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
  303 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 0.687 
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: A  428 ARG cc_start: 0.9080 (mmp80) cc_final: 0.8671 (mmp80)
REVERT: A  575 ARG cc_start: 0.8495 (ptt90) cc_final: 0.7567 (ptm-80)
REVERT: A  644 PHE cc_start: 0.9107 (p90) cc_final: 0.8640 (p90)
REVERT: A  731 GLU cc_start: 0.8580 (pt0) cc_final: 0.7510 (pp20)
REVERT: A  807 MET cc_start: 0.7978 (mpp) cc_final: 0.7546 (mpp)
REVERT: A  872 ASN cc_start: 0.9151 (p0) cc_final: 0.8904 (p0)
REVERT: A  960 LYS cc_start: 0.9295 (mttt) cc_final: 0.8504 (mptt)
REVERT: A 1005 GLU cc_start: 0.8627 (pt0) cc_final: 0.8153 (pt0)
REVERT: B    1 MET cc_start: 0.6648 (tpp) cc_final: 0.6263 (tpp)
REVERT: B   29 TYR cc_start: 0.7876 (m-80) cc_final: 0.7604 (m-80)
REVERT: B   46 PHE cc_start: 0.8305 (m-80) cc_final: 0.8029 (m-80)
REVERT: B   64 ASN cc_start: 0.8695 (m-40) cc_final: 0.8265 (p0)
REVERT: B  150 LYS cc_start: 0.8376 (mppt) cc_final: 0.8140 (mppt)
REVERT: B  162 MET cc_start: 0.7839 (ptt) cc_final: 0.7504 (ptt)
REVERT: B  222 HIS cc_start: 0.8374 (t-90) cc_final: 0.7835 (t-90)
REVERT: B  280 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7971 (tp30)
REVERT: C  495 LEU cc_start: 0.8767 (mt) cc_final: 0.8509 (mt)
REVERT: C  555 ASP cc_start: 0.8556 (m-30) cc_final: 0.8073 (m-30)
REVERT: C  589 LEU cc_start: 0.9139 (mm) cc_final: 0.8814 (tp)
REVERT: C  619 CYS cc_start: 0.9108 (p) cc_final: 0.8738 (t)
REVERT: C  680 MET cc_start: 0.8846 (pmm) cc_final: 0.8554 (pmm)
REVERT: C  689 THR cc_start: 0.9163 (m) cc_final: 0.8925 (m)
REVERT: C  806 PHE cc_start: 0.9207 (p90) cc_final: 0.8988 (p90)
REVERT: C  904 LEU cc_start: 0.8651 (tt) cc_final: 0.7783 (pp)
REVERT: C  916 ARG cc_start: 0.8381 (tpt170) cc_final: 0.8095 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8523 (p0) cc_final: 0.8127 (p0)
REVERT: C  938 PHE cc_start: 0.8928 (t80) cc_final: 0.8086 (t80)
REVERT: C  989 LEU cc_start: 0.8750 (mt) cc_final: 0.8497 (mt)
REVERT: D   31 PHE cc_start: 0.8453 (t80) cc_final: 0.8205 (t80)
REVERT: D   45 ILE cc_start: 0.9448 (mm) cc_final: 0.9133 (mm)
REVERT: D   91 LEU cc_start: 0.9256 (mm) cc_final: 0.8938 (mm)
REVERT: D  108 MET cc_start: 0.8154 (tpt) cc_final: 0.7759 (tpt)
REVERT: D  109 LEU cc_start: 0.9067 (tt) cc_final: 0.8857 (tt)
REVERT: D  117 ASN cc_start: 0.8559 (t0) cc_final: 0.8002 (p0)
REVERT: D  184 LEU cc_start: 0.7955 (tp) cc_final: 0.7657 (tp)
REVERT: D  218 PHE cc_start: 0.7981 (m-80) cc_final: 0.7245 (m-80)
REVERT: D  324 LYS cc_start: 0.8833 (mttp) cc_final: 0.8346 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 303
  average time/residue: 0.1578
  time to fit residues: 73.1540
Evaluate side-chains
  223 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 169 optimal weight:    0.5980
   chunk 77 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 181 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 188 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 175 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 414 HIS
A 425 HIS
A 910 GLN
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 ASN
B  16 GLN
B 173 ASN
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 501 HIS
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.085870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.069348 restraints weight = 90614.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071260 restraints weight = 50770.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.072560 restraints weight = 32718.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.073414 restraints weight = 23472.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.073945 restraints weight = 18459.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3408
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
r_final: 0.3408
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.6948

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= 0.164
  Angle     :  0.706  13.115  29159  Z= 0.382
  Chirality :  0.041   0.197   3192
  Planarity :  0.005   0.070   2994
  Dihedral  : 24.845 176.493   4568
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.44 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  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 aren not related in a simple way.
