Starting phenix.real_space_refine
on Sun Aug 24 02:38:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5wrg_6679/08_2025/5wrg_6679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5wrg_6679/08_2025/5wrg_6679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5wrg_6679/08_2025/5wrg_6679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5wrg_6679/08_2025/5wrg_6679.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5wrg_6679/08_2025/5wrg_6679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5wrg_6679/08_2025/5wrg_6679.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      87      5.16       5
     C   10281      2.51       5
     N    2760      2.21       5
     O    3189      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16317
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 736, 5439
          Classifications: {'peptide': 736}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 76}
          Link IDs: {'CIS': 26, 'PCIS': 1, 'PTRANS': 34, 'TRANS': 674}
          Chain breaks: 4
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 298
          Unresolved non-hydrogen angles: 388
          Unresolved non-hydrogen dihedrals: 255
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 5, 'TRP:plan': 1, 'ARG:plan': 4, 'TYR:plan': 6, 'PHE:plan': 6, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 166
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 4.89, per 1000 atoms: 0.30
  Number of scatterers: 16317
  At special positions: 0
  Unit cell: (109.56, 108.24, 149.16, 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      87     16.00
     O    3189      8.00
     N    2760      7.00
     C   10281      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 288 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 366 " - pdb=" SG  CYS A 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 467 " - pdb=" SG  CYS A 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 524 " - pdb=" SG  CYS A 576 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 648 " - pdb=" SG  CYS A 657 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 720 " - pdb=" SG  CYS A 742 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 725 " - pdb=" SG  CYS A 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 278 " - pdb=" SG  CYS B 288 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 278 " - pdb=" SG  CYS C 288 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 323 " - pdb=" SG  CYS B 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 323 " - pdb=" SG  CYS C 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 366 " - pdb=" SG  CYS B 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 366 " - pdb=" SG  CYS C 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 467 " - pdb=" SG  CYS B 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 467 " - pdb=" SG  CYS C 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 524 " - pdb=" SG  CYS B 576 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 524 " - pdb=" SG  CYS C 576 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 648 " - pdb=" SG  CYS B 657 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 648 " - pdb=" SG  CYS C 657 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 720 " - pdb=" SG  CYS B 742 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 720 " - pdb=" SG  CYS C 742 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 725 " - pdb=" SG  CYS B 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 725 " - pdb=" SG  CYS C 731 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.38
  Conformation dependent library (CDL) restraints added in 626.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4140

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 24 sheets defined
      28.4% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 281 through 290
      removed outlier: 3.952A  pdb=" N   LEU A 286 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 351 through 357
      removed outlier: 3.867A  pdb=" N   LEU A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 395
      removed outlier: 3.812A  pdb=" N   VAL A 394 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG A 395 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 391 through 395'
    Processing helix  chain 'A' and resid 402 through 409
      removed outlier: 4.131A  pdb=" N   ALA A 406 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 719 through 724
    Processing helix  chain 'A' and resid 728 through 734
    Processing helix  chain 'A' and resid 743 through 765
      removed outlier: 3.931A  pdb=" N   LEU A 749 " --> pdb=" O   LEU A 745 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE A 752 " --> pdb=" O   ALA A 748 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 753 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN A 759 " --> pdb=" O   GLU A 755 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 806
      removed outlier: 3.897A  pdb=" N   ASP A 802 " --> pdb=" O   SER A 798 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASN A 806 " --> pdb=" O   ASP A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 848 through 860
      removed outlier: 3.874A  pdb=" N   ALA A 858 " --> pdb=" O   ALA A 854 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU A 859 " --> pdb=" O   TYR A 855 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL A 860 " --> pdb=" O   THR A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 891
      removed outlier: 3.504A  pdb=" N   ILE A 891 " --> pdb=" O   ARG A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 898
    Processing helix  chain 'A' and resid 901 through 917
      removed outlier: 3.677A  pdb=" N   ALA A 906 " --> pdb=" O   GLN A 902 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA A 912 " --> pdb=" O   GLN A 908 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLN A 915 " --> pdb=" O   LYS A 911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 949
      removed outlier: 3.591A  pdb=" N   VAL A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 934 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA A 940 " --> pdb=" O   GLN A 936 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER A 949 " --> pdb=" O   VAL A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 966
      removed outlier: 4.102A  pdb=" N   ILE A 962 " --> pdb=" O   VAL A 958 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   SER A 964 " --> pdb=" O   ASN A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 1011
      removed outlier: 3.601A  pdb=" N   ASP A 976 " --> pdb=" O   GLU A 972 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A 977 " --> pdb=" O   VAL A 973 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR A 980 " --> pdb=" O   ASP A 976 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLY A 981 " --> pdb=" O   ARG A 977 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE A 995 " --> pdb=" O   THR A 991 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ARG A 996 " --> pdb=" O   GLN A 992 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 290
      removed outlier: 3.951A  pdb=" N   LEU B 286 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS B 287 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 330
    Processing helix  chain 'B' and resid 351 through 357
      removed outlier: 3.868A  pdb=" N   LEU B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 395
      removed outlier: 3.812A  pdb=" N   VAL B 394 " --> pdb=" O   GLY B 391 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG B 395 " --> pdb=" O   ASP B 392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 391 through 395'
    Processing helix  chain 'B' and resid 402 through 409
      removed outlier: 4.130A  pdb=" N   ALA B 406 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 603 through 609
    Processing helix  chain 'B' and resid 719 through 724
    Processing helix  chain 'B' and resid 728 through 734
    Processing helix  chain 'B' and resid 743 through 765
      removed outlier: 3.931A  pdb=" N   LEU B 749 " --> pdb=" O   LEU B 745 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE B 752 " --> pdb=" O   ALA B 748 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B 753 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASP B 757 " --> pdb=" O   ALA B 753 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN B 759 " --> pdb=" O   GLU B 755 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR B 760 " --> pdb=" O   GLN B 756 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 798 through 806
      removed outlier: 3.899A  pdb=" N   ASP B 802 " --> pdb=" O   SER B 798 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN B 806 " --> pdb=" O   ASP B 802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 848 through 860
      removed outlier: 3.874A  pdb=" N   ALA B 858 " --> pdb=" O   ALA B 854 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU B 859 " --> pdb=" O   TYR B 855 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B 860 " --> pdb=" O   THR B 856 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 880 through 891
      removed outlier: 3.504A  pdb=" N   ILE B 891 " --> pdb=" O   ARG B 887 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 898
    Processing helix  chain 'B' and resid 901 through 917
      removed outlier: 3.678A  pdb=" N   ALA B 906 " --> pdb=" O   GLN B 902 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA B 912 " --> pdb=" O   GLN B 908 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLN B 915 " --> pdb=" O   LYS B 911 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 927 through 949
      removed outlier: 3.591A  pdb=" N   VAL B 933 " --> pdb=" O   LYS B 929 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B 934 " --> pdb=" O   LEU B 930 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ALA B 940 " --> pdb=" O   GLN B 936 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER B 949 " --> pdb=" O   VAL B 945 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 958 through 966
      removed outlier: 4.101A  pdb=" N   ILE B 962 " --> pdb=" O   VAL B 958 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER B 964 " --> pdb=" O   ASN B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 970 through 1011
      removed outlier: 3.599A  pdb=" N   ASP B 976 " --> pdb=" O   GLU B 972 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG B 977 " --> pdb=" O   VAL B 973 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR B 980 " --> pdb=" O   ASP B 976 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY B 981 " --> pdb=" O   ARG B 977 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 991 " --> pdb=" O   GLN B 987 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE B 995 " --> pdb=" O   THR B 991 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ARG B 996 " --> pdb=" O   GLN B 992 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 290
      removed outlier: 3.952A  pdb=" N   LEU C 286 " --> pdb=" O   PRO C 282 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS C 287 " --> pdb=" O   LEU C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 330
    Processing helix  chain 'C' and resid 351 through 357
      removed outlier: 3.868A  pdb=" N   LEU C 355 " --> pdb=" O   ASP C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 395
      removed outlier: 3.811A  pdb=" N   VAL C 394 " --> pdb=" O   GLY C 391 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG C 395 " --> pdb=" O   ASP C 392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 391 through 395'
    Processing helix  chain 'C' and resid 402 through 409
      removed outlier: 4.131A  pdb=" N   ALA C 406 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 603 through 609
    Processing helix  chain 'C' and resid 719 through 724
    Processing helix  chain 'C' and resid 728 through 734
    Processing helix  chain 'C' and resid 743 through 765
      removed outlier: 3.931A  pdb=" N   LEU C 749 " --> pdb=" O   LEU C 745 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE C 752 " --> pdb=" O   ALA C 748 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA C 753 " --> pdb=" O   LEU C 749 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASP C 757 " --> pdb=" O   ALA C 753 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASN C 759 " --> pdb=" O   GLU C 755 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR C 760 " --> pdb=" O   GLN C 756 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 798 through 806
      removed outlier: 3.898A  pdb=" N   ASP C 802 " --> pdb=" O   SER C 798 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN C 806 " --> pdb=" O   ASP C 802 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 848 through 860
      removed outlier: 3.874A  pdb=" N   ALA C 858 " --> pdb=" O   ALA C 854 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU C 859 " --> pdb=" O   TYR C 855 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL C 860 " --> pdb=" O   THR C 856 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 880 through 891
      removed outlier: 3.504A  pdb=" N   ILE C 891 " --> pdb=" O   ARG C 887 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 898
    Processing helix  chain 'C' and resid 901 through 917
      removed outlier: 3.677A  pdb=" N   ALA C 906 " --> pdb=" O   GLN C 902 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA C 912 " --> pdb=" O   GLN C 908 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLN C 915 " --> pdb=" O   LYS C 911 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 927 through 949
      removed outlier: 3.591A  pdb=" N   VAL C 933 " --> pdb=" O   LYS C 929 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL C 934 " --> pdb=" O   LEU C 930 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA C 940 " --> pdb=" O   GLN C 936 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER C 949 " --> pdb=" O   VAL C 945 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 958 through 966
      removed outlier: 4.101A  pdb=" N   ILE C 962 " --> pdb=" O   VAL C 958 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER C 964 " --> pdb=" O   ASN C 960 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 970 through 1011
      removed outlier: 3.600A  pdb=" N   ASP C 976 " --> pdb=" O   GLU C 972 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG C 977 " --> pdb=" O   VAL C 973 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR C 980 " --> pdb=" O   ASP C 976 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLY C 981 " --> pdb=" O   ARG C 977 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR C 991 " --> pdb=" O   GLN C 987 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE C 995 " --> pdb=" O   THR C 991 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ARG C 996 " --> pdb=" O   GLN C 992 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 303
      removed outlier: 3.700A  pdb=" N   GLY A 580 " --> pdb=" O   SER A 303 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 595 " --> pdb=" O   VAL A 583 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 344
      removed outlier: 4.461A  pdb=" N   GLU A 341 " --> pdb=" O   SER A 386 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER A 386 " --> pdb=" O   GLU A 341 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   CYS A 419 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY A 418 " --> pdb=" O   TYR A 367 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441
      removed outlier: 3.697A  pdb=" N   ASN A 479 " --> pdb=" O   TYR A 440 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 537 through 539
      removed outlier: 3.681A  pdb=" N   SER A 574 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR A 539 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 700 through 701
    Processing sheet with id=AA7, first strand: chain 'A' and resid 704 through 710
      removed outlier: 3.555A  pdb=" N   GLU A 707 " --> pdb=" O   PHE A1044 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 716 through 718
    Processing sheet with id=AA9, first strand: chain 'B' and resid 266 through 267
    Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 303
      removed outlier: 3.699A  pdb=" N   GLY B 580 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA B 595 " --> pdb=" O   VAL B 583 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 341 through 344
      removed outlier: 4.461A  pdb=" N   GLU B 341 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   SER B 386 " --> pdb=" O   GLU B 341 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   CYS B 419 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY B 418 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 440 through 441
      removed outlier: 3.698A  pdb=" N   ASN B 479 " --> pdb=" O   TYR B 440 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 537 through 539
      removed outlier: 3.681A  pdb=" N   SER B 574 " --> pdb=" O   VAL B 537 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR B 539 " --> pdb=" O   ASP B 572 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 700 through 701
    Processing sheet with id=AB6, first strand: chain 'B' and resid 704 through 710
      removed outlier: 3.556A  pdb=" N   GLU B 707 " --> pdb=" O   PHE B1044 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 716 through 718
    Processing sheet with id=AB8, first strand: chain 'C' and resid 266 through 267
    Processing sheet with id=AB9, first strand: chain 'C' and resid 302 through 303
      removed outlier: 3.700A  pdb=" N   GLY C 580 " --> pdb=" O   SER C 303 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA C 595 " --> pdb=" O   VAL C 583 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 344
      removed outlier: 4.461A  pdb=" N   GLU C 341 " --> pdb=" O   SER C 386 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   SER C 386 " --> pdb=" O   GLU C 341 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   CYS C 419 " --> pdb=" O   LEU C 499 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY C 418 " --> pdb=" O   TYR C 367 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 440 through 441
      removed outlier: 3.697A  pdb=" N   ASN C 479 " --> pdb=" O   TYR C 440 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 537 through 539
      removed outlier: 3.681A  pdb=" N   SER C 574 " --> pdb=" O   VAL C 537 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR C 539 " --> pdb=" O   ASP C 572 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 700 through 701
    Processing sheet with id=AC5, first strand: chain 'C' and resid 704 through 710
      removed outlier: 3.555A  pdb=" N   GLU C 707 " --> pdb=" O   PHE C1044 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 716 through 718

