Starting phenix.real_space_refine
on Wed Jul 30 15:43:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k2x_62000/07_2025/9k2x_62000.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k2x_62000/07_2025/9k2x_62000.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k2x_62000/07_2025/9k2x_62000.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k2x_62000/07_2025/9k2x_62000.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k2x_62000/07_2025/9k2x_62000.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k2x_62000/07_2025/9k2x_62000.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      81      5.16       5
     C    7850      2.51       5
     N    2140      2.21       5
     O    2305      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12376
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 4311
          Classifications: {'peptide': 524}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 496}
    Chain: "B"
      Number of atoms: 8065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1027, 8065
          Classifications: {'peptide': 1027}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21}
          Link IDs: {'CIS': 4, 'PTRANS': 65, 'TRANS': 957}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 85
  Time building chain proxies: 6.90, per 1000 atoms: 0.56
  Number of scatterers: 12376
  At special positions: 0
  Unit cell: (91.135, 156.034, 133.941, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      81     16.00
     O    2305      8.00
     N    2140      7.00
     C    7850      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: 3.09
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2922

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 15 sheets defined
      33.3% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 560 through 562
      No H-bonds generated for 'chain 'A' and resid 560 through 562'
    Processing helix  chain 'A' and resid 571 through 575
    Processing helix  chain 'A' and resid 601 through 614
    Processing helix  chain 'A' and resid 616 through 618
      No H-bonds generated for 'chain 'A' and resid 616 through 618'
    Processing helix  chain 'A' and resid 647 through 652
    Processing helix  chain 'A' and resid 666 through 671
    Processing helix  chain 'A' and resid 712 through 724
      removed outlier: 3.678A  pdb=" N   LEU A 716 " --> pdb=" O   LYS A 712 " (cutoff:3.500A)
      Proline residue:  A 718  - end of helix
    Processing helix  chain 'A' and resid 752 through 757
    Processing helix  chain 'A' and resid 772 through 778
    Processing helix  chain 'A' and resid 782 through 792
    Processing helix  chain 'A' and resid 818 through 831
    Processing helix  chain 'A' and resid 833 through 835
      No H-bonds generated for 'chain 'A' and resid 833 through 835'
    Processing helix  chain 'A' and resid 860 through 866
    Processing helix  chain 'A' and resid 884 through 890
    Processing helix  chain 'A' and resid 917 through 929
    Processing helix  chain 'A' and resid 958 through 962
    Processing helix  chain 'A' and resid 976 through 980
      removed outlier: 3.873A  pdb=" N   VAL A 980 " --> pdb=" O   LEU A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1029
      removed outlier: 3.763A  pdb=" N   VAL A1020 " --> pdb=" O   HIS A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1038
    Processing helix  chain 'A' and resid 1059 through 1063
    Processing helix  chain 'B' and resid 496 through 519
    Processing helix  chain 'B' and resid 523 through 534
    Processing helix  chain 'B' and resid 546 through 553
    Processing helix  chain 'B' and resid 553 through 568
WARNING: missing atoms!
      removed outlier: 3.608A  pdb=" N   ALA B 567 " --> pdb=" O   SER B 563 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   GLY B 568 " --> pdb=" O   TYR B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 577
    Processing helix  chain 'B' and resid 578 through 588
    Processing helix  chain 'B' and resid 621 through 632
    Processing helix  chain 'B' and resid 633 through 636
      removed outlier: 4.073A  pdb=" N   ILE B 636 " --> pdb=" O   ALA B 633 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 633 through 636'
    Processing helix  chain 'B' and resid 656 through 661
    Processing helix  chain 'B' and resid 686 through 690
      removed outlier: 3.929A  pdb=" N   ARG B 690 " --> pdb=" O   GLN B 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 691 through 704
    Processing helix  chain 'B' and resid 801 through 803
      No H-bonds generated for 'chain 'B' and resid 801 through 803'
    Processing helix  chain 'B' and resid 805 through 809
    Processing helix  chain 'B' and resid 826 through 828
      No H-bonds generated for 'chain 'B' and resid 826 through 828'
    Processing helix  chain 'B' and resid 842 through 846
    Processing helix  chain 'B' and resid 850 through 855
    Processing helix  chain 'B' and resid 885 through 889
    Processing helix  chain 'B' and resid 893 through 907
      removed outlier: 3.525A  pdb=" N   ILE B 907 " --> pdb=" O   ARG B 903 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 971 through 976
      removed outlier: 3.590A  pdb=" N   ARG B 974 " --> pdb=" O   GLU B 971 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1030 through 1035
    Processing helix  chain 'B' and resid 1054 through 1056
      No H-bonds generated for 'chain 'B' and resid 1054 through 1056'
    Processing helix  chain 'B' and resid 1071 through 1079
      removed outlier: 3.502A  pdb=" N   TYR B1075 " --> pdb=" O   CYS B1071 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLY B1079 " --> pdb=" O   TYR B1075 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1100 through 1104
    Processing helix  chain 'B' and resid 1149 through 1159
    Processing helix  chain 'B' and resid 1170 through 1181
    Processing helix  chain 'B' and resid 1190 through 1201
      removed outlier: 3.672A  pdb=" N   LEU B1194 " --> pdb=" O   ASP B1190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1236 through 1244
    Processing helix  chain 'B' and resid 1246 through 1259
      removed outlier: 4.043A  pdb=" N   SER B1250 " --> pdb=" O   SER B1246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1270 through 1274
      removed outlier: 3.608A  pdb=" N   PHE B1274 " --> pdb=" O   PHE B1271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1277 through 1291
    Processing helix  chain 'B' and resid 1302 through 1305
      removed outlier: 3.737A  pdb=" N   GLY B1305 " --> pdb=" O   GLY B1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1302 through 1305'
    Processing helix  chain 'B' and resid 1335 through 1339
    Processing helix  chain 'B' and resid 1367 through 1372
    Processing helix  chain 'B' and resid 1394 through 1402
      removed outlier: 3.637A  pdb=" N   GLY B1402 " --> pdb=" O   ARG B1398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1418 through 1427
    Processing helix  chain 'B' and resid 1435 through 1439
    Processing helix  chain 'B' and resid 1476 through 1480
    Processing helix  chain 'B' and resid 1498 through 1503
    Processing helix  chain 'B' and resid 1504 through 1511
      removed outlier: 4.017A  pdb=" N   ASN B1508 " --> pdb=" O   ASN B1505 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   HIS B1509 " --> pdb=" O   ARG B1506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1549 through 1558
    Processing helix  chain 'B' and resid 1568 through 1579
      removed outlier: 3.566A  pdb=" N   ALA B1579 " --> pdb=" O   GLN B1575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1581 through 1600
      removed outlier: 3.694A  pdb=" N   GLU B1591 " --> pdb=" O   ALA B1587 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA B1600 " --> pdb=" O   MET B1596 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 592 through 597
      removed outlier: 5.294A  pdb=" N   THR A 659 " --> pdb=" O   MET A 625 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 698 through 708
      removed outlier: 4.692A  pdb=" N   LEU A 689 " --> pdb=" O   CYS A 702 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   HIS A 704 " --> pdb=" O   LEU A 687 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU A 687 " --> pdb=" O   HIS A 704 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   TYR A 706 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL A 685 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