  whole: -0.76 (0.18), residues: 1938
  helix:  0.13 (0.21), residues: 616
  sheet:  0.65 (0.29), residues: 298
  loop : -1.28 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 783 
 TYR   0.026   0.002   TYR C1020 
 PHE   0.014   0.002   PHE A 454 
 TRP   0.034   0.002   TRP C 782 
 HIS   0.012   0.001   HIS C 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (20880)
  covalent geometry    : angle       0.70644 (29159)
  hydrogen bonds       : bond        0.04899 (  810)
  hydrogen bonds       : angle       5.00193 ( 2266)
  metal coordination   : bond        0.00189 (    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
  309 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 0.723 
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  428 ARG cc_start: 0.8954 (mmp80) cc_final: 0.8622 (mmp80)
REVERT: A  622 MET cc_start: 0.4784 (mtp) cc_final: 0.4141 (mtt)
REVERT: A  644 PHE cc_start: 0.9126 (p90) cc_final: 0.8563 (p90)
REVERT: A  688 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: A  705 MET cc_start: 0.8611 (mmp) cc_final: 0.8330 (mmp)
REVERT: A  731 GLU cc_start: 0.8438 (pt0) cc_final: 0.7416 (pp20)
REVERT: A  891 LEU cc_start: 0.8622 (tp) cc_final: 0.8305 (tp)
REVERT: A  960 LYS cc_start: 0.9305 (mttt) cc_final: 0.8454 (mptt)
REVERT: A 1005 GLU cc_start: 0.8585 (pt0) cc_final: 0.8119 (pt0)
REVERT: B   64 ASN cc_start: 0.8613 (m-40) cc_final: 0.8297 (p0)
REVERT: B  162 MET cc_start: 0.7622 (ptt) cc_final: 0.7341 (ptt)
REVERT: B  222 HIS cc_start: 0.8351 (t-90) cc_final: 0.7722 (t-90)
REVERT: B  280 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7967 (tp30)
REVERT: C  495 LEU cc_start: 0.8728 (mt) cc_final: 0.8495 (mt)
REVERT: C  555 ASP cc_start: 0.8561 (m-30) cc_final: 0.8104 (m-30)
REVERT: C  619 CYS cc_start: 0.9269 (p) cc_final: 0.8982 (t)
REVERT: C  640 VAL cc_start: 0.9156 (t) cc_final: 0.8652 (t)
REVERT: C  722 PHE cc_start: 0.7706 (m-80) cc_final: 0.7353 (m-10)
REVERT: C  729 TYR cc_start: 0.8317 (m-10) cc_final: 0.7825 (m-10)
REVERT: C  818 CYS cc_start: 0.9301 (t) cc_final: 0.8590 (t)
REVERT: C  896 GLU cc_start: 0.8318 (mp0) cc_final: 0.7902 (pt0)
REVERT: C  904 LEU cc_start: 0.8635 (tt) cc_final: 0.7784 (pp)
REVERT: C  915 TRP cc_start: 0.8984 (p-90) cc_final: 0.8064 (p-90)
REVERT: C  926 ASP cc_start: 0.8420 (p0) cc_final: 0.7940 (p0)
REVERT: C  938 PHE cc_start: 0.8913 (t80) cc_final: 0.8259 (t80)
REVERT: C  989 LEU cc_start: 0.8796 (mt) cc_final: 0.8526 (mt)
REVERT: D   22 LEU cc_start: 0.8925 (mp) cc_final: 0.8616 (mt)
REVERT: D   31 PHE cc_start: 0.8426 (t80) cc_final: 0.8201 (t80)
REVERT: D   45 ILE cc_start: 0.9358 (mm) cc_final: 0.9134 (mm)
REVERT: D  108 MET cc_start: 0.8180 (tpt) cc_final: 0.7812 (tpt)
REVERT: D  117 ASN cc_start: 0.8561 (t0) cc_final: 0.8038 (p0)
REVERT: D  184 LEU cc_start: 0.7918 (tp) cc_final: 0.7613 (tp)
REVERT: D  218 PHE cc_start: 0.7880 (m-80) cc_final: 0.7057 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.1617
  time to fit residues: 75.9601
Evaluate side-chains
  233 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 63 optimal weight:    0.7980
   chunk 160 optimal weight:    6.9990
   chunk 143 optimal weight:    8.9990
   chunk 141 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 125 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 169 optimal weight:    7.9990
   chunk 137 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 414 HIS
** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 ASN
B 173 ASN
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 501 HIS