    465 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 5001
        1.33 -     1.45: 2872
        1.45 -     1.57: 8618
        1.57 -     1.69: 3
        1.69 -     1.81: 114
  Bond restraints: 16608
  Sorted by residual:
  bond pdb=" CA  PRO A 547 "
       pdb=" C   PRO A 547 "
    ideal  model  delta    sigma   weight residual
    1.516  1.569 -0.052 1.42e-02 4.96e+03 1.36e+01
  bond pdb=" CA  PRO B 547 "
       pdb=" C   PRO B 547 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 1.42e-02 4.96e+03 1.35e+01
  bond pdb=" CA  PRO C 547 "
       pdb=" C   PRO C 547 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 1.42e-02 4.96e+03 1.32e+01
  bond pdb=" CA  VAL B 675 "
       pdb=" C   VAL B 675 "
    ideal  model  delta    sigma   weight residual
    1.525  1.585 -0.060 2.10e-02 2.27e+03 8.04e+00
  bond pdb=" CA  VAL A 675 "
       pdb=" C   VAL A 675 "
    ideal  model  delta    sigma   weight residual
    1.525  1.583 -0.058 2.10e-02 2.27e+03 7.72e+00
  ... (remaining 16603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.01: 21707
        3.01 -     6.02: 666
        6.02 -     9.03: 148
        9.03 -    12.03: 63
       12.03 -    15.04: 21
  Bond angle restraints: 22605
  Sorted by residual:
  angle pdb=" C   GLU C1013 "
        pdb=" N   CYS C1014 "
        pdb=" CA  CYS C1014 "
      ideal   model   delta    sigma   weight residual
     121.70  136.74  -15.04 1.80e+00 3.09e-01 6.98e+01
  angle pdb=" C   GLU A1013 "
        pdb=" N   CYS A1014 "
        pdb=" CA  CYS A1014 "
      ideal   model   delta    sigma   weight residual
     121.70  136.71  -15.01 1.80e+00 3.09e-01 6.95e+01
  angle pdb=" C   GLU B1013 "
        pdb=" N   CYS B1014 "
        pdb=" CA  CYS B1014 "
      ideal   model   delta    sigma   weight residual
     121.70  136.67  -14.97 1.80e+00 3.09e-01 6.91e+01
  angle pdb=" N   PRO C 547 "
        pdb=" CA  PRO C 547 "
        pdb=" C   PRO C 547 "
      ideal   model   delta    sigma   weight residual
     113.40  124.33  -10.93 1.34e+00 5.57e-01 6.66e+01
  angle pdb=" N   PRO B 547 "
        pdb=" CA  PRO B 547 "
        pdb=" C   PRO B 547 "
      ideal   model   delta    sigma   weight residual
     113.40  124.31  -10.91 1.34e+00 5.57e-01 6.63e+01
  ... (remaining 22600 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 9312
       16.79 -    33.58: 530
       33.58 -    50.37: 94
       50.37 -    67.17: 15
       67.17 -    83.96: 27
  Dihedral angle restraints: 9978
    sinusoidal: 3561
      harmonic: 6417
  Sorted by residual:
  dihedral pdb=" CA  CYS B 524 "
           pdb=" C   CYS B 524 "
           pdb=" N   VAL B 525 "
           pdb=" CA  VAL B 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -96.04  -83.96     0      5.00e+00 4.00e-02 2.82e+02
  dihedral pdb=" CA  CYS A 524 "
           pdb=" C   CYS A 524 "
           pdb=" N   VAL A 525 "
           pdb=" CA  VAL A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -96.07  -83.93     0      5.00e+00 4.00e-02 2.82e+02
  dihedral pdb=" CA  CYS C 524 "
           pdb=" C   CYS C 524 "
           pdb=" N   VAL C 525 "
           pdb=" CA  VAL C 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -96.11  -83.89     0      5.00e+00 4.00e-02 2.81e+02
  ... (remaining 9975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 2319
       0.092 -    0.184: 274
       0.184 -    0.277: 41
       0.277 -    0.369: 9
       0.369 -    0.461: 3
  Chirality restraints: 2646
  Sorted by residual:
  chirality pdb=" CB  VAL A 525 "
            pdb=" CA  VAL A 525 "
            pdb=" CG1 VAL A 525 "
            pdb=" CG2 VAL A 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.31e+00
  chirality pdb=" CB  VAL C 525 "
            pdb=" CA  VAL C 525 "
            pdb=" CG1 VAL C 525 "
            pdb=" CG2 VAL C 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.28e+00
  chirality pdb=" CB  VAL B 525 "
            pdb=" CA  VAL B 525 "
            pdb=" CG1 VAL B 525 "
            pdb=" CG2 VAL B 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.25e+00
  ... (remaining 2643 not shown)