      removed outlier: 8.287A  pdb=" N   ILE A 766 " --> pdb=" O   MET A 686 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   PHE A 688 " --> pdb=" O   ILE A 766 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   PHE A 768 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LYS A 690 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
      removed outlier: 8.590A  pdb=" N   LYS A 770 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   TYR A 692 " --> pdb=" O   LYS A 770 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ILE A 765 " --> pdb=" O   GLU A 737 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU A 742 " --> pdb=" O   VAL A 738 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 814
      removed outlier: 4.878A  pdb=" N   LYS A 874 " --> pdb=" O   ASP A 795 " (cutoff:3.500A)
      removed outlier: 8.724A  pdb=" N   LYS A 875 " --> pdb=" O   SER A 842 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   SER A 842 " --> pdb=" O   LYS A 875 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   PHE A 839 " --> pdb=" O   PRO A 852 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   LYS A 841 " --> pdb=" O   GLY A 850 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 905 through 910
      removed outlier: 5.063A  pdb=" N   PHE A 970 " --> pdb=" O   LYS A 895 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   GLU A 974 " --> pdb=" O   LEU A 899 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LEU A 941 " --> pdb=" O   HIS A 953 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   VAL A 945 " --> pdb=" O   ILE A 949 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   ILE A 949 " --> pdb=" O   VAL A 945 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1002 through 1011
      removed outlier: 7.485A  pdb=" N   ILE A1005 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   HIS A 994 " --> pdb=" O   ILE A1005 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 732 through 734
      removed outlier: 4.279A  pdb=" N   VAL B 750 " --> pdb=" O   VAL B 734 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 739 through 740
      removed outlier: 5.555A  pdb=" N   LEU B 776 " --> pdb=" O   PHE B 797 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   HIS B 793 " --> pdb=" O   THR B 780 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU B 782 " --> pdb=" O   MET B 791 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   MET B 791 " --> pdb=" O   LEU B 782 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   GLU B 819 " --> pdb=" O   TRP B 796 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   CYS B 798 " --> pdb=" O   VAL B 817 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   VAL B 817 " --> pdb=" O   CYS B 798 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   LEU B 814 " --> pdb=" O   LEU B 867 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   TYR B 869 " --> pdb=" O   LEU B 814 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU B 816 " --> pdb=" O   TYR B 869 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ILE B 835 " --> pdb=" O   TYR B 865 " (cutoff:3.500A)
      removed outlier: 8.573A  pdb=" N   LEU B 867 " --> pdb=" O   ILE B 835 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 830 through 832
      removed outlier: 3.545A  pdb=" N   SER B 830 " --> pdb=" O   SER B 764 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   CYS B 762 " --> pdb=" O   VAL B 832 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   LEU B 776 " --> pdb=" O   PHE B 797 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   HIS B 793 " --> pdb=" O   THR B 780 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU B 782 " --> pdb=" O   MET B 791 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   MET B 791 " --> pdb=" O   LEU B 782 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   GLU B 819 " --> pdb=" O   TRP B 796 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   CYS B 798 " --> pdb=" O   VAL B 817 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   VAL B 817 " --> pdb=" O   CYS B 798 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   LEU B 814 " --> pdb=" O   LEU B 867 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   TYR B 869 " --> pdb=" O   LEU B 814 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU B 816 " --> pdb=" O   TYR B 869 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 909 through 916
      removed outlier: 7.681A  pdb=" N   ARG B 909 " --> pdb=" O   LYS B 928 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   LYS B 928 " --> pdb=" O   ARG B 909 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   LEU B 911 " --> pdb=" O   ALA B 926 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   ALA B 926 " --> pdb=" O   LEU B 911 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   GLN B 913 " --> pdb=" O   TYR B 924 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   TYR B 924 " --> pdb=" O   GLN B 913 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE B 999 " --> pdb=" O   TYR B 923 " (cutoff:3.500A)
      removed outlier: 9.743A  pdb=" N   SER B 925 " --> pdb=" O   LYS B 997 " (cutoff:3.500A)
      removed outlier: 12.262A  pdb=" N   LYS B 997 " --> pdb=" O   SER B 925 " (cutoff:3.500A)
      removed outlier: 15.444A  pdb=" N   THR B 927 " --> pdb=" O   ARG B 995 " (cutoff:3.500A)
      removed outlier: 16.944A  pdb=" N   ARG B 995 " --> pdb=" O   THR B 927 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   ILE B 993 " --> pdb=" O   PHE B1021 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ARG B1017 " --> pdb=" O   LYS B 997 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   ILE B 999 " --> pdb=" O   LYS B1015 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   LYS B1015 " --> pdb=" O   ILE B 999 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS B1020 " --> pdb=" O   GLU B1047 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   GLU B1047 " --> pdb=" O   LYS B1020 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   TYR B1022 " --> pdb=" O   SER B1045 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   SER B1045 " --> pdb=" O   TYR B1022 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 931 through 934
      removed outlier: 4.074A  pdb=" N   ILE B 999 " --> pdb=" O   TYR B 923 " (cutoff:3.500A)
      removed outlier: 9.743A  pdb=" N   SER B 925 " --> pdb=" O   LYS B 997 " (cutoff:3.500A)
      removed outlier: 12.262A  pdb=" N   LYS B 997 " --> pdb=" O   SER B 925 " (cutoff:3.500A)
      removed outlier: 15.444A  pdb=" N   THR B 927 " --> pdb=" O   ARG B 995 " (cutoff:3.500A)
      removed outlier: 16.944A  pdb=" N   ARG B 995 " --> pdb=" O   THR B 927 " (cutoff:3.500A)
      removed outlier: 8.803A  pdb=" N   PHE B1083 " --> pdb=" O   ARG B1059 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   THR B1061 " --> pdb=" O   PHE B1083 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   PHE B1085 " --> pdb=" O   THR B1061 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   GLU B1063 " --> pdb=" O   PHE B1085 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1088 through 1090
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1185 through 1187
      removed outlier: 8.969A  pdb=" N   THR B1185 " --> pdb=" O   ASP B1162 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU B1164 " --> pdb=" O   THR B1185 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   PHE B1187 " --> pdb=" O   LEU B1164 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA B1166 " --> pdb=" O   PHE B1187 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   LEU B1139 " --> pdb=" O   ASP B1162 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU B1164 " --> pdb=" O   LEU B1139 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   THR B1141 " --> pdb=" O   LEU B1164 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   ALA B1166 " --> pdb=" O   THR B1141 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ASP B1143 " --> pdb=" O   ALA B1166 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 1343 through 1344
    Processing sheet with id=AB5, first strand: chain 'B' and resid 1385 through 1386
    Processing sheet with id=AB6, first strand: chain 'B' and resid 1444 through 1445
      removed outlier: 4.043A  pdb=" N   VAL B1444 " --> pdb=" O   ALA B1452 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ALA B1452 " --> pdb=" O   VAL B1444 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6

