Starting phenix.real_space_refine
on Sat Jun 14 04:47:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b3q_7041/06_2025/6b3q_7041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b3q_7041/06_2025/6b3q_7041.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6b3q_7041/06_2025/6b3q_7041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b3q_7041/06_2025/6b3q_7041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b3q_7041/06_2025/6b3q_7041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b3q_7041/06_2025/6b3q_7041.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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      52      5.16       5
     C   10128      2.51       5
     N    2638      2.21       5
     O    2909      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15727
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 948, 7743
          Classifications: {'peptide': 948}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 51, 'TRANS': 896}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 7665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 938, 7665
          Classifications: {'peptide': 938}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 48, 'TRANS': 889}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "a"
      Number of atoms: 208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 208
          Classifications: {'peptide': 28}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 27}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "b"
      Number of atoms: 111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 111
          Classifications: {'peptide': 15}
          Link IDs: {'TRANS': 14}
  Time building chain proxies: 9.93, per 1000 atoms: 0.63
  Number of scatterers: 15727
  At special positions: 0
  Unit cell: (106.227, 121.249, 154.512, 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      52     16.00
     O    2909      8.00
     N    2638      7.00
     C   10128      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS a   7 " - pdb=" SG  CYS a 182 " distance=2.02
    Simple disulfide: pdb=" SG  CYS a  19 " - pdb=" SG  CYS a 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 181 " - pdb=" SG  CYS a 186 " distance=2.04
    Simple disulfide: pdb=" SG  CYS b   6 " - pdb=" SG  CYS b  11 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.78
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3676

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 11 sheets defined
      43.9% alpha, 14.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.686A  pdb=" N   SER A  98 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ASP A  99 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 95 through 99'
    Processing helix  chain 'A' and resid 105 through 115
      removed outlier: 3.928A  pdb=" N   PHE A 115 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 133
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 4.501A  pdb=" N   ARG A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   PHE A 168 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 193
      removed outlier: 3.523A  pdb=" N   LYS A 179 " --> pdb=" O   ASP A 175 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   VAL A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   ASN A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ALA A 185 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 208
      removed outlier: 3.762A  pdb=" N   LEU A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   PHE A 202 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
      removed outlier: 3.524A  pdb=" N   ASN A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 249
    Processing helix  chain 'A' and resid 267 through 272
    Processing helix  chain 'A' and resid 294 through 298
      removed outlier: 3.553A  pdb=" N   LEU A 298 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'A' and resid 345 through 353
      removed outlier: 3.913A  pdb=" N   LEU A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 403
    Processing helix  chain 'A' and resid 407 through 424
      removed outlier: 3.597A  pdb=" N   PHE A 411 " --> pdb=" O   GLN A 407 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE A 424 " --> pdb=" O   VAL A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 440
      removed outlier: 3.639A  pdb=" N   TYR A 433 " --> pdb=" O   ARG A 429 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR A 434 " --> pdb=" O   PRO A 430 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   SER A 435 " --> pdb=" O   ARG A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 470
      removed outlier: 3.696A  pdb=" N   ILE A 464 " --> pdb=" O   ARG A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 514
      removed outlier: 4.303A  pdb=" N   ILE A 510 " --> pdb=" O   PRO A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 615
      removed outlier: 4.453A  pdb=" N   GLU A 606 " --> pdb=" O   ASP A 602 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   TYR A 607 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   ALA A 610 " --> pdb=" O   GLU A 606 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   ALA A 611 " --> pdb=" O   TYR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 651
      removed outlier: 3.663A  pdb=" N   LEU A 641 " --> pdb=" O   LYS A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 671
      removed outlier: 3.780A  pdb=" N   GLU A 664 " --> pdb=" O   GLU A 660 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER A 669 " --> pdb=" O   ALA A 665 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN A 671 " --> pdb=" O   MET A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 674
      No H-bonds generated for 'chain 'A' and resid 672 through 674'
    Processing helix  chain 'A' and resid 677 through 689
      removed outlier: 3.747A  pdb=" N   ARG A 687 " --> pdb=" O   MET A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 701
      removed outlier: 3.683A  pdb=" N   LEU A 700 " --> pdb=" O   THR A 696 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LYS A 701 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 696 through 701'
    Processing helix  chain 'A' and resid 708 through 720