  Planarity restraints: 2958
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 741 "    0.022 2.00e-02 2.50e+03   4.50e-02 2.03e+01
        pdb=" C   PHE C 741 "   -0.078 2.00e-02 2.50e+03
        pdb=" O   PHE C 741 "    0.029 2.00e-02 2.50e+03
        pdb=" N   CYS C 742 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 741 "   -0.022 2.00e-02 2.50e+03   4.50e-02 2.02e+01
        pdb=" C   PHE B 741 "    0.078 2.00e-02 2.50e+03
        pdb=" O   PHE B 741 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   CYS B 742 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 741 "   -0.022 2.00e-02 2.50e+03   4.46e-02 1.99e+01
        pdb=" C   PHE A 741 "    0.077 2.00e-02 2.50e+03
        pdb=" O   PHE A 741 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   CYS A 742 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 2955 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1551
        2.73 -     3.27: 16254
        3.27 -     3.82: 26901
        3.82 -     4.36: 30472
        4.36 -     4.90: 48791
  Nonbonded interactions: 123969
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 646 "
            pdb=" OH  TYR A 677 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   TYR C 646 "
            pdb=" OH  TYR C 677 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   TYR B 646 "
            pdb=" OH  TYR B 677 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   PHE C 741 "
            pdb=" N   GLN C 744 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   PHE A 741 "
            pdb=" N   GLN A 744 "
     model   vdw
     2.264 3.120
  ... (remaining 123964 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.760
  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:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.890
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  16632  Z= 0.355
  Angle     :  1.400  15.044  22653  Z= 0.769
  Chirality :  0.066   0.461   2646
  Planarity :  0.007   0.049   2958
  Dihedral  : 12.061  83.958   5766
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.69 %
    Allowed  : 17.95 %
    Favored  : 81.36 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  4.27 %
    Favored  : 95.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.15 %
    Twisted Proline : 9.09 %
    Twisted General : 1.58 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.05 (0.15), residues: 2178
  helix: -3.26 (0.14), residues: 534
  sheet: -2.15 (0.33), residues: 228
  loop : -3.86 (0.14), residues: 1416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B1001 
 TYR   0.018   0.003   TYR C 899 
 PHE   0.028   0.003   PHE B1024 
 TRP   0.007   0.001   TRP A 423 
 HIS   0.003   0.001   HIS B 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 (16608)
  covalent geometry    : angle       1.39874 (22605)
  SS BOND              : bond        0.00998 (   24)
  SS BOND              : angle       1.84652 (   48)
  hydrogen bonds       : bond        0.28541 (  465)
  hydrogen bonds       : angle      10.37160 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  417 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 408
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  709 MET cc_start: 0.8259 (mmt) cc_final: 0.8018 (mmt)
REVERT: A  838 ASN cc_start: 0.8566 (p0) cc_final: 0.8107 (p0)
REVERT: A  851 MET cc_start: 0.8697 (tpt) cc_final: 0.8461 (tpp)
REVERT: A  974 GLN cc_start: 0.8454 (mm110) cc_final: 0.8155 (mm-40)
REVERT: A  984 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: B  340 TRP cc_start: 0.7825 (p-90) cc_final: 0.7127 (p-90)
REVERT: B  518 ASP cc_start: 0.6730 (m-30) cc_final: 0.6439 (p0)
REVERT: B  557 ASP cc_start: 0.8269 (m-30) cc_final: 0.8006 (m-30)
REVERT: B  715 LYS cc_start: 0.8288 (tttt) cc_final: 0.8071 (ttmt)
REVERT: B  740 SER cc_start: 0.7861 (t) cc_final: 0.7027 (t)
REVERT: C  532 LEU cc_start: 0.8370 (pt) cc_final: 0.7780 (mp)
REVERT: C  558 PHE cc_start: 0.8459 (m-10) cc_final: 0.8239 (m-10)
REVERT: C  708 VAL cc_start: 0.9375 (m) cc_final: 0.8749 (m)
REVERT: C  733 ASN cc_start: 0.8867 (t0) cc_final: 0.8452 (t0)
REVERT: C  743 THR cc_start: 0.9290 (p) cc_final: 0.9052 (t)
REVERT: C  932 ASP cc_start: 0.8279 (t70) cc_final: 0.8027 (t70)
  outliers start: 9
  outliers final: 3
  residues processed: 417
  average time/residue: 0.1346
  time to fit residues: 81.1520
Evaluate side-chains
  228 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 225
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 216 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0370
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.0970
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 200 optimal weight:    3.9990
   chunk 212 optimal weight:    0.9980
   overall best weight:    0.3654