    448 hydrogen bonds defined for protein.
    1161 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.33

  Time building geometry restraints manager: 3.55 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2658
        1.33 -     1.45: 2856
        1.45 -     1.57: 7028
        1.57 -     1.70: 1
        1.70 -     1.82: 123
  Bond restraints: 12666
  Sorted by residual:
  bond pdb=" CG  GLN A 626 "
       pdb=" CD  GLN A 626 "
    ideal  model  delta    sigma   weight residual
    1.516  1.445  0.071 2.50e-02 1.60e+03 8.03e+00
  bond pdb=" CB  PRO B1260 "
       pdb=" CG  PRO B1260 "
    ideal  model  delta    sigma   weight residual
    1.492  1.630 -0.138 5.00e-02 4.00e+02 7.58e+00
  bond pdb=" CG  PRO B1260 "
       pdb=" CD  PRO B1260 "
    ideal  model  delta    sigma   weight residual
    1.503  1.426  0.077 3.40e-02 8.65e+02 5.17e+00
  bond pdb=" CA  MET A 625 "
       pdb=" C   MET A 625 "
    ideal  model  delta    sigma   weight residual
    1.524  1.550 -0.026 1.26e-02 6.30e+03 4.29e+00
  bond pdb=" N   GLN A 626 "
       pdb=" CA  GLN A 626 "
    ideal  model  delta    sigma   weight residual
    1.455  1.478 -0.023 1.23e-02 6.61e+03 3.54e+00
  ... (remaining 12661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 16904
        3.15 -     6.29: 193
        6.29 -     9.44: 25
        9.44 -    12.58: 6
       12.58 -    15.73: 3
  Bond angle restraints: 17131
  Sorted by residual:
  angle pdb=" CA  PRO B1260 "
        pdb=" N   PRO B1260 "
        pdb=" CD  PRO B1260 "
      ideal   model   delta    sigma   weight residual
     112.00   97.98   14.02 1.40e+00 5.10e-01 1.00e+02
  angle pdb=" C   GLU B 711 "
        pdb=" N   MET B 712 "
        pdb=" CA  MET B 712 "
      ideal   model   delta    sigma   weight residual
     121.70  137.43  -15.73 1.80e+00 3.09e-01 7.63e+01
  angle pdb=" CA  ARG A 871 "
        pdb=" CB  ARG A 871 "
        pdb=" CG  ARG A 871 "
      ideal   model   delta    sigma   weight residual
     114.10  127.08  -12.98 2.00e+00 2.50e-01 4.21e+01
  angle pdb=" CA  MET A1045 "
        pdb=" CB  MET A1045 "
        pdb=" CG  MET A1045 "
      ideal   model   delta    sigma   weight residual
     114.10  124.57  -10.47 2.00e+00 2.50e-01 2.74e+01
  angle pdb=" C   HIS A 915 "
        pdb=" N   GLY A 916 "
        pdb=" CA  GLY A 916 "
      ideal   model   delta    sigma   weight residual
     122.17  117.56    4.61 8.90e-01 1.26e+00 2.68e+01
  ... (remaining 17126 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6654
       17.98 -    35.96: 763
       35.96 -    53.94: 210
       53.94 -    71.91: 45
       71.91 -    89.89: 27
  Dihedral angle restraints: 7699
    sinusoidal: 3175
      harmonic: 4524
  Sorted by residual:
  dihedral pdb=" CA  LYS A1033 "
           pdb=" C   LYS A1033 "
           pdb=" N   GLU A1034 "
           pdb=" CA  GLU A1034 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.27   34.73     0      5.00e+00 4.00e-02 4.82e+01
  dihedral pdb=" CA  GLU A1032 "
           pdb=" C   GLU A1032 "
           pdb=" N   LYS A1033 "
           pdb=" CA  LYS A1033 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.94  -28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  TYR B1405 "
           pdb=" C   TYR B1405 "
           pdb=" N   GLN B1406 "
           pdb=" CA  GLN B1406 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.86   25.14     0      5.00e+00 4.00e-02 2.53e+01
  ... (remaining 7696 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1567
       0.066 -    0.132: 236
       0.132 -    0.198: 21
       0.198 -    0.264: 6
       0.264 -    0.329: 2
  Chirality restraints: 1832
  Sorted by residual:
  chirality pdb=" CB  ILE A 797 "
            pdb=" CA  ILE A 797 "
            pdb=" CG1 ILE A 797 "
            pdb=" CG2 ILE A 797 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" CA  ARG A 871 "
            pdb=" N   ARG A 871 "
            pdb=" C   ARG A 871 "
            pdb=" CB  ARG A 871 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  LYS A 633 "
            pdb=" N   LYS A 633 "
            pdb=" C   LYS A 633 "
            pdb=" CB  LYS A 633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1829 not shown)