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3677 r_free = 0.3677 target = 0.085809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.069329 restraints weight = 90437.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.071281 restraints weight = 50077.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.072546 restraints weight = 32007.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.073475 restraints weight = 23060.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.074065 restraints weight = 17938.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3413 r_free = 0.3413    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
r_final: 0.3413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.7139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  20886  Z= 0.165
  Angle     :  0.705  10.634  29159  Z= 0.381
  Chirality :  0.041   0.287   3192
  Planarity :  0.005   0.074   2994
  Dihedral  : 24.828 177.629   4568
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.75 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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 aren not related in a simple way.
  whole: -0.75 (0.18), residues: 1938
  helix:  0.21 (0.21), residues: 615
  sheet:  0.62 (0.29), residues: 300
  loop : -1.30 (0.18), residues: 1023

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 284 
 TYR   0.023   0.002   TYR C1020 
 PHE   0.019   0.002   PHE C 437 
 TRP   0.029   0.002   TRP C 782 
 HIS   0.010   0.001   HIS C 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (20880)
  covalent geometry    : angle       0.70461 (29159)
  hydrogen bonds       : bond        0.04860 (  810)
  hydrogen bonds       : angle       4.96017 ( 2266)
  metal coordination   : bond        0.00294 (    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
  310 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.679 
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: A  428 ARG cc_start: 0.8959 (mmp80) cc_final: 0.8603 (mmp80)
REVERT: A  565 ASP cc_start: 0.8515 (p0) cc_final: 0.8271 (p0)
REVERT: A  622 MET cc_start: 0.4939 (mtp) cc_final: 0.4298 (mtt)
REVERT: A  640 VAL cc_start: 0.9082 (t) cc_final: 0.8876 (t)
REVERT: A  644 PHE cc_start: 0.9097 (p90) cc_final: 0.8608 (p90)
REVERT: A  688 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7967 (mm-30)
REVERT: A  705 MET cc_start: 0.8691 (mmp) cc_final: 0.8465 (mmp)
REVERT: A  731 GLU cc_start: 0.8379 (pt0) cc_final: 0.7836 (pp20)
REVERT: A  960 LYS cc_start: 0.9309 (mttt) cc_final: 0.8467 (mptt)
REVERT: A 1005 GLU cc_start: 0.8578 (pt0) cc_final: 0.8121 (pt0)
REVERT: B    1 MET cc_start: 0.5809 (tpp) cc_final: 0.5257 (tpp)
REVERT: B   46 PHE cc_start: 0.8139 (m-80) cc_final: 0.7934 (m-80)
REVERT: B   64 ASN cc_start: 0.8618 (m-40) cc_final: 0.8363 (p0)
REVERT: B  162 MET cc_start: 0.7373 (ptt) cc_final: 0.7002 (ptt)
REVERT: B  222 HIS cc_start: 0.8486 (t-90) cc_final: 0.8230 (t70)
REVERT: B  280 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7832 (tp30)
REVERT: C  555 ASP cc_start: 0.8559 (m-30) cc_final: 0.8089 (m-30)
REVERT: C  589 LEU cc_start: 0.9050 (mm) cc_final: 0.8694 (tp)
REVERT: C  640 VAL cc_start: 0.9080 (t) cc_final: 0.8733 (t)
REVERT: C  651 ILE cc_start: 0.8710 (pt) cc_final: 0.8430 (tp)
REVERT: C  729 TYR cc_start: 0.8073 (m-10) cc_final: 0.7570 (m-10)
REVERT: C  737 MET cc_start: 0.7954 (ptp) cc_final: 0.6544 (ptp)
REVERT: C  818 CYS cc_start: 0.9276 (t) cc_final: 0.8817 (t)
REVERT: C  865 LEU cc_start: 0.9246 (mt) cc_final: 0.9034 (mt)
REVERT: C  871 MET cc_start: 0.8880 (tmm) cc_final: 0.7959 (tmm)
REVERT: C  904 LEU cc_start: 0.8560 (tt) cc_final: 0.7995 (pp)
REVERT: C  915 TRP cc_start: 0.8964 (p-90) cc_final: 0.8070 (p-90)
REVERT: C  916 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7695 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8328 (p0) cc_final: 0.7872 (p0)
REVERT: C  989 LEU cc_start: 0.8748 (mt) cc_final: 0.8518 (mt)
REVERT: D   22 LEU cc_start: 0.8912 (mp) cc_final: 0.8625 (mt)
REVERT: D   31 PHE cc_start: 0.8316 (t80) cc_final: 0.8068 (t80)
REVERT: D   45 ILE cc_start: 0.9386 (mm) cc_final: 0.9132 (mm)