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
A 401 GLN
A 910 ASN
A 960 ASN
A1046 HIS
B 381 ASN
B 401 GLN
B 910 ASN
B1018 GLN
B1046 HIS
C 401 GLN
C 910 ASN
C 960 ASN
C 987 GLN
C1018 GLN
C1046 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.116992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.089244 restraints weight = 58319.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.090993 restraints weight = 39588.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.092157 restraints weight = 29625.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.093043 restraints weight = 23945.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.093584 restraints weight = 20423.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16632  Z= 0.177
  Angle     :  0.967  13.120  22653  Z= 0.513
  Chirality :  0.051   0.225   2646
  Planarity :  0.005   0.045   2958
  Dihedral  :  8.290  48.443   2343
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 15.52 %
    Favored  : 84.34 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.26 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.44 %
    Twisted Proline : 6.06 %
    Twisted General : 0.67 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.35 (0.15), residues: 2178
  helix: -1.79 (0.18), residues: 558
  sheet: -1.73 (0.33), residues: 249
  loop : -3.85 (0.14), residues: 1371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 306 
 TYR   0.018   0.001   TYR C 738 
 PHE   0.021   0.002   PHE B 741 
 TRP   0.007   0.001   TRP C 476 
 HIS   0.003   0.001   HIS B 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (16608)
  covalent geometry    : angle       0.96511 (22605)
  SS BOND              : bond        0.00325 (   24)
  SS BOND              : angle       1.56990 (   48)
  hydrogen bonds       : bond        0.05402 (  465)
  hydrogen bonds       : angle       6.65807 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 316
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LYS cc_start: 0.9020 (tmmt) cc_final: 0.8754 (ttpp)
REVERT: A  441 ARG cc_start: 0.6081 (ttm-80) cc_final: 0.5839 (mtt-85)
REVERT: A  444 ARG cc_start: 0.5469 (ttt-90) cc_final: 0.4951 (mtp-110)
REVERT: A  480 ASP cc_start: 0.5903 (m-30) cc_final: 0.5666 (m-30)
REVERT: A  532 LEU cc_start: 0.8941 (pt) cc_final: 0.8619 (pt)
REVERT: A  709 MET cc_start: 0.8563 (mmt) cc_final: 0.8268 (mmm)
REVERT: A  942 ASN cc_start: 0.8521 (m-40) cc_final: 0.8129 (m110)
REVERT: A  946 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8270 (tmmt)
REVERT: A  969 VAL cc_start: 0.9506 (t) cc_final: 0.8785 (t)
REVERT: A  976 ASP cc_start: 0.9211 (m-30) cc_final: 0.8789 (p0)
REVERT: A  984 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: A  988 THR cc_start: 0.9403 (m) cc_final: 0.9015 (m)
REVERT: A  992 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8419 (tp-100)
REVERT: A  999 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8046 (tm-30)
REVERT: B  263 MET cc_start: 0.0698 (mmm) cc_final: 0.0401 (tpp)
REVERT: B  340 TRP cc_start: 0.5966 (p-90) cc_final: 0.5720 (p-90)
REVERT: B  518 ASP cc_start: 0.7228 (m-30) cc_final: 0.6718 (p0)
REVERT: B  557 ASP cc_start: 0.8233 (m-30) cc_final: 0.8005 (m-30)
REVERT: B  558 PHE cc_start: 0.8671 (m-10) cc_final: 0.8413 (m-10)
REVERT: B  636 LEU cc_start: 0.9108 (tp) cc_final: 0.8892 (tp)
REVERT: B  762 GLU cc_start: 0.8328 (tt0) cc_final: 0.7999 (tt0)
REVERT: B  987 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8773 (tp-100)
REVERT: B  999 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: C  294 GLU cc_start: 0.7939 (tt0) cc_final: 0.7613 (tt0)
REVERT: C  417 MET cc_start: 0.6549 (ttt) cc_final: 0.6277 (ttp)
REVERT: C  532 LEU cc_start: 0.8997 (pt) cc_final: 0.8516 (mp)
REVERT: C  558 PHE cc_start: 0.8447 (m-10) cc_final: 0.8129 (m-10)
REVERT: C  650 ILE cc_start: 0.9291 (mt) cc_final: 0.8847 (mt)
REVERT: C  707 GLU cc_start: 0.6442 (tm-30) cc_final: 0.6017 (pp20)
REVERT: C  708 VAL cc_start: 0.9336 (m) cc_final: 0.8883 (p)
REVERT: C  733 ASN cc_start: 0.9493 (t0) cc_final: 0.9087 (t0)
REVERT: C  743 THR cc_start: 0.9446 (p) cc_final: 0.9232 (t)
REVERT: C 1000 ILE cc_start: 0.9683 (mt) cc_final: 0.9422 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 319
  average time/residue: 0.1178
  time to fit residues: 56.5308
Evaluate side-chains
  221 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 105 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 184 optimal weight:    0.0040
   chunk 131 optimal weight:    0.0870
   chunk 23 optimal weight:    6.9990
   chunk 147 optimal weight:    5.9990
   chunk 214 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0980
   chunk 27 optimal weight:    0.8980
   chunk 175 optimal weight:    3.9990
   overall best weight:    0.2770