  Planarity restraints: 2250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B1259 "    0.110 5.00e-02 4.00e+02   1.54e-01 3.80e+01
        pdb=" N   PRO B1260 "   -0.266 5.00e-02 4.00e+02
        pdb=" CA  PRO B1260 "    0.079 5.00e-02 4.00e+02
        pdb=" CD  PRO B1260 "    0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 624 "    0.022 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        pdb=" C   PRO A 624 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   PRO A 624 "    0.029 2.00e-02 2.50e+03
        pdb=" N   MET A 625 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1018 "   -0.017 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   ARG A1018 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ARG A1018 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLU A1019 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2247 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 348
        2.69 -     3.24: 12381
        3.24 -     3.80: 19817
        3.80 -     4.35: 24880
        4.35 -     4.90: 40166
  Nonbonded interactions: 97592
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B1023 "
            pdb=" O   PRO B1361 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" OG1 THR B 885 "
            pdb=" OD1 ASN B 888 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG1 THR B1494 "
            pdb=" O   ILE B1496 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG1 THR B 780 "
            pdb=" O   PHE B 892 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OH  TYR B 524 "
            pdb=" OE2 GLU B 547 "
     model   vdw
     2.208 3.040
  ... (remaining 97587 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     30.110
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
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      :  0.004   0.138  12666  Z= 0.167
  Angle     :  0.869  15.728  17131  Z= 0.469
  Chirality :  0.049   0.329   1832
  Planarity :  0.006   0.154   2250
  Dihedral  : 17.380  89.893   4777
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 23.81 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.21), residues: 1535
  helix: -0.08 (0.26), residues: 383
  sheet: -0.64 (0.28), residues: 298
  loop : -0.16 (0.22), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B1395 
 HIS   0.008   0.001   HIS A 578 
 PHE   0.033   0.002   PHE B1274 
 TYR   0.015   0.002   TYR A 857 
 ARG   0.012   0.001   ARG A 723 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15696 (  436)
  hydrogen bonds       : angle       6.98713 ( 1161)
  covalent geometry    : bond        0.00379 (12666)
  covalent geometry    : angle       0.86877 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 1.338 
Fit side-chains
TARDY: cannot create tardy model for: "VAL B 561 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  632 PHE cc_start: 0.8470 (m-80) cc_final: 0.8123 (m-80)
REVERT: B 1136 LEU cc_start: 0.9259 (mm) cc_final: 0.8929 (mt)
REVERT: B 1260 PRO cc_start: 0.9186 (Cg_exo) cc_final: 0.8701 (Cg_endo)
REVERT: B 1544 GLN cc_start: 0.8143 (mt0) cc_final: 0.7899 (mt0)
  outliers start: 6
  outliers final: 4
  residues processed: 123
  average time/residue: 0.2064
  time to fit residues: 39.2608
Evaluate side-chains
  114 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain B residue  561 VAL
Chi-restraints excluded: chain B residue  937 ASP
Chi-restraints excluded: chain B residue  999 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 39 optimal weight:   20.0000
   chunk 78 optimal weight:    0.0570
   chunk 62 optimal weight:   20.0000
   chunk 120 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 73 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 139 optimal weight:    0.2980
   overall best weight:    0.8702

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

Flipped N/Q/H residues before XYZ refinement:
A 818 ASN
A 821 GLN
A 855 HIS
A 994 HIS
A1059 ASN
B 529 ASN
B 790 GLN
B 829 HIS
B 888 ASN
B1026 ASN
B1270 ASN
** B1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1427 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.158248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.097635 restraints weight = 28166.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.100479 restraints weight = 14470.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.102167 restraints weight = 9803.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12666  Z= 0.122
  Angle     :  0.608  10.080  17131  Z= 0.309
  Chirality :  0.043   0.185   1832
  Planarity :  0.005   0.073   2250
  Dihedral  :  4.630  53.056   1702
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.90 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.22), residues: 1535
  helix:  0.60 (0.27), residues: 400
  sheet: -0.35 (0.28), residues: 297
  loop :  0.11 (0.23), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B1395 
 HIS   0.004   0.001   HIS B1028 
 PHE   0.021   0.001   PHE B1274 
 TYR   0.014   0.001   TYR A 857 
 ARG   0.004   0.000   ARG B1023 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  436)
  hydrogen bonds       : angle       5.43807 ( 1161)
  covalent geometry    : bond        0.00273 (12666)
  covalent geometry    : angle       0.60765 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 1.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  611 GLN cc_start: 0.7968 (mm110) cc_final: 0.7711 (mm110)
REVERT: A  637 MET cc_start: 0.5871 (tpp) cc_final: 0.5335 (mmt)
REVERT: A  648 MET cc_start: 0.4341 (pmm) cc_final: 0.4017 (pmm)
REVERT: B  632 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8202 (m-80)
REVERT: B  712 MET cc_start: 0.4219 (mpp) cc_final: 0.3998 (mpp)
REVERT: B  753 ASP cc_start: 0.8611 (t70) cc_final: 0.8266 (p0)
REVERT: B  902 MET cc_start: 0.8850 (tpp) cc_final: 0.8624 (mmm)
REVERT: B 1136 LEU cc_start: 0.9093 (mm) cc_final: 0.8869 (mt)
REVERT: B 1397 GLN cc_start: 0.6776 (mt0) cc_final: 0.6339 (mt0)
REVERT: B 1413 ILE cc_start: 0.8556 (pt) cc_final: 0.8283 (pt)
REVERT: B 1533 MET cc_start: 0.6839 (ptp) cc_final: 0.6550 (ptm)
  outliers start: 34
  outliers final: 8
  residues processed: 151
  average time/residue: 0.2107
  time to fit residues: 49.9594
Evaluate side-chains
  119 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1590 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 135 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 51 optimal weight:   40.0000
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 115 optimal weight:    0.0020
   chunk 0 optimal weight:    9.9990
   overall best weight:    2.7794