      removed outlier: 3.545A  pdb=" N   ILE A 716 " --> pdb=" O   LEU A 712 " (cutoff:3.500A)
      Proline residue:  A 717  - end of helix
    Processing helix  chain 'A' and resid 734 through 754
      removed outlier: 3.515A  pdb=" N   HIS A 754 " --> pdb=" O   ILE A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 763
      removed outlier: 3.805A  pdb=" N   LEU A 763 " --> pdb=" O   PRO A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 815
      removed outlier: 4.042A  pdb=" N   LEU A 808 " --> pdb=" O   GLU A 804 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE A 815 " --> pdb=" O   PHE A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 824
      removed outlier: 4.037A  pdb=" N   PHE A 820 " --> pdb=" O   SER A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.679A  pdb=" N   LEU A 859 " --> pdb=" O   PRO A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 893
      removed outlier: 3.516A  pdb=" N   PHE A 882 " --> pdb=" O   THR A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 912
      removed outlier: 3.825A  pdb=" N   LYS A 906 " --> pdb=" O   ALA A 902 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY A 909 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   GLU A 910 " --> pdb=" O   LYS A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 921
      removed outlier: 3.901A  pdb=" N   ARG A 920 " --> pdb=" O   ASN A 917 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ASP A 921 " --> pdb=" O   PHE A 918 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 917 through 921'
    Processing helix  chain 'A' and resid 922 through 929
    Processing helix  chain 'A' and resid 932 through 945
      removed outlier: 3.750A  pdb=" N   ILE A 936 " --> pdb=" O   THR A 932 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE A 937 " --> pdb=" O   LYS A 933 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   GLU A 942 " --> pdb=" O   LYS A 938 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   MET A 943 " --> pdb=" O   PHE A 939 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA A 945 " --> pdb=" O   LYS A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 999
    Processing helix  chain 'B' and resid 106 through 115
      removed outlier: 3.971A  pdb=" N   PHE B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 133
      removed outlier: 3.913A  pdb=" N   GLU B 133 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 166
    Processing helix  chain 'B' and resid 167 through 169
      No H-bonds generated for 'chain 'B' and resid 167 through 169'
    Processing helix  chain 'B' and resid 175 through 179
    Processing helix  chain 'B' and resid 181 through 192
      removed outlier: 3.683A  pdb=" N   ALA B 185 " --> pdb=" O   ARG B 181 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LYS B 192 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 207
      removed outlier: 3.818A  pdb=" N   PHE B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 222 through 227
    Processing helix  chain 'B' and resid 227 through 234
      removed outlier: 3.692A  pdb=" N   ASN B 231 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 247
      removed outlier: 3.505A  pdb=" N   GLU B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 276
      removed outlier: 3.681A  pdb=" N   LEU B 267 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASN B 269 " --> pdb=" O   ASP B 265 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU B 270 " --> pdb=" O   ASP B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 339
      removed outlier: 3.715A  pdb=" N   TYR B 333 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 353
      removed outlier: 3.626A  pdb=" N   LYS B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 405
    Processing helix  chain 'B' and resid 408 through 424
      removed outlier: 3.546A  pdb=" N   ASN B 418 " --> pdb=" O   LEU B 414 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 424 " --> pdb=" O   VAL B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 440
      removed outlier: 3.648A  pdb=" N   LYS B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE B 437 " --> pdb=" O   TYR B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 443
      No H-bonds generated for 'chain 'B' and resid 441 through 443'
    Processing helix  chain 'B' and resid 460 through 470
      removed outlier: 3.725A  pdb=" N   ILE B 464 " --> pdb=" O   ARG B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 476
      removed outlier: 3.700A  pdb=" N   VAL B 476 " --> pdb=" O   PRO B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 486
    Processing helix  chain 'B' and resid 506 through 514
      removed outlier: 3.933A  pdb=" N   ILE B 510 " --> pdb=" O   PRO B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 603
    Processing helix  chain 'B' and resid 604 through 613
      removed outlier: 5.069A  pdb=" N   ALA B 610 " --> pdb=" O   GLU B 606 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA B 611 " --> pdb=" O   TYR B 607 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU B 613 " --> pdb=" O   TYR B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 650
      removed outlier: 3.521A  pdb=" N   LEU B 641 " --> pdb=" O   LYS B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 672
    Processing helix  chain 'B' and resid 677 through 690
      removed outlier: 3.517A  pdb=" N   HIS B 681 " --> pdb=" O   GLN B 677 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA B 682 " --> pdb=" O   PRO B 678 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   MET B 683 " --> pdb=" O   HIS B 679 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 704
    Processing helix  chain 'B' and resid 705 through 707
      No H-bonds generated for 'chain 'B' and resid 705 through 707'
    Processing helix  chain 'B' and resid 708 through 714
      removed outlier: 3.887A  pdb=" N   ALA B 714 " --> pdb=" O   PRO B 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 720
    Processing helix  chain 'B' and resid 734 through 753
      removed outlier: 4.025A  pdb=" N   LEU B 739 " --> pdb=" O   LYS B 735 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL B 745 " --> pdb=" O   ILE B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 759 through 763