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

Flipped N/Q/H residues before XYZ refinement:
A 759 ASN
A 960 ASN
B1018 GLN
C 301 GLN
** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 960 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.117659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.089907 restraints weight = 59341.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.091707 restraints weight = 44048.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.093019 restraints weight = 29937.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.093184 restraints weight = 25503.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.093449 restraints weight = 22446.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  16632  Z= 0.164
  Angle     :  0.918  14.206  22653  Z= 0.483
  Chirality :  0.050   0.246   2646
  Planarity :  0.005   0.060   2958
  Dihedral  :  7.436  47.997   2343
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 15.24 %
    Favored  : 84.57 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.80 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.58 %
    Twisted Proline : 6.06 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.91 (0.16), residues: 2178
  helix: -1.05 (0.20), residues: 555
  sheet: -1.47 (0.34), residues: 249
  loop : -3.75 (0.14), residues: 1374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 306 
 TYR   0.010   0.001   TYR C 723 
 PHE   0.015   0.001   PHE A 293 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (16608)
  covalent geometry    : angle       0.91785 (22605)
  SS BOND              : bond        0.00186 (   24)
  SS BOND              : angle       1.01296 (   48)
  hydrogen bonds       : bond        0.04484 (  465)
  hydrogen bonds       : angle       5.94168 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 279
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LYS cc_start: 0.8933 (tmmt) cc_final: 0.8285 (ttpp)
REVERT: A  373 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7510 (mppt)
REVERT: A  444 ARG cc_start: 0.5987 (ttt-90) cc_final: 0.5465 (mtp-110)
REVERT: A  532 LEU cc_start: 0.9057 (pt) cc_final: 0.8848 (mp)
REVERT: A  709 MET cc_start: 0.8382 (mmt) cc_final: 0.7990 (mmm)
REVERT: A  932 ASP cc_start: 0.8836 (t70) cc_final: 0.8624 (t0)
REVERT: A  935 ASN cc_start: 0.9244 (m-40) cc_final: 0.8916 (m-40)
REVERT: A  942 ASN cc_start: 0.8506 (m-40) cc_final: 0.8214 (m-40)
REVERT: A  945 VAL cc_start: 0.9181 (t) cc_final: 0.8908 (m)
REVERT: A  976 ASP cc_start: 0.9242 (m-30) cc_final: 0.8779 (p0)
REVERT: A  984 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: A  988 THR cc_start: 0.9526 (m) cc_final: 0.9226 (m)
REVERT: A  992 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8525 (tm-30)
REVERT: B  340 TRP cc_start: 0.6620 (p-90) cc_final: 0.6192 (p-90)
REVERT: B  518 ASP cc_start: 0.7478 (m-30) cc_final: 0.6871 (p0)
REVERT: B  557 ASP cc_start: 0.8333 (m-30) cc_final: 0.8040 (m-30)
REVERT: B  558 PHE cc_start: 0.8580 (m-10) cc_final: 0.8352 (m-10)
REVERT: B  636 LEU cc_start: 0.9126 (tp) cc_final: 0.8879 (tp)
REVERT: B  762 GLU cc_start: 0.8208 (tt0) cc_final: 0.7936 (tt0)
REVERT: B  987 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8605 (tp40)
REVERT: C  263 MET cc_start: 0.1718 (tpt) cc_final: 0.1400 (tpt)
REVERT: C  532 LEU cc_start: 0.8845 (pt) cc_final: 0.8374 (mp)
REVERT: C  558 PHE cc_start: 0.8497 (m-10) cc_final: 0.8168 (m-10)
REVERT: C  650 ILE cc_start: 0.9173 (mt) cc_final: 0.8893 (mt)
REVERT: C  708 VAL cc_start: 0.9393 (m) cc_final: 0.9076 (p)
REVERT: C  733 ASN cc_start: 0.9528 (t0) cc_final: 0.9171 (t0)
REVERT: C  743 THR cc_start: 0.9413 (p) cc_final: 0.9206 (t)
REVERT: C  894 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7543 (p)
REVERT: C 1000 ILE cc_start: 0.9642 (mt) cc_final: 0.9225 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 282
  average time/residue: 0.1096
  time to fit residues: 47.0007
Evaluate side-chains
  215 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 214
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 168 optimal weight:    5.9990
   chunk 206 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 153 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 170 optimal weight:    6.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 766 GLN
A 902 GLN
A 960 ASN
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 902 GLN
B 917 GLN
B1018 GLN
C 381 ASN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 902 GLN
C 939 GLN
** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 960 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.111347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.082554 restraints weight = 60234.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.084324 restraints weight = 40627.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.085587 restraints weight = 30190.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.086437 restraints weight = 24192.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.086945 restraints weight = 20626.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  16632  Z= 0.230
  Angle     :  0.970  14.107  22653  Z= 0.509
  Chirality :  0.050   0.280   2646
  Planarity :  0.005   0.061   2958
  Dihedral  :  7.431  50.010   2343
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 17.95 %
    Favored  : 81.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.63 %
    Twisted Proline : 5.05 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.73 (0.17), residues: 2178
  helix: -0.67 (0.22), residues: 573
  sheet: -1.60 (0.33), residues: 246
  loop : -3.73 (0.15), residues: 1359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B1001 
 TYR   0.021   0.002   TYR A 723 
 PHE   0.017   0.002   PHE B 578 
 TRP   0.007   0.001   TRP C 423 
 HIS   0.009   0.002   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (16608)
  covalent geometry    : angle       0.96938 (22605)
  SS BOND              : bond        0.00381 (   24)
  SS BOND              : angle       1.24080 (   48)
  hydrogen bonds       : bond        0.04405 (  465)
  hydrogen bonds       : angle       5.91083 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 ARG cc_start: 0.5813 (ttt-90) cc_final: 0.5194 (mtp-110)
REVERT: A  650 ILE cc_start: 0.9058 (mt) cc_final: 0.8646 (mm)
REVERT: A  709 MET cc_start: 0.8089 (mmt) cc_final: 0.7855 (mmt)
REVERT: A  719 ASP cc_start: 0.8636 (t0) cc_final: 0.8276 (t0)
REVERT: A  935 ASN cc_start: 0.9260 (m-40) cc_final: 0.8937 (m-40)
REVERT: A  942 ASN cc_start: 0.8629 (m-40) cc_final: 0.8339 (m110)
REVERT: A  969 VAL cc_start: 0.9154 (t) cc_final: 0.8944 (t)
REVERT: A  976 ASP cc_start: 0.9240 (m-30) cc_final: 0.8805 (p0)
REVERT: A  992 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8617 (tm-30)
REVERT: B  286 LEU cc_start: 0.9620 (mt) cc_final: 0.9288 (mt)
REVERT: B  518 ASP cc_start: 0.7785 (m-30) cc_final: 0.6902 (p0)
REVERT: B  557 ASP cc_start: 0.8230 (m-30) cc_final: 0.7889 (m-30)
REVERT: B  636 LEU cc_start: 0.9066 (tp) cc_final: 0.8832 (tp)
REVERT: B  738 TYR cc_start: 0.6117 (p90) cc_final: 0.5662 (p90)
REVERT: B  758 ARG cc_start: 0.8643 (tpm170) cc_final: 0.8191 (tpp-160)
REVERT: B  762 GLU cc_start: 0.8410 (tt0) cc_final: 0.8160 (tt0)
REVERT: B  983 LEU cc_start: 0.9532 (tp) cc_final: 0.9275 (tt)
REVERT: B  987 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8688 (tp-100)
REVERT: B  999 GLU cc_start: 0.8129 (tp30) cc_final: 0.7830 (tp30)
REVERT: C  381 ASN cc_start: 0.5934 (m110) cc_final: 0.5146 (m110)
REVERT: C  557 ASP cc_start: 0.8009 (t70) cc_final: 0.7723 (t70)
REVERT: C  715 LYS cc_start: 0.8313 (tttt) cc_final: 0.8012 (mmmt)
REVERT: C  733 ASN cc_start: 0.9560 (t0) cc_final: 0.9222 (t0)
REVERT: C  758 ARG cc_start: 0.8467 (tpm170) cc_final: 0.8211 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1100
  time to fit residues: 43.4669
Evaluate side-chains
  192 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 176 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 166 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 130 optimal weight:    0.9980
   chunk 82 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0070
   chunk 108 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 96 optimal weight:   20.0000
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
A 522 ASN
A 902 GLN
B 902 GLN
B 947 GLN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN
C 902 GLN
C 960 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.113787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.085334 restraints weight = 58886.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.087784 restraints weight = 41940.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.089200 restraints weight = 27446.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.089847 restraints weight = 21956.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.089915 restraints weight = 18129.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16632  Z= 0.160
  Angle     :  0.913  13.934  22653  Z= 0.476
  Chirality :  0.049   0.260   2646
  Planarity :  0.004   0.040   2958
  Dihedral  :  7.086  48.548   2343
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 15.11 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.14 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.63 %
    Twisted Proline : 5.05 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.41 (0.17), residues: 2178
  helix: -0.18 (0.22), residues: 579
  sheet: -1.37 (0.33), residues: 243
  loop : -3.65 (0.15), residues: 1356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 306 
 TYR   0.012   0.001   TYR C 300 
 PHE   0.017   0.001   PHE A 529 
 TRP   0.003   0.000   TRP B 340 
 HIS   0.004   0.001   HIS A1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (16608)
  covalent geometry    : angle       0.91204 (22605)
  SS BOND              : bond        0.00326 (   24)
  SS BOND              : angle       1.18238 (   48)
  hydrogen bonds       : bond        0.03854 (  465)
  hydrogen bonds       : angle       5.48141 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 266
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LYS cc_start: 0.8832 (pptt) cc_final: 0.8511 (ptmm)
REVERT: A  444 ARG cc_start: 0.5726 (ttt-90) cc_final: 0.5008 (mtp-110)
REVERT: A  557 ASP cc_start: 0.8501 (m-30) cc_final: 0.8262 (m-30)
REVERT: A  650 ILE cc_start: 0.8982 (mt) cc_final: 0.8568 (mm)
REVERT: A  709 MET cc_start: 0.8231 (mmt) cc_final: 0.7993 (mmm)
REVERT: A  719 ASP cc_start: 0.8499 (t0) cc_final: 0.8133 (t0)
REVERT: A  935 ASN cc_start: 0.9269 (m-40) cc_final: 0.8927 (m-40)
REVERT: A  942 ASN cc_start: 0.8672 (m-40) cc_final: 0.8367 (m110)
REVERT: A  969 VAL cc_start: 0.9213 (t) cc_final: 0.8996 (t)
REVERT: A  976 ASP cc_start: 0.9124 (m-30) cc_final: 0.8831 (p0)
REVERT: A  992 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8550 (tm-30)
REVERT: A 1011 MET cc_start: 0.8132 (tmm) cc_final: 0.7920 (tmm)
REVERT: B  340 TRP cc_start: 0.6823 (p-90) cc_final: 0.6278 (p-90)
REVERT: B  518 ASP cc_start: 0.7809 (m-30) cc_final: 0.7028 (p0)
REVERT: B  557 ASP cc_start: 0.7881 (m-30) cc_final: 0.7580 (m-30)
REVERT: B  715 LYS cc_start: 0.8263 (tttt) cc_final: 0.8015 (tttt)
REVERT: B  738 TYR cc_start: 0.5990 (p90) cc_final: 0.5319 (p90)
REVERT: B  758 ARG cc_start: 0.8489 (tpm170) cc_final: 0.8093 (tpp-160)
REVERT: B  762 GLU cc_start: 0.8184 (tt0) cc_final: 0.7933 (tt0)
REVERT: B  935 ASN cc_start: 0.9326 (m-40) cc_final: 0.9039 (m-40)
REVERT: B  952 PHE cc_start: 0.6961 (t80) cc_final: 0.6617 (m-80)
REVERT: B  987 GLN cc_start: 0.9192 (tp-100) cc_final: 0.8567 (tp-100)
REVERT: C  381 ASN cc_start: 0.5872 (m110) cc_final: 0.5333 (m110)
REVERT: C  417 MET cc_start: 0.6404 (ttp) cc_final: 0.6019 (ttp)
REVERT: C  449 ARG cc_start: 0.0699 (ptt-90) cc_final: 0.0214 (ptp-170)
REVERT: C  557 ASP cc_start: 0.7855 (t70) cc_final: 0.7630 (t70)
REVERT: C  599 GLN cc_start: 0.8714 (mt0) cc_final: 0.8490 (mt0)
REVERT: C  650 ILE cc_start: 0.9279 (mt) cc_final: 0.8912 (mt)
REVERT: C  715 LYS cc_start: 0.8258 (tttt) cc_final: 0.7967 (mmmt)
REVERT: C  718 VAL cc_start: 0.9488 (t) cc_final: 0.9282 (m)
REVERT: C  733 ASN cc_start: 0.9577 (t0) cc_final: 0.9224 (t0)
REVERT: C  992 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8385 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1140
  time to fit residues: 45.8775
Evaluate side-chains
  201 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0050
   chunk 205 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 22 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.3998