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

Flipped N/Q/H residues before XYZ refinement:
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 792 HIS
** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 994 HIS
A1012 HIS
** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 529 ASN
** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1332 HIS
B1573 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.155961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.100584 restraints weight = 28601.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.100203 restraints weight = 16232.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.102200 restraints weight = 11456.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12666  Z= 0.200
  Angle     :  0.625   8.966  17131  Z= 0.319
  Chirality :  0.044   0.175   1832
  Planarity :  0.005   0.058   2250
  Dihedral  :  4.480  28.829   1694
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.71 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.19 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.21), residues: 1535
  helix:  0.56 (0.26), residues: 408
  sheet: -0.51 (0.28), residues: 310
  loop : -0.00 (0.22), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B1395 
 HIS   0.006   0.001   HIS B 719 
 PHE   0.020   0.002   PHE B1274 
 TYR   0.015   0.002   TYR B1022 
 ARG   0.005   0.000   ARG B1023 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  436)
  hydrogen bonds       : angle       5.38145 ( 1161)
  covalent geometry    : bond        0.00455 (12666)
  covalent geometry    : angle       0.62505 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 112
  time to evaluate  : 2.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  611 GLN cc_start: 0.8195 (mm110) cc_final: 0.7967 (mm110)
REVERT: A  637 MET cc_start: 0.6290 (tpp) cc_final: 0.6028 (tpp)
REVERT: A  818 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6605 (p0)
REVERT: B  504 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8324 (mp0)
REVERT: B  632 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8369 (m-80)
REVERT: B  712 MET cc_start: 0.3931 (mpp) cc_final: 0.3710 (mpp)
REVERT: B 1136 LEU cc_start: 0.9194 (mm) cc_final: 0.8927 (mt)
REVERT: B 1334 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7282 (t80)
REVERT: B 1462 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7679 (mmm160)
REVERT: B 1490 ARG cc_start: 0.7332 (ttt180) cc_final: 0.7020 (ttt180)
REVERT: B 1533 MET cc_start: 0.7110 (ptp) cc_final: 0.6784 (ptm)
REVERT: B 1544 GLN cc_start: 0.8147 (mt0) cc_final: 0.7875 (mt0)
  outliers start: 44
  outliers final: 29
  residues processed: 146
  average time/residue: 0.2118
  time to fit residues: 47.8895
Evaluate side-chains
  138 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  818 ASN
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  529 ASN
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  803 THR
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  832 VAL
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1235 PHE
Chi-restraints excluded: chain B residue 1248 VAL
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1374 LEU
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1420 LEU
Chi-restraints excluded: chain B residue 1421 VAL
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1548 VAL
Chi-restraints excluded: chain B residue 1562 THR
Chi-restraints excluded: chain B residue 1590 LEU
Chi-restraints excluded: chain B residue 1594 LEU
Chi-restraints excluded: chain B residue 1596 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 116 optimal weight:    5.9990
   chunk 76 optimal weight:    9.9990
   chunk 142 optimal weight:   10.0000
   chunk 100 optimal weight:    3.9990
   chunk 35 optimal weight:   20.0000
   chunk 79 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 98 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 87 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 562 HIS
A 728 GLN
** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1308 GLN
** B1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1573 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.153420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.098653 restraints weight = 27871.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.097773 restraints weight = 15900.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.099801 restraints weight = 11578.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  12666  Z= 0.269
  Angle     :  0.666  11.506  17131  Z= 0.340
  Chirality :  0.045   0.189   1832
  Planarity :  0.006   0.083   2250
  Dihedral  :  4.654  32.406   1694
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.17 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 20.97 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.21), residues: 1535
  helix:  0.35 (0.25), residues: 407
  sheet: -0.64 (0.28), residues: 311
  loop : -0.17 (0.22), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B1395 
 HIS   0.012   0.001   HIS A1012 
 PHE   0.023   0.002   PHE B1274 
 TYR   0.020   0.002   TYR B1022 
 ARG   0.008   0.001   ARG B1445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03821 (  436)
  hydrogen bonds       : angle       5.50632 ( 1161)
  covalent geometry    : bond        0.00609 (12666)
  covalent geometry    : angle       0.66639 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 104
  time to evaluate  : 2.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  611 GLN cc_start: 0.8261 (mm110) cc_final: 0.8030 (mm110)
REVERT: A  648 MET cc_start: 0.5584 (pmm) cc_final: 0.5292 (pmm)
REVERT: A  742 LEU cc_start: 0.9046 (tp) cc_final: 0.8762 (tp)
REVERT: A  780 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7729 (mm)
REVERT: A  801 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7775 (ttpp)
REVERT: B  504 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8279 (mp0)
REVERT: B  632 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8293 (m-80)
REVERT: B  753 ASP cc_start: 0.8846 (t70) cc_final: 0.8614 (p0)
REVERT: B  889 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8851 (mmmt)
REVERT: B 1136 LEU cc_start: 0.9202 (mm) cc_final: 0.8934 (mt)
REVERT: B 1334 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7262 (t80)
REVERT: B 1462 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7761 (mmm160)
REVERT: B 1490 ARG cc_start: 0.7635 (ttt180) cc_final: 0.7372 (ttt180)
  outliers start: 57
  outliers final: 40
  residues processed: 150
  average time/residue: 0.2525
  time to fit residues: 58.3642
Evaluate side-chains
  145 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 101
  time to evaluate  : 1.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  801 LYS
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  624 VAL
Chi-restraints excluded: chain B residue  630 THR
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  832 VAL
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1163 THR
Chi-restraints excluded: chain B residue 1165 TRP
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1248 VAL
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1279 VAL
Chi-restraints excluded: chain B residue 1284 LEU
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1351 VAL
Chi-restraints excluded: chain B residue 1365 ILE
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1420 LEU
Chi-restraints excluded: chain B residue 1421 VAL
Chi-restraints excluded: chain B residue 1492 PHE
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1548 VAL
Chi-restraints excluded: chain B residue 1562 THR
Chi-restraints excluded: chain B residue 1590 LEU
Chi-restraints excluded: chain B residue 1594 LEU
Chi-restraints excluded: chain B residue 1596 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 56 optimal weight:    0.0770
   chunk 108 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 7 optimal weight:    6.9990
   chunk 127 optimal weight:    5.9990
   overall best weight:    2.3544

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

Flipped N/Q/H residues before XYZ refinement:
** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 828 GLN
** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
A1025 GLN
** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1156 HIS
B1573 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.153485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.092407 restraints weight = 27893.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.095110 restraints weight = 14748.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.096863 restraints weight = 10296.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12666  Z= 0.176
  Angle     :  0.605  10.688  17131  Z= 0.304
  Chirality :  0.043   0.168   1832
  Planarity :  0.005   0.074   2250
  Dihedral  :  4.487  28.890   1694
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.67 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.21), residues: 1535
  helix:  0.61 (0.26), residues: 410
  sheet: -0.59 (0.28), residues: 309
  loop : -0.07 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B1395 
 HIS   0.009   0.001   HIS A 562 
 PHE   0.021   0.001   PHE B1274 
 TYR   0.014   0.001   TYR B1022 
 ARG   0.006   0.000   ARG B1445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03434 (  436)
  hydrogen bonds       : angle       5.22799 ( 1161)
  covalent geometry    : bond        0.00402 (12666)
  covalent geometry    : angle       0.60515 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 103
  time to evaluate  : 2.762 
Fit side-chains
   revert: symmetry clash
REVERT: A  611 GLN cc_start: 0.8103 (mm110) cc_final: 0.7840 (mm110)
REVERT: A  637 MET cc_start: 0.6510 (tpp) cc_final: 0.6207 (tpp)
REVERT: A  648 MET cc_start: 0.5044 (pmm) cc_final: 0.4733 (pmm)
REVERT: A  821 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.7039 (mp10)
REVERT: B  504 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8249 (mp0)
REVERT: B  632 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8222 (m-80)
REVERT: B  712 MET cc_start: 0.4163 (mpp) cc_final: 0.3892 (mpp)
REVERT: B  753 ASP cc_start: 0.8521 (t0) cc_final: 0.8292 (p0)
REVERT: B  885 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7319 (p)
REVERT: B 1136 LEU cc_start: 0.9064 (mm) cc_final: 0.8854 (mt)
REVERT: B 1329 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6877 (mm-30)
REVERT: B 1334 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.7281 (t80)
REVERT: B 1490 ARG cc_start: 0.7605 (ttt180) cc_final: 0.7363 (ttt180)
  outliers start: 58
  outliers final: 34
  residues processed: 150
  average time/residue: 0.3070
  time to fit residues: 70.1434
Evaluate side-chains
  140 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 101
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  821 GLN
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  655 VAL
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  803 THR
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  832 VAL
Chi-restraints excluded: chain B residue  885 THR
Chi-restraints excluded: chain B residue  999 ILE
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1235 PHE
Chi-restraints excluded: chain B residue 1248 VAL
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1256 ASP
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1284 LEU
Chi-restraints excluded: chain B residue 1329 GLU
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1351 VAL
Chi-restraints excluded: chain B residue 1374 LEU
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1418 SER
Chi-restraints excluded: chain B residue 1420 LEU
Chi-restraints excluded: chain B residue 1421 VAL
Chi-restraints excluded: chain B residue 1446 LEU
Chi-restraints excluded: chain B residue 1492 PHE
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1536 GLN
Chi-restraints excluded: chain B residue 1594 LEU
Chi-restraints excluded: chain B residue 1596 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 56 optimal weight:    0.0770
   chunk 105 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 147 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9980
   chunk 118 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   overall best weight:    1.6144