REVERT: D  108 MET cc_start: 0.8113 (tpt) cc_final: 0.7742 (tpt)
REVERT: D  117 ASN cc_start: 0.8565 (t0) cc_final: 0.8055 (p0)
REVERT: D  184 LEU cc_start: 0.7903 (tp) cc_final: 0.7592 (tp)
REVERT: D  218 PHE cc_start: 0.7851 (m-80) cc_final: 0.7070 (m-80)
REVERT: D  317 TRP cc_start: 0.7774 (p-90) cc_final: 0.7514 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 310
  average time/residue: 0.1542
  time to fit residues: 72.6191
Evaluate side-chains
  237 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 193 optimal weight:    6.9990
   chunk 143 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 102 optimal weight:    9.9990
   chunk 182 optimal weight:   10.0000
   chunk 179 optimal weight:   20.0000
   chunk 173 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 687 HIS
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 ASN
** B  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 GLN
B 173 ASN
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 501 HIS
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.083344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.067019 restraints weight = 92550.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.068905 restraints weight = 51080.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.070156 restraints weight = 32644.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.070947 restraints weight = 23441.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.071545 restraints weight = 18588.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       59 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       60 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.7467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  20886  Z= 0.201
  Angle     :  0.742   9.657  29159  Z= 0.400
  Chirality :  0.042   0.284   3192
  Planarity :  0.005   0.068   2994
  Dihedral  : 24.898 179.183   4568
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.11 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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 aren not related in a simple way.
  whole: -0.92 (0.18), residues: 1938
  helix:  0.06 (0.20), residues: 623
  sheet:  0.58 (0.29), residues: 291
  loop : -1.42 (0.18), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 675 
 TYR   0.024   0.002   TYR D  29 
 PHE   0.019   0.002   PHE C 681 
 TRP   0.031   0.003   TRP A 782 
 HIS   0.009   0.002   HIS C 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (20880)
  covalent geometry    : angle       0.74236 (29159)
  hydrogen bonds       : bond        0.05086 (  810)
  hydrogen bonds       : angle       5.13571 ( 2266)
  metal coordination   : bond        0.00294 (    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
  294 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 ARG cc_start: 0.8987 (mmp80) cc_final: 0.8695 (mmp80)
REVERT: A  565 ASP cc_start: 0.8533 (p0) cc_final: 0.8046 (p0)
REVERT: A  622 MET cc_start: 0.5050 (mtp) cc_final: 0.4789 (mtp)
REVERT: A  644 PHE cc_start: 0.9096 (p90) cc_final: 0.8594 (p90)
REVERT: A  688 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8507 (mm-30)
REVERT: A  705 MET cc_start: 0.8712 (mmp) cc_final: 0.8452 (mmp)
REVERT: A  731 GLU cc_start: 0.8588 (pt0) cc_final: 0.7606 (pp20)
REVERT: A  880 MET cc_start: 0.8630 (tpt) cc_final: 0.8333 (tpp)
REVERT: A  895 GLU cc_start: 0.7441 (tp30) cc_final: 0.7089 (tp30)
REVERT: A  960 LYS cc_start: 0.9273 (mttt) cc_final: 0.8179 (tttt)
REVERT: A  988 LYS cc_start: 0.8973 (tptm) cc_final: 0.8626 (tptm)
REVERT: A 1005 GLU cc_start: 0.8617 (pt0) cc_final: 0.8166 (pt0)
REVERT: B    1 MET cc_start: 0.6003 (tpp) cc_final: 0.5523 (tpp)
REVERT: B   23 ASP cc_start: 0.7989 (t0) cc_final: 0.7383 (p0)
REVERT: B   29 TYR cc_start: 0.8086 (m-10) cc_final: 0.7863 (m-10)