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

Flipped N/Q/H residues before XYZ refinement:
A 522 ASN
A 902 GLN
A 917 GLN
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 947 GLN
C 301 GLN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN
C 902 GLN
C 960 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.111973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.083462 restraints weight = 60030.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.085105 restraints weight = 41723.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.086316 restraints weight = 31680.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.087099 restraints weight = 25728.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.087649 restraints weight = 22199.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16632  Z= 0.178
  Angle     :  0.917  14.359  22653  Z= 0.480
  Chirality :  0.049   0.255   2646
  Planarity :  0.004   0.051   2958
  Dihedral  :  7.027  48.131   2343
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 17.13 %
    Favored  : 82.69 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.73 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.63 %
    Twisted Proline : 3.03 %
    Twisted General : 0.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.34 (0.17), residues: 2178
  helix: -0.05 (0.23), residues: 579
  sheet: -1.43 (0.33), residues: 252
  loop : -3.63 (0.15), residues: 1347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C1001 
 TYR   0.016   0.001   TYR A 723 
 PHE   0.023   0.002   PHE A 361 
 TRP   0.003   0.001   TRP A 423 
 HIS   0.007   0.001   HIS A 641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (16608)
  covalent geometry    : angle       0.91537 (22605)
  SS BOND              : bond        0.00736 (   24)
  SS BOND              : angle       1.59115 (   48)
  hydrogen bonds       : bond        0.03728 (  465)
  hydrogen bonds       : angle       5.47018 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 252
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LYS cc_start: 0.8587 (pptt) cc_final: 0.7966 (ptmm)
REVERT: A  423 TRP cc_start: 0.8326 (p90) cc_final: 0.8083 (p90)
REVERT: A  444 ARG cc_start: 0.5491 (ttt-90) cc_final: 0.5021 (mtp-110)
REVERT: A  557 ASP cc_start: 0.8457 (m-30) cc_final: 0.8224 (m-30)
REVERT: A  707 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6237 (pp20)
REVERT: A  719 ASP cc_start: 0.8648 (t0) cc_final: 0.8278 (t0)
REVERT: A  935 ASN cc_start: 0.9228 (m-40) cc_final: 0.8843 (m-40)
REVERT: A  942 ASN cc_start: 0.8765 (m-40) cc_final: 0.8409 (m-40)
REVERT: A  969 VAL cc_start: 0.9200 (t) cc_final: 0.8982 (t)
REVERT: A  992 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8571 (tm-30)
REVERT: A 1011 MET cc_start: 0.8039 (tmm) cc_final: 0.7790 (tmm)
REVERT: B  518 ASP cc_start: 0.7876 (m-30) cc_final: 0.7043 (p0)
REVERT: B  557 ASP cc_start: 0.7877 (m-30) cc_final: 0.7551 (m-30)
REVERT: B  558 PHE cc_start: 0.8788 (m-10) cc_final: 0.8242 (m-10)
REVERT: B  738 TYR cc_start: 0.6079 (p90) cc_final: 0.5278 (p90)
REVERT: B  758 ARG cc_start: 0.8544 (tpm170) cc_final: 0.7996 (tpp-160)
REVERT: B  762 GLU cc_start: 0.8309 (tt0) cc_final: 0.8080 (tt0)
REVERT: B  983 LEU cc_start: 0.9489 (tp) cc_final: 0.9242 (tt)
REVERT: B  987 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8514 (tp-100)
REVERT: C  417 MET cc_start: 0.6582 (ttp) cc_final: 0.6365 (ttp)
REVERT: C  449 ARG cc_start: 0.0227 (ptt-90) cc_final: -0.0241 (ptp-170)
REVERT: C  650 ILE cc_start: 0.9305 (mt) cc_final: 0.8950 (mt)
REVERT: C  733 ASN cc_start: 0.9551 (t0) cc_final: 0.9296 (t0)
REVERT: C  992 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8412 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1164
  time to fit residues: 44.3711
Evaluate side-chains
  191 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 208 optimal weight:    0.9990
   chunk 139 optimal weight:    0.6980
   chunk 167 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 155 optimal weight:   10.0000
   chunk 150 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 104 optimal weight:    0.6980
   chunk 145 optimal weight:    0.1980
   chunk 107 optimal weight:    0.0870
   chunk 133 optimal weight:    5.9990
   overall best weight:    0.5360

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

Flipped N/Q/H residues before XYZ refinement:
A 960 ASN
B 902 GLN
B 947 GLN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN
C 960 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.114234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.085484 restraints weight = 59266.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.087367 restraints weight = 41261.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.088563 restraints weight = 30838.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.089328 restraints weight = 25089.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.089925 restraints weight = 21695.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.5422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  16632  Z= 0.153
  Angle     :  0.909  14.353  22653  Z= 0.472
  Chirality :  0.049   0.300   2646
  Planarity :  0.004   0.047   2958
  Dihedral  :  6.800  47.276   2343
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 14.46 %
    Favored  : 85.40 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.61 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.68 %
    Twisted Proline : 3.03 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.17), residues: 2178
  helix:  0.00 (0.22), residues: 579
  sheet: -1.18 (0.34), residues: 243
  loop : -3.55 (0.15), residues: 1356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1001 
 TYR   0.012   0.001   TYR B 723 
 PHE   0.017   0.001   PHE A 361 
 TRP   0.007   0.001   TRP B 340 
 HIS   0.003   0.001   HIS B1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (16608)
  covalent geometry    : angle       0.90809 (22605)
  SS BOND              : bond        0.00302 (   24)
  SS BOND              : angle       1.40615 (   48)
  hydrogen bonds       : bond        0.03586 (  465)
  hydrogen bonds       : angle       5.23983 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TRP cc_start: 0.8239 (p90) cc_final: 0.7990 (p90)
REVERT: A  444 ARG cc_start: 0.5690 (ttt-90) cc_final: 0.5368 (mtp-110)
REVERT: A  558 PHE cc_start: 0.9017 (m-10) cc_final: 0.8629 (m-10)
REVERT: A  707 GLU cc_start: 0.7731 (tm-30) cc_final: 0.5755 (tm-30)
REVERT: A  713 MET cc_start: 0.8295 (ttt) cc_final: 0.7892 (ttp)
REVERT: A  719 ASP cc_start: 0.8532 (t0) cc_final: 0.8115 (t0)
REVERT: A  935 ASN cc_start: 0.9267 (m-40) cc_final: 0.8902 (m-40)
REVERT: A  942 ASN cc_start: 0.8696 (m-40) cc_final: 0.8337 (m-40)
REVERT: A  969 VAL cc_start: 0.9209 (t) cc_final: 0.8998 (t)
REVERT: A  992 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8547 (tm-30)
REVERT: A 1011 MET cc_start: 0.7969 (tmm) cc_final: 0.7683 (tmm)
REVERT: B  340 TRP cc_start: 0.6775 (p-90) cc_final: 0.6237 (p-90)
REVERT: B  518 ASP cc_start: 0.7891 (m-30) cc_final: 0.7200 (p0)
REVERT: B  557 ASP cc_start: 0.7726 (m-30) cc_final: 0.7391 (m-30)
REVERT: B  738 TYR cc_start: 0.6125 (p90) cc_final: 0.5471 (p90)
REVERT: B  758 ARG cc_start: 0.8491 (tpm170) cc_final: 0.7961 (tpp-160)
REVERT: B  762 GLU cc_start: 0.8369 (tt0) cc_final: 0.8133 (tt0)
REVERT: B  935 ASN cc_start: 0.9196 (m-40) cc_final: 0.8912 (m-40)
REVERT: B  952 PHE cc_start: 0.6954 (t80) cc_final: 0.6728 (m-80)
REVERT: B  983 LEU cc_start: 0.9469 (tp) cc_final: 0.9224 (tp)
REVERT: B  987 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8380 (tp-100)
REVERT: C  304 ASN cc_start: 0.8605 (t0) cc_final: 0.8299 (t0)
REVERT: C  381 ASN cc_start: 0.5876 (m110) cc_final: 0.5392 (m110)
REVERT: C  417 MET cc_start: 0.6592 (ttp) cc_final: 0.6378 (tmm)
REVERT: C  449 ARG cc_start: 0.0087 (ptt-90) cc_final: -0.0331 (ptp-170)
REVERT: C  558 PHE cc_start: 0.8398 (m-80) cc_final: 0.7987 (m-10)
REVERT: C  599 GLN cc_start: 0.8631 (mt0) cc_final: 0.8366 (mt0)
REVERT: C  650 ILE cc_start: 0.9264 (mt) cc_final: 0.8923 (mt)
REVERT: C  706 THR cc_start: 0.8770 (p) cc_final: 0.8522 (p)
REVERT: C  733 ASN cc_start: 0.9516 (t0) cc_final: 0.9288 (t0)
REVERT: C  762 GLU cc_start: 0.8037 (tp30) cc_final: 0.7762 (tp30)
REVERT: C  984 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: C  992 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8367 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 254
  average time/residue: 0.1147
  time to fit residues: 44.2408
Evaluate side-chains
  199 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 166 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 196 optimal weight:    7.9990
   chunk 145 optimal weight:    0.6980
   chunk 93 optimal weight:    8.9990
   chunk 204 optimal weight:    1.9990
   chunk 206 optimal weight:    4.9990
   chunk 180 optimal weight:    0.0030
   chunk 58 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 213 optimal weight:    0.8980
   overall best weight:    0.9194