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

Flipped N/Q/H residues before XYZ refinement:
** A 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1573 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.154408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.094393 restraints weight = 28006.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.097046 restraints weight = 14589.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.098920 restraints weight = 10059.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12666  Z= 0.139
  Angle     :  0.596  10.081  17131  Z= 0.295
  Chirality :  0.042   0.171   1832
  Planarity :  0.005   0.067   2250
  Dihedral  :  4.348  26.196   1694
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 20.97 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.22), residues: 1535
  helix:  0.87 (0.26), residues: 404
  sheet: -0.40 (0.29), residues: 311
  loop :  0.06 (0.23), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B1395 
 HIS   0.006   0.001   HIS A 562 
 PHE   0.019   0.001   PHE B1274 
 TYR   0.012   0.001   TYR A 857 
 ARG   0.006   0.000   ARG B1462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (  436)
  hydrogen bonds       : angle       5.05076 ( 1161)
  covalent geometry    : bond        0.00323 (12666)
  covalent geometry    : angle       0.59560 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 115
  time to evaluate  : 1.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  565 MET cc_start: 0.8493 (pmm) cc_final: 0.7821 (pmm)
REVERT: A  637 MET cc_start: 0.6273 (tpp) cc_final: 0.5977 (tpp)
REVERT: A  648 MET cc_start: 0.5478 (pmm) cc_final: 0.5166 (pmm)
REVERT: B  504 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8203 (mp0)
REVERT: B  632 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8357 (m-80)
REVERT: B  712 MET cc_start: 0.4008 (mpp) cc_final: 0.3667 (mpp)
REVERT: B  753 ASP cc_start: 0.8581 (t0) cc_final: 0.8286 (p0)
REVERT: B  892 PHE cc_start: 0.7459 (t80) cc_final: 0.7065 (t80)
REVERT: B 1082 ARG cc_start: 0.8616 (mtt180) cc_final: 0.8140 (mtt180)
REVERT: B 1329 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6887 (mm-30)
REVERT: B 1334 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7269 (t80)
REVERT: B 1399 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: B 1439 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7466 (tt)
REVERT: B 1490 ARG cc_start: 0.7528 (ttt180) cc_final: 0.7304 (ttt180)
  outliers start: 55
  outliers final: 37
  residues processed: 160
  average time/residue: 0.2325
  time to fit residues: 57.7453
Evaluate side-chains
  145 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 104
  time to evaluate  : 1.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  736 GLU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  832 VAL
Chi-restraints excluded: chain B residue  985 LEU
Chi-restraints excluded: chain B residue  999 ILE
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1163 THR
Chi-restraints excluded: chain B residue 1165 TRP
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1235 PHE
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1256 ASP
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1284 LEU
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1329 GLU
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1351 VAL
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1374 LEU
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1439 LEU
Chi-restraints excluded: chain B residue 1492 PHE
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1536 GLN
Chi-restraints excluded: chain B residue 1580 VAL
Chi-restraints excluded: chain B residue 1594 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 102 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 65 optimal weight:   30.0000
   chunk 16 optimal weight:    0.6980
   chunk 116 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 94 optimal weight:    8.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    2.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 GLN
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1573 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.152723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.091656 restraints weight = 27962.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.094094 restraints weight = 15044.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095643 restraints weight = 10442.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12666  Z= 0.204
  Angle     :  0.637  10.813  17131  Z= 0.318
  Chirality :  0.044   0.294   1832
  Planarity :  0.005   0.069   2250
  Dihedral  :  4.470  29.380   1694
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.36 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 21.19 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.22), residues: 1535
  helix:  0.75 (0.26), residues: 405
  sheet: -0.47 (0.29), residues: 311
  loop : -0.05 (0.23), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B1395 
 HIS   0.005   0.001   HIS A 562 
 PHE   0.020   0.002   PHE B1274 
 TYR   0.015   0.002   TYR B1022 
 ARG   0.006   0.000   ARG B1445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (  436)
  hydrogen bonds       : angle       5.16516 ( 1161)
  covalent geometry    : bond        0.00468 (12666)
  covalent geometry    : angle       0.63653 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 103
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  565 MET cc_start: 0.8458 (pmm) cc_final: 0.7814 (pmm)
REVERT: A  637 MET cc_start: 0.6556 (tpp) cc_final: 0.6238 (tpp)
REVERT: A  648 MET cc_start: 0.5688 (pmm) cc_final: 0.5351 (pmm)
REVERT: A  787 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8644 (t80)
REVERT: B  504 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8224 (mp0)
REVERT: B  632 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8221 (m-80)
REVERT: B  885 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7187 (p)
REVERT: B  892 PHE cc_start: 0.7597 (t80) cc_final: 0.7154 (t80)
REVERT: B 1329 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6900 (mm-30)
REVERT: B 1334 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.7263 (t80)
REVERT: B 1439 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7539 (tt)
REVERT: B 1451 MET cc_start: 0.7245 (tmm) cc_final: 0.6608 (tmm)
REVERT: B 1490 ARG cc_start: 0.7670 (ttt180) cc_final: 0.7404 (ttt180)
  outliers start: 61
  outliers final: 45
  residues processed: 154
  average time/residue: 0.2092
  time to fit residues: 49.4789
Evaluate side-chains
  152 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 101
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  787 PHE
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue 1012 HIS
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  630 THR
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  655 VAL
Chi-restraints excluded: chain B residue  736 GLU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  804 VAL
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  832 VAL
Chi-restraints excluded: chain B residue  885 THR
Chi-restraints excluded: chain B residue  985 LEU
Chi-restraints excluded: chain B residue  999 ILE
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1038 ASP
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1163 THR
Chi-restraints excluded: chain B residue 1165 TRP
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1248 VAL
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1256 ASP
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1284 LEU
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1329 GLU
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1351 VAL
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1374 LEU
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1418 SER
Chi-restraints excluded: chain B residue 1439 LEU
Chi-restraints excluded: chain B residue 1492 PHE
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1536 GLN
Chi-restraints excluded: chain B residue 1562 THR
Chi-restraints excluded: chain B residue 1573 HIS
Chi-restraints excluded: chain B residue 1580 VAL
Chi-restraints excluded: chain B residue 1594 LEU
Chi-restraints excluded: chain B residue 1596 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 152 optimal weight:    0.7980
   chunk 143 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9980
   chunk 12 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   chunk 79 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 86 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 39 optimal weight:   10.0000
   overall best weight:    2.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1573 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.153288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.092263 restraints weight = 28108.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.094902 restraints weight = 14769.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.096625 restraints weight = 10272.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12666  Z= 0.164
  Angle     :  0.620  10.289  17131  Z= 0.307
  Chirality :  0.043   0.295   1832
  Planarity :  0.005   0.065   2250
  Dihedral  :  4.417  27.973   1694
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 22.16 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.22), residues: 1535
  helix:  0.89 (0.26), residues: 399
  sheet: -0.38 (0.29), residues: 306
  loop : -0.02 (0.23), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B1395 
 HIS   0.023   0.001   HIS B1573 
 PHE   0.018   0.001   PHE B1274 
 TYR   0.012   0.001   TYR B1022 
 ARG   0.004   0.000   ARG B1023 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  436)
  hydrogen bonds       : angle       5.04728 ( 1161)
  covalent geometry    : bond        0.00379 (12666)
  covalent geometry    : angle       0.62008 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 105
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
REVERT: A  637 MET cc_start: 0.6523 (tpp) cc_final: 0.6243 (tpp)
REVERT: A  648 MET cc_start: 0.5809 (pmm) cc_final: 0.5527 (pmm)
REVERT: A  787 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8597 (t80)
REVERT: A  801 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7806 (ttpp)
REVERT: B  504 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8256 (mp0)
REVERT: B  555 GLN cc_start: 0.7370 (pp30) cc_final: 0.7158 (tm-30)
REVERT: B  632 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8118 (m-80)
REVERT: B  712 MET cc_start: 0.3993 (mpp) cc_final: 0.3679 (mpp)
REVERT: B  885 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7366 (p)
REVERT: B  892 PHE cc_start: 0.7582 (t80) cc_final: 0.7138 (t80)
REVERT: B 1082 ARG cc_start: 0.8714 (mtt180) cc_final: 0.7979 (mtt90)
REVERT: B 1232 MET cc_start: 0.7141 (ttp) cc_final: 0.6861 (tmm)
REVERT: B 1274 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7101 (t80)
REVERT: B 1329 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6929 (mm-30)
REVERT: B 1334 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7259 (t80)
REVERT: B 1439 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7504 (tt)
REVERT: B 1451 MET cc_start: 0.7217 (tmm) cc_final: 0.6565 (tmm)
REVERT: B 1490 ARG cc_start: 0.7664 (ttt180) cc_final: 0.7379 (ttt180)
  outliers start: 54
  outliers final: 40
  residues processed: 152
  average time/residue: 0.2196
  time to fit residues: 51.0528
Evaluate side-chains
  150 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 102
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  787 PHE
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  801 LYS
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  736 GLU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  832 VAL
Chi-restraints excluded: chain B residue  885 THR
Chi-restraints excluded: chain B residue  985 LEU
Chi-restraints excluded: chain B residue  999 ILE
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1163 THR
Chi-restraints excluded: chain B residue 1165 TRP
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1248 VAL
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1256 ASP
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1284 LEU
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1329 GLU
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1351 VAL
Chi-restraints excluded: chain B residue 1365 ILE
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1374 LEU
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1418 SER
Chi-restraints excluded: chain B residue 1439 LEU
Chi-restraints excluded: chain B residue 1492 PHE
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1536 GLN
Chi-restraints excluded: chain B residue 1562 THR
Chi-restraints excluded: chain B residue 1580 VAL
Chi-restraints excluded: chain B residue 1592 ILE
Chi-restraints excluded: chain B residue 1594 LEU
Chi-restraints excluded: chain B residue 1596 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0070
   chunk 88 optimal weight:    7.9990
   chunk 147 optimal weight:    0.9990
   chunk 58 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 123 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9990
   chunk 148 optimal weight:    8.9990
   overall best weight:    3.2006