REVERT: B   46 PHE cc_start: 0.8290 (m-80) cc_final: 0.7995 (m-80)
REVERT: B  162 MET cc_start: 0.7727 (ptt) cc_final: 0.7377 (ptt)
REVERT: B  280 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7900 (tp30)
REVERT: B  322 LEU cc_start: 0.8611 (mt) cc_final: 0.7848 (tt)
REVERT: C  555 ASP cc_start: 0.8614 (m-30) cc_final: 0.8113 (m-30)
REVERT: C  689 THR cc_start: 0.9110 (m) cc_final: 0.8903 (m)
REVERT: C  722 PHE cc_start: 0.7820 (m-80) cc_final: 0.7504 (m-10)
REVERT: C  871 MET cc_start: 0.8833 (tmm) cc_final: 0.8115 (tmm)
REVERT: C  904 LEU cc_start: 0.8548 (tt) cc_final: 0.8026 (pp)
REVERT: C  915 TRP cc_start: 0.8994 (p-90) cc_final: 0.8251 (p-90)
REVERT: C  916 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.7698 (tpp-160)
REVERT: C  926 ASP cc_start: 0.8443 (p0) cc_final: 0.7907 (p0)
REVERT: C  984 GLU cc_start: 0.8242 (tp30) cc_final: 0.7765 (tp30)
REVERT: C  989 LEU cc_start: 0.8685 (mt) cc_final: 0.8435 (mt)
REVERT: D   22 LEU cc_start: 0.8899 (mp) cc_final: 0.8673 (mt)
REVERT: D   91 LEU cc_start: 0.9236 (mm) cc_final: 0.8937 (mm)
REVERT: D  108 MET cc_start: 0.8148 (tpt) cc_final: 0.7632 (tpt)
REVERT: D  109 LEU cc_start: 0.8939 (tt) cc_final: 0.8629 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 294
  average time/residue: 0.1422
  time to fit residues: 64.6400
Evaluate side-chains
  219 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 200 optimal weight:   10.0000
   chunk 158 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 178 optimal weight:    8.9990
   chunk 76 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0970
   chunk 93 optimal weight:    5.9990
   chunk 107 optimal weight:    0.0070
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
A 425 HIS
** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 ASN
B  83 GLN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 ASN
** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 347 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.086577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.070220 restraints weight = 91470.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.072136 restraints weight = 51557.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.073438 restraints weight = 33226.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.074293 restraints weight = 23874.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.074812 restraints weight = 18827.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       60 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       62 |
|-----------------------------------------------------------------------------|
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.7591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  20886  Z= 0.152
  Angle     :  0.710  11.583  29159  Z= 0.380
  Chirality :  0.041   0.263   3192
  Planarity :  0.005   0.065   2994
  Dihedral  : 24.821 178.792   4568
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.39 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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 aren not related in a simple way.
  whole: -0.83 (0.18), residues: 1938
  helix:  0.17 (0.21), residues: 622
  sheet:  0.44 (0.29), residues: 320
  loop : -1.36 (0.18), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 675 
 TYR   0.017   0.002   TYR C 747 
 PHE   0.021   0.002   PHE D  31 
 TRP   0.033   0.002   TRP C 782 
 HIS   0.010   0.001   HIS C 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (20880)
  covalent geometry    : angle       0.71042 (29159)
  hydrogen bonds       : bond        0.04933 (  810)
  hydrogen bonds       : angle       4.91904 ( 2266)
  metal coordination   : bond        0.00171 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3297.25 seconds
wall clock time: 58 minutes 9.08 seconds (3489.08 seconds total)