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

Flipped N/Q/H residues before XYZ refinement:
A 721 ASN
A 744 GLN
** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 744 GLN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN
C 960 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.113526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.085168 restraints weight = 59651.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.086930 restraints weight = 41096.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.088130 restraints weight = 30915.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.088967 restraints weight = 25148.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.089501 restraints weight = 21601.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.5606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16632  Z= 0.159
  Angle     :  0.911  14.126  22653  Z= 0.472
  Chirality :  0.049   0.240   2646
  Planarity :  0.005   0.079   2958
  Dihedral  :  6.751  47.543   2343
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 16.16 %
    Favored  : 83.70 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.84 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.63 %
    Twisted Proline : 3.03 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.24 (0.17), residues: 2178
  helix:  0.01 (0.22), residues: 579
  sheet: -1.31 (0.33), residues: 255
  loop : -3.58 (0.15), residues: 1344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C1001 
 TYR   0.016   0.001   TYR B 300 
 PHE   0.017   0.001   PHE A 529 
 TRP   0.004   0.001   TRP A 423 
 HIS   0.004   0.001   HIS B1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (16608)
  covalent geometry    : angle       0.90868 (22605)
  SS BOND              : bond        0.00237 (   24)
  SS BOND              : angle       1.59873 (   48)
  hydrogen bonds       : bond        0.03573 (  465)
  hydrogen bonds       : angle       5.30428 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LYS cc_start: 0.8824 (pptt) cc_final: 0.8315 (ptmm)
REVERT: A  441 ARG cc_start: 0.6296 (mtt180) cc_final: 0.5360 (mtt180)
REVERT: A  444 ARG cc_start: 0.5791 (ttt-90) cc_final: 0.5398 (mtp-110)
REVERT: A  558 PHE cc_start: 0.9003 (m-10) cc_final: 0.8626 (m-10)
REVERT: A  707 GLU cc_start: 0.7386 (tm-30) cc_final: 0.5706 (tm-30)
REVERT: A  719 ASP cc_start: 0.8578 (t0) cc_final: 0.8231 (t0)
REVERT: A  935 ASN cc_start: 0.9253 (m-40) cc_final: 0.8841 (m-40)
REVERT: A  942 ASN cc_start: 0.8728 (m-40) cc_final: 0.8375 (m-40)
REVERT: A  969 VAL cc_start: 0.9193 (t) cc_final: 0.8952 (t)
REVERT: A  976 ASP cc_start: 0.9150 (m-30) cc_final: 0.8879 (p0)
REVERT: A  992 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8522 (tm-30)
REVERT: B  340 TRP cc_start: 0.6869 (p-90) cc_final: 0.6273 (p-90)
REVERT: B  518 ASP cc_start: 0.7915 (m-30) cc_final: 0.7203 (p0)
REVERT: B  557 ASP cc_start: 0.7629 (m-30) cc_final: 0.7304 (m-30)
REVERT: B  558 PHE cc_start: 0.8805 (m-10) cc_final: 0.8221 (m-80)
REVERT: B  709 MET cc_start: 0.7593 (mmm) cc_final: 0.7381 (mmm)
REVERT: B  738 TYR cc_start: 0.6298 (p90) cc_final: 0.5501 (p90)
REVERT: B  758 ARG cc_start: 0.8667 (tpm170) cc_final: 0.8132 (tpp-160)
REVERT: B  947 GLN cc_start: 0.8276 (tp40) cc_final: 0.8009 (tp-100)
REVERT: B  952 PHE cc_start: 0.7054 (t80) cc_final: 0.6475 (t80)
REVERT: B  968 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8204 (tptp)
REVERT: B  987 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8464 (tp-100)
REVERT: C  304 ASN cc_start: 0.8669 (t0) cc_final: 0.8367 (t0)
REVERT: C  449 ARG cc_start: 0.0122 (ptt-90) cc_final: -0.0302 (ptp-170)
REVERT: C  650 ILE cc_start: 0.9299 (mt) cc_final: 0.8917 (mt)
REVERT: C  733 ASN cc_start: 0.9570 (t0) cc_final: 0.9363 (t0)
REVERT: C  758 ARG cc_start: 0.8441 (tpm170) cc_final: 0.8039 (tpp-160)
REVERT: C  762 GLU cc_start: 0.8124 (tp30) cc_final: 0.7904 (tp30)
REVERT: C  984 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8632 (tm-30)
REVERT: C  992 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8490 (tm-30)
REVERT: C 1011 MET cc_start: 0.7752 (tmm) cc_final: 0.7461 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1308
  time to fit residues: 48.6023
Evaluate side-chains
  192 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 209 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 174 optimal weight:    5.9990
   chunk 192 optimal weight:    0.6980
   chunk 53 optimal weight:    0.4980
   chunk 1 optimal weight:   10.0000
   chunk 164 optimal weight:    5.9990
   chunk 109 optimal weight:    1.9990
   chunk 195 optimal weight:    0.4980
   chunk 96 optimal weight:   10.0000
   chunk 204 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 GLN
C 744 GLN
** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 960 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.114329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.085768 restraints weight = 58893.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.087599 restraints weight = 41215.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.088839 restraints weight = 30892.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.089678 restraints weight = 25009.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.090199 restraints weight = 21515.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.5829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16632  Z= 0.154
  Angle     :  0.916  14.189  22653  Z= 0.474
  Chirality :  0.049   0.240   2646
  Planarity :  0.004   0.053   2958
  Dihedral  :  6.698  46.851   2343
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 14.83 %
    Favored  : 85.03 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.95 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.68 %
    Twisted Proline : 3.03 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.17), residues: 2178
  helix:  0.10 (0.22), residues: 579
  sheet: -1.14 (0.34), residues: 252
  loop : -3.56 (0.15), residues: 1347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 965 
 TYR   0.013   0.001   TYR B 300 
 PHE   0.017   0.001   PHE A 529 
 TRP   0.004   0.000   TRP A 340 
 HIS   0.003   0.001   HIS B1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (16608)
  covalent geometry    : angle       0.91349 (22605)
  SS BOND              : bond        0.00220 (   24)
  SS BOND              : angle       1.65097 (   48)
  hydrogen bonds       : bond        0.03486 (  465)
  hydrogen bonds       : angle       5.20862 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 252
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TRP cc_start: 0.8140 (p90) cc_final: 0.7896 (p90)
REVERT: A  441 ARG cc_start: 0.6477 (mtt180) cc_final: 0.5537 (mtt180)
REVERT: A  444 ARG cc_start: 0.5783 (ttt-90) cc_final: 0.5475 (mtp-110)
REVERT: A  558 PHE cc_start: 0.8946 (m-10) cc_final: 0.8531 (m-10)
REVERT: A  707 GLU cc_start: 0.7447 (tm-30) cc_final: 0.5751 (tm-30)
REVERT: A  719 ASP cc_start: 0.8485 (t0) cc_final: 0.8173 (t0)
REVERT: A  935 ASN cc_start: 0.9248 (m-40) cc_final: 0.8852 (m-40)
REVERT: A  942 ASN cc_start: 0.8699 (m-40) cc_final: 0.8348 (m-40)
REVERT: A  973 VAL cc_start: 0.9310 (t) cc_final: 0.9091 (t)
REVERT: A  976 ASP cc_start: 0.9137 (m-30) cc_final: 0.8857 (p0)
REVERT: A  992 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8573 (tm-30)
REVERT: A 1011 MET cc_start: 0.7705 (tmm) cc_final: 0.7360 (tmm)
REVERT: B  340 TRP cc_start: 0.6912 (p-90) cc_final: 0.6282 (p-90)
REVERT: B  518 ASP cc_start: 0.7881 (m-30) cc_final: 0.7171 (p0)
REVERT: B  557 ASP cc_start: 0.7527 (m-30) cc_final: 0.7199 (m-30)
REVERT: B  709 MET cc_start: 0.7542 (mmm) cc_final: 0.7325 (mmm)
REVERT: B  722 MET cc_start: 0.8918 (tpp) cc_final: 0.8591 (tpp)
REVERT: B  758 ARG cc_start: 0.8504 (tpm170) cc_final: 0.7985 (tpp-160)
REVERT: B  947 GLN cc_start: 0.8230 (tp40) cc_final: 0.7954 (tp-100)
REVERT: B  952 PHE cc_start: 0.7012 (t80) cc_final: 0.6477 (t80)
REVERT: B  968 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8167 (tptp)
REVERT: B  987 GLN cc_start: 0.9163 (tp-100) cc_final: 0.8407 (tp-100)
REVERT: B  992 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8151 (tm-30)
REVERT: C  417 MET cc_start: 0.5916 (ttp) cc_final: 0.5623 (tmm)
REVERT: C  449 ARG cc_start: 0.0148 (ptt-90) cc_final: -0.0289 (ptp-170)
REVERT: C  558 PHE cc_start: 0.8408 (m-80) cc_final: 0.7920 (m-10)
REVERT: C  709 MET cc_start: 0.8294 (mmp) cc_final: 0.7975 (mmm)
REVERT: C  984 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8615 (tm-30)
REVERT: C  992 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8468 (tm-30)
REVERT: C 1011 MET cc_start: 0.7402 (tmm) cc_final: 0.7053 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1198
  time to fit residues: 45.6875
Evaluate side-chains
  193 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 205 optimal weight:    1.9990
   chunk 169 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 211 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 200 optimal weight:    4.9990
   chunk 178 optimal weight:    4.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 960 ASN
B 737 GLN
B 744 GLN
B 746 ASN
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN
** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 917 GLN
C 960 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.111596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.083162 restraints weight = 60078.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.084906 restraints weight = 41273.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.086092 restraints weight = 31033.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.086862 restraints weight = 25193.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.087475 restraints weight = 21773.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.6032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  16632  Z= 0.190
  Angle     :  0.936  14.075  22653  Z= 0.486
  Chirality :  0.049   0.336   2646
  Planarity :  0.005   0.059   2958
  Dihedral  :  6.847  47.380   2343
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 16.94 %
    Favored  : 82.92 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.47 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.63 %
    Twisted Proline : 3.03 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.17), residues: 2178
  helix:  0.06 (0.22), residues: 582
  sheet: -1.25 (0.33), residues: 255
  loop : -3.58 (0.15), residues: 1341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 306 
 TYR   0.017   0.001   TYR B 300 
 PHE   0.041   0.002   PHE A 529 
 TRP   0.006   0.001   TRP A 423 
 HIS   0.004   0.001   HIS C1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (16608)
  covalent geometry    : angle       0.93357 (22605)
  SS BOND              : bond        0.00248 (   24)
  SS BOND              : angle       1.62663 (   48)
  hydrogen bonds       : bond        0.03624 (  465)
  hydrogen bonds       : angle       5.30157 ( 1296)