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

Flipped N/Q/H residues before XYZ refinement:
** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 888 ASN
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1181 ASN
** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1573 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.151503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.094931 restraints weight = 28343.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.097258 restraints weight = 17051.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.097915 restraints weight = 10334.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12666  Z= 0.224
  Angle     :  0.670  13.811  17131  Z= 0.333
  Chirality :  0.044   0.234   1832
  Planarity :  0.005   0.063   2250
  Dihedral  :  4.634  30.932   1694
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.63 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 22.16 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.22), residues: 1535
  helix:  0.79 (0.26), residues: 391
  sheet: -0.57 (0.29), residues: 308
  loop : -0.14 (0.22), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B1395 
 HIS   0.007   0.001   HIS A1012 
 PHE   0.020   0.002   PHE B1274 
 TYR   0.018   0.002   TYR B1022 
 ARG   0.005   0.001   ARG B1023 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  436)
  hydrogen bonds       : angle       5.25330 ( 1161)
  covalent geometry    : bond        0.00514 (12666)
  covalent geometry    : angle       0.67008 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 100
  time to evaluate  : 1.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  565 MET cc_start: 0.9070 (pmm) cc_final: 0.8301 (pmm)
REVERT: A  637 MET cc_start: 0.6744 (tpp) cc_final: 0.6438 (tpp)
REVERT: A  648 MET cc_start: 0.6176 (pmm) cc_final: 0.5896 (pmm)
REVERT: A  787 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8834 (t80)
REVERT: A  801 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7874 (ttpp)
REVERT: A 1021 MET cc_start: 0.1203 (OUTLIER) cc_final: 0.0892 (tmm)
REVERT: B  504 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8278 (mp0)
REVERT: B  632 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8382 (m-80)
REVERT: B  712 MET cc_start: 0.3562 (mpp) cc_final: 0.2908 (pmm)
REVERT: B  885 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8089 (p)
REVERT: B 1073 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6090 (tm-30)
REVERT: B 1082 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8125 (mtt180)
REVERT: B 1235 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8194 (m-80)
REVERT: B 1274 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7045 (t80)
REVERT: B 1329 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6958 (mm-30)
REVERT: B 1334 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.7264 (t80)
REVERT: B 1451 MET cc_start: 0.7119 (tmm) cc_final: 0.6588 (tmm)
REVERT: B 1490 ARG cc_start: 0.7866 (ttt180) cc_final: 0.7661 (ttt180)
  outliers start: 56
  outliers final: 41
  residues processed: 150
  average time/residue: 0.2444
  time to fit residues: 57.4149
Evaluate side-chains
  148 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 97
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  787 PHE
Chi-restraints excluded: chain A residue  801 LYS
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  655 VAL
Chi-restraints excluded: chain B residue  736 GLU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  770 SER
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  832 VAL
Chi-restraints excluded: chain B residue  885 THR
Chi-restraints excluded: chain B residue  985 LEU
Chi-restraints excluded: chain B residue  999 ILE
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1038 ASP
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain B residue 1073 GLN
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1163 THR
Chi-restraints excluded: chain B residue 1165 TRP
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1235 PHE
Chi-restraints excluded: chain B residue 1248 VAL
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1256 ASP
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1284 LEU
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1329 GLU
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1351 VAL
Chi-restraints excluded: chain B residue 1365 ILE
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1374 LEU
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1414 CYS
Chi-restraints excluded: chain B residue 1418 SER
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1536 GLN
Chi-restraints excluded: chain B residue 1562 THR
Chi-restraints excluded: chain B residue 1580 VAL
Chi-restraints excluded: chain B residue 1594 LEU
Chi-restraints excluded: chain B residue 1596 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 60 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 40 optimal weight:   20.0000
   chunk 85 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 529 ASN
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1573 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.154581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.095313 restraints weight = 27796.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 89)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.096534 restraints weight = 14249.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.098494 restraints weight = 9621.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12666  Z= 0.121
  Angle     :  0.637  16.030  17131  Z= 0.308
  Chirality :  0.043   0.271   1832
  Planarity :  0.004   0.064   2250
  Dihedral  :  4.341  25.439   1694
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.13 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.22), residues: 1535
  helix:  1.04 (0.27), residues: 393
  sheet: -0.37 (0.30), residues: 300
  loop :  0.09 (0.23), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B1395 
 HIS   0.004   0.001   HIS A1012 
 PHE   0.017   0.001   PHE B1274 
 TYR   0.011   0.001   TYR A 857 
 ARG   0.005   0.000   ARG B1023 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03182 (  436)
  hydrogen bonds       : angle       4.93369 ( 1161)
  covalent geometry    : bond        0.00283 (12666)
  covalent geometry    : angle       0.63714 (17131)