      removed outlier: 3.764A  pdb=" N   LEU B 763 " --> pdb=" O   PRO B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 801 through 815
      removed outlier: 3.627A  pdb=" N   MET B 806 " --> pdb=" O   THR B 802 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE B 807 " --> pdb=" O   SER B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 825
    Processing helix  chain 'B' and resid 855 through 876
      removed outlier: 4.414A  pdb=" N   SER B 861 " --> pdb=" O   HIS B 857 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ARG B 862 " --> pdb=" O   TYR B 858 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL B 863 " --> pdb=" O   LEU B 859 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 875 " --> pdb=" O   GLU B 871 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP B 876 " --> pdb=" O   LYS B 872 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 878 through 893
      removed outlier: 3.713A  pdb=" N   LEU B 889 " --> pdb=" O   HIS B 885 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA B 890 " --> pdb=" O   ILE B 886 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 899 through 912
      removed outlier: 3.607A  pdb=" N   GLU B 903 " --> pdb=" O   LYS B 899 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLY B 909 " --> pdb=" O   ALA B 905 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 919 through 929
      removed outlier: 3.515A  pdb=" N   LYS B 929 " --> pdb=" O   VAL B 925 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 934 through 944
      removed outlier: 3.520A  pdb=" N   GLU B 942 " --> pdb=" O   LYS B 938 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET B 943 " --> pdb=" O   PHE B 939 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 994 through 1001
      removed outlier: 4.087A  pdb=" N   GLY B1001 " --> pdb=" O   GLU B 997 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.115A  pdb=" N   LYS A  74 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL A 258 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU A  76 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   GLY A 260 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ILE A  78 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER A  87 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA A  88 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR A 150 " --> pdb=" O   ASN A 139 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASN A 139 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360
      removed outlier: 3.624A  pdb=" N   GLU A 503 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492
    Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 563
      removed outlier: 6.215A  pdb=" N   LYS A 562 " --> pdb=" O   GLY A 731 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   HIS A 724 " --> pdb=" O   PHE A 579 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 728 " --> pdb=" O   ASN A 575 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 834
      removed outlier: 4.618A  pdb=" N   ILE A 832 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN A 851 " --> pdb=" O   ILE A 832 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 840 " --> pdb=" O   ILE A 843 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 834
      removed outlier: 4.618A  pdb=" N   ILE A 832 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN A 851 " --> pdb=" O   ILE A 832 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   GLN A 844 " --> pdb=" O   THR A 797 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 793 " --> pdb=" O   PHE A 848 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 990 " --> pdb=" O   TRP A 776 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL A 778 " --> pdb=" O   GLU A 990 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.517A  pdb=" N   GLU B  63 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LYS B  74 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   VAL B 258 " --> pdb=" O   LYS B  74 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LEU B  76 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   GLY B 260 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   ILE B  78 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA B  88 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASN B 148 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE B 141 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 304
      removed outlier: 4.612A  pdb=" N   THR B 358 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 301 through 304
      removed outlier: 3.562A  pdb=" N   PHE B 370 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA B 367 " --> pdb=" O   PHE B 370 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE B 372 " --> pdb=" O   GLU B 365 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   GLU B 365 " --> pdb=" O   PHE B 372 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 549 through 553
      removed outlier: 6.712A  pdb=" N   LEU B 550 " --> pdb=" O   PHE B 561 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   PHE B 561 " --> pdb=" O   LEU B 550 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS B 552 " --> pdb=" O   LEU B 559 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LYS B 558 " --> pdb=" O   ALA B 727 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   LEU B 729 " --> pdb=" O   LYS B 558 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   TRP B 560 " --> pdb=" O   LEU B 729 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 782
      removed outlier: 6.325A  pdb=" N   PHE B 777 " --> pdb=" O   SER B 955 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   HIS B 957 " --> pdb=" O   PHE B 777 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   TYR B 779 " --> pdb=" O   HIS B 957 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   LEU B 959 " --> pdb=" O   TYR B 779 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   GLN B 781 " --> pdb=" O   LEU B 959 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU B 792 " --> pdb=" O   VAL B 956 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE B 850 " --> pdb=" O   ILE B 791 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY B 836 " --> pdb=" O   ARG B 847 " (cutoff:3.500A)

    626 hydrogen bonds defined for protein.