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

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

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4356 Ramachandran restraints generated.
    2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 237
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 ARG cc_start: 0.5828 (ttt-90) cc_final: 0.5433 (mtp-110)
REVERT: A  558 PHE cc_start: 0.9092 (m-10) cc_final: 0.8684 (m-10)
REVERT: A  713 MET cc_start: 0.8427 (ttt) cc_final: 0.7881 (ttp)
REVERT: A  719 ASP cc_start: 0.8539 (t0) cc_final: 0.8336 (t0)
REVERT: A  942 ASN cc_start: 0.8742 (m-40) cc_final: 0.8387 (m-40)
REVERT: A  976 ASP cc_start: 0.9126 (m-30) cc_final: 0.8861 (p0)
REVERT: A  992 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8545 (tm-30)
REVERT: A 1011 MET cc_start: 0.7682 (tmm) cc_final: 0.7248 (tmm)
REVERT: B  340 TRP cc_start: 0.7044 (p-90) cc_final: 0.6501 (p-90)
REVERT: B  518 ASP cc_start: 0.8105 (m-30) cc_final: 0.7301 (p0)
REVERT: B  557 ASP cc_start: 0.7379 (m-30) cc_final: 0.7154 (m-30)
REVERT: B  709 MET cc_start: 0.7664 (mmm) cc_final: 0.7390 (mmm)
REVERT: B  738 TYR cc_start: 0.6419 (p90) cc_final: 0.6042 (p90)
REVERT: B  758 ARG cc_start: 0.8476 (tpm170) cc_final: 0.8023 (tpp-160)
REVERT: B  939 GLN cc_start: 0.8746 (pm20) cc_final: 0.8415 (pm20)
REVERT: B  947 GLN cc_start: 0.8392 (tp40) cc_final: 0.8114 (tp-100)
REVERT: B  952 PHE cc_start: 0.7280 (t80) cc_final: 0.6815 (t80)
REVERT: B  968 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8220 (tptp)
REVERT: C  417 MET cc_start: 0.5939 (ttp) cc_final: 0.5626 (tmm)
REVERT: C  449 ARG cc_start: -0.0433 (ptt-90) cc_final: -0.0702 (ptp-170)
REVERT: C  650 ILE cc_start: 0.9253 (mt) cc_final: 0.8949 (mt)
REVERT: C  709 MET cc_start: 0.8252 (mmp) cc_final: 0.7964 (mmm)
REVERT: C  992 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8493 (tm-30)
REVERT: C 1011 MET cc_start: 0.7440 (tmm) cc_final: 0.7175 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1215
  time to fit residues: 43.7265
Evaluate side-chains
  178 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 219
   random chunks:
   chunk 190 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 192 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 119 optimal weight:    0.9980
   chunk 144 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
B 987 GLN
C 445 HIS
** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN
** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 960 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.110026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.081866 restraints weight = 60764.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.083561 restraints weight = 41987.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.084742 restraints weight = 31413.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.085531 restraints weight = 25390.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.085974 restraints weight = 21869.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.6366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16632  Z= 0.199
  Angle     :  0.948  14.071  22653  Z= 0.494
  Chirality :  0.050   0.265   2646
  Planarity :  0.005   0.062   2958
  Dihedral  :  6.956  46.792   2343
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 16.21 %
    Favored  : 83.65 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.30 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 3.68 %
    Twisted Proline : 5.05 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.23 (0.17), residues: 2178
  helix: -0.02 (0.22), residues: 594
  sheet: -1.40 (0.33), residues: 258
  loop : -3.57 (0.15), residues: 1326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 306 
 TYR   0.014   0.001   TYR B 598 
 PHE   0.031   0.002   PHE A 529 
 TRP   0.008   0.001   TRP C 423 
 HIS   0.004   0.001   HIS B1030 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (16608)
  covalent geometry    : angle       0.94618 (22605)
  SS BOND              : bond        0.00260 (   24)
  SS BOND              : angle       1.60747 (   48)
  hydrogen bonds       : bond        0.03704 (  465)
  hydrogen bonds       : angle       5.31932 ( 1296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2625.64 seconds
wall clock time: 46 minutes 9.54 seconds (2769.54 seconds total)