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

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

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3070 Ramachandran restraints generated.
    1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 97
  time to evaluate  : 2.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  565 MET cc_start: 0.8666 (pmm) cc_final: 0.8008 (pmm)
REVERT: A  625 MET cc_start: 0.8135 (tpp) cc_final: 0.7865 (tpp)
REVERT: A  637 MET cc_start: 0.6475 (tpp) cc_final: 0.6211 (tpp)
REVERT: A  648 MET cc_start: 0.5818 (pmm) cc_final: 0.5614 (pmm)
REVERT: A  787 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8607 (t80)
REVERT: A  817 MET cc_start: 0.7822 (tpp) cc_final: 0.7572 (tpp)
REVERT: A 1021 MET cc_start: 0.0713 (OUTLIER) cc_final: 0.0504 (tmm)
REVERT: B  504 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8282 (mp0)
REVERT: B  632 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8178 (m-80)
REVERT: B  712 MET cc_start: 0.4342 (mpp) cc_final: 0.3658 (pmm)
REVERT: B  753 ASP cc_start: 0.8682 (t70) cc_final: 0.8412 (p0)
REVERT: B  892 PHE cc_start: 0.7518 (t80) cc_final: 0.7224 (t80)
REVERT: B 1082 ARG cc_start: 0.8691 (mtt180) cc_final: 0.8263 (mtt180)
REVERT: B 1284 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8310 (mm)
REVERT: B 1329 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6998 (mm-30)
REVERT: B 1334 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7277 (t80)
REVERT: B 1439 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7626 (tt)
REVERT: B 1451 MET cc_start: 0.7175 (tmm) cc_final: 0.6616 (tmm)
REVERT: B 1490 ARG cc_start: 0.7687 (ttt180) cc_final: 0.7420 (ttt180)
  outliers start: 44
  outliers final: 31
  residues processed: 136
  average time/residue: 0.2879
  time to fit residues: 63.5905
Evaluate side-chains
  133 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 95
  time to evaluate  : 3.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  727 ILE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  787 PHE
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  632 PHE
Chi-restraints excluded: chain B residue  736 GLU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  795 HIS
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  825 LEU
Chi-restraints excluded: chain B residue  999 ILE
Chi-restraints excluded: chain B residue 1020 LYS
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain B residue 1148 CYS
Chi-restraints excluded: chain B residue 1163 THR
Chi-restraints excluded: chain B residue 1217 VAL
Chi-restraints excluded: chain B residue 1249 VAL
Chi-restraints excluded: chain B residue 1256 ASP
Chi-restraints excluded: chain B residue 1274 PHE
Chi-restraints excluded: chain B residue 1284 LEU
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1329 GLU
Chi-restraints excluded: chain B residue 1334 PHE
Chi-restraints excluded: chain B residue 1351 VAL
Chi-restraints excluded: chain B residue 1367 VAL
Chi-restraints excluded: chain B residue 1374 LEU
Chi-restraints excluded: chain B residue 1377 VAL
Chi-restraints excluded: chain B residue 1439 LEU
Chi-restraints excluded: chain B residue 1492 PHE
Chi-restraints excluded: chain B residue 1527 VAL
Chi-restraints excluded: chain B residue 1528 THR
Chi-restraints excluded: chain B residue 1536 GLN
Chi-restraints excluded: chain B residue 1580 VAL
Chi-restraints excluded: chain B residue 1594 LEU
Chi-restraints excluded: chain B residue 1596 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 104 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 143 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 62 optimal weight:   30.0000
   chunk 49 optimal weight:   40.0000
   chunk 38 optimal weight:   20.0000
   chunk 51 optimal weight:    0.0570
   chunk 146 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.8106

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

Flipped N/Q/H residues before XYZ refinement:
** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1573 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.151758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.090618 restraints weight = 28180.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.093258 restraints weight = 15139.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.095030 restraints weight = 10768.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  12666  Z= 0.203
  Angle     :  0.667  15.124  17131  Z= 0.330
  Chirality :  0.044   0.198   1832
  Planarity :  0.005   0.063   2250
  Dihedral  :  4.487  28.877   1694
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.82 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.76 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.10 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.22), residues: 1535
  helix:  0.99 (0.27), residues: 392
  sheet: -0.46 (0.30), residues: 298
  loop :  0.00 (0.23), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B1395 
 HIS   0.005   0.001   HIS B1541 
 PHE   0.020   0.002   PHE B 631 
 TYR   0.018   0.002   TYR B1022 
 ARG   0.004   0.000   ARG B1445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  436)
  hydrogen bonds       : angle       5.11474 ( 1161)
  covalent geometry    : bond        0.00469 (12666)
  covalent geometry    : angle       0.66668 (17131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6557.99 seconds
wall clock time: 119 minutes 44.73 seconds (7184.73 seconds total)