    1803 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: 5.47

  Time building geometry restraints manager: 4.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 5046
        1.34 -     1.48: 3978
        1.48 -     1.61: 6992
        1.61 -     1.74: 0
        1.74 -     1.88: 95
  Bond restraints: 16111
  Sorted by residual:
  bond pdb=" C   GLN A 638 "
       pdb=" N   PRO A 639 "
    ideal  model  delta    sigma   weight residual
    1.334  1.408 -0.074 2.34e-02 1.83e+03 9.98e+00
  bond pdb=" CB  CYS b   6 "
       pdb=" SG  CYS b   6 "
    ideal  model  delta    sigma   weight residual
    1.808  1.877 -0.069 3.30e-02 9.18e+02 4.31e+00
  bond pdb=" CG1 ILE B 307 "
       pdb=" CD1 ILE B 307 "
    ideal  model  delta    sigma   weight residual
    1.513  1.446  0.067 3.90e-02 6.57e+02 2.98e+00
  bond pdb=" C   GLU A 817 "
       pdb=" N   PRO A 818 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.022 1.25e-02 6.40e+03 2.97e+00
  bond pdb=" CG1 ILE A 843 "
       pdb=" CD1 ILE A 843 "
    ideal  model  delta    sigma   weight residual
    1.513  1.446  0.067 3.90e-02 6.57e+02 2.95e+00
  ... (remaining 16106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 20684
        2.10 -     4.20: 923
        4.20 -     6.30: 118
        6.30 -     8.40: 46
        8.40 -    10.50: 16
  Bond angle restraints: 21787
  Sorted by residual:
  angle pdb=" C   CYS b   6 "
        pdb=" N   CYS b   7 "
        pdb=" CA  CYS b   7 "
      ideal   model   delta    sigma   weight residual
     121.54  130.34   -8.80 1.91e+00 2.74e-01 2.12e+01
  angle pdb=" C   ASN A 222 "
        pdb=" N   LYS A 223 "
        pdb=" CA  LYS A 223 "
      ideal   model   delta    sigma   weight residual
     121.54  130.23   -8.69 1.91e+00 2.74e-01 2.07e+01
  angle pdb=" C   GLN A 167 "
        pdb=" N   PHE A 168 "
        pdb=" CA  PHE A 168 "
      ideal   model   delta    sigma   weight residual
     120.38  126.50   -6.12 1.37e+00 5.33e-01 1.99e+01
  angle pdb=" C   SER A 154 "
        pdb=" N   HIS A 155 "
        pdb=" CA  HIS A 155 "
      ideal   model   delta    sigma   weight residual
     121.19  127.90   -6.71 1.59e+00 3.96e-01 1.78e+01
  angle pdb=" C   GLN B 502 "
        pdb=" N   GLU B 503 "
        pdb=" CA  GLU B 503 "
      ideal   model   delta    sigma   weight residual
     121.54  129.28   -7.74 1.91e+00 2.74e-01 1.64e+01
  ... (remaining 21782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.86: 8905
       15.86 -    31.72: 648
       31.72 -    47.58: 174
       47.58 -    63.44: 16
       63.44 -    79.30: 14
  Dihedral angle restraints: 9757
    sinusoidal: 4071
      harmonic: 5686
  Sorted by residual:
  dihedral pdb=" CB  CYS a   7 "
           pdb=" SG  CYS a   7 "
           pdb=" SG  CYS a 182 "
           pdb=" CB  CYS a 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.66  -74.34     1      1.00e+01 1.00e-02 7.01e+01
  dihedral pdb=" CB  CYS a  19 "
           pdb=" SG  CYS a  19 "
           pdb=" SG  CYS a 195 "
           pdb=" CB  CYS a 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.04   57.04     1      1.00e+01 1.00e-02 4.38e+01
  dihedral pdb=" CA  LYS A 511 "
           pdb=" C   LYS A 511 "
           pdb=" N   LYS A 512 "
           pdb=" CA  LYS A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.04   27.96     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 9754 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1593
       0.054 -    0.108: 589
       0.108 -    0.161: 145
       0.161 -    0.215: 19
       0.215 -    0.269: 6
  Chirality restraints: 2352
  Sorted by residual:
  chirality pdb=" CB  ILE A 103 "
            pdb=" CA  ILE A 103 "
            pdb=" CG1 ILE A 103 "
            pdb=" CG2 ILE A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  ILE A 733 "
            pdb=" CA  ILE A 733 "
            pdb=" CG1 ILE A 733 "
            pdb=" CG2 ILE A 733 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  ILE b  10 "
            pdb=" CA  ILE b  10 "
            pdb=" CG1 ILE b  10 "
            pdb=" CG2 ILE b  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 2349 not shown)

  Planarity restraints: 2815
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 821 "   -0.022 2.00e-02 2.50e+03   4.47e-02 2.00e+01
        pdb=" C   ASN B 821 "    0.077 2.00e-02 2.50e+03
        pdb=" O   ASN B 821 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   THR B 822 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 223 "   -0.021 2.00e-02 2.50e+03   4.26e-02 1.81e+01
        pdb=" C   LYS A 223 "    0.074 2.00e-02 2.50e+03
        pdb=" O   LYS A 223 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   TYR A 224 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 224 "    0.018 2.00e-02 2.50e+03   3.69e-02 1.36e+01
        pdb=" C   TYR A 224 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   TYR A 224 "    0.024 2.00e-02 2.50e+03
        pdb=" N   THR A 225 "    0.022 2.00e-02 2.50e+03
  ... (remaining 2812 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1605
        2.75 -     3.29: 14793
        3.29 -     3.82: 25685
        3.82 -     4.36: 29714
        4.36 -     4.90: 51397
  Nonbonded interactions: 123194
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 831 "
            pdb=" O   LEU a 188 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OG1 THR A 623 "
            pdb=" O   GLY A 626 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OH  TYR B 831 "
            pdb=" O   LEU b  13 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OG  SER A  87 "
            pdb=" O   PHE A 151 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG1 THR A  55 "
            pdb=" OE2 GLU A 447 "
     model   vdw
     2.318 3.040
  ... (remaining 123189 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 47 through 656 or (resid 657 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 658 through 704 or (resid 705 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 706 through 763 or (resid 7 \ 
64 through 765 and (name N or name CA or name C or name O or name CB )) or resid \ 
 766 through 962 or resid 990 through 1011))
  selection = (chain 'B' and (resid 47 through 541 or (resid 542 through 544 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 545 through 1011))
}

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:             1.870
  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:          0.650
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     37.500
  Find NCS groups from input model:        0.690
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
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      :  0.005   0.074  16115  Z= 0.246
  Angle     :  1.035  10.496  21795  Z= 0.551
  Chirality :  0.059   0.269   2352
  Planarity :  0.008   0.085   2815
  Dihedral  : 12.289  79.296   6069
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.53 (0.15), residues: 1914
  helix: -3.51 (0.12), residues: 745
  sheet: -2.18 (0.27), residues: 320
  loop : -2.71 (0.17), residues: 849

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.004   TRP A 776 
 HIS   0.013   0.002   HIS B 155 
 PHE   0.056   0.003   PHE A 168 
 TYR   0.050   0.003   TYR A 831 
 ARG   0.017   0.001   ARG B 477 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19775 (  609)
  hydrogen bonds       : angle       8.75826 ( 1803)
  SS BOND              : bond        0.00824 (    4)
  SS BOND              : angle       3.68065 (    8)
  covalent geometry    : bond        0.00535 (16111)
  covalent geometry    : angle       1.03247 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 374
  time to evaluate  : 1.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 MET cc_start: 0.7615 (pmt) cc_final: 0.7305 (pmt)
REVERT: A  556 MET cc_start: 0.8428 (tpp) cc_final: 0.8164 (tpp)
REVERT: A  806 MET cc_start: 0.7929 (mmp) cc_final: 0.6982 (mmp)
REVERT: A  872 LYS cc_start: 0.8856 (tptp) cc_final: 0.8161 (tppt)
REVERT: B  150 TYR cc_start: 0.8553 (p90) cc_final: 0.8329 (p90)
REVERT: B  240 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: B  242 LEU cc_start: 0.9026 (mm) cc_final: 0.8716 (mp)
REVERT: B  495 TRP cc_start: 0.7379 (m-90) cc_final: 0.6911 (m-90)
REVERT: B  553 ASP cc_start: 0.8295 (t0) cc_final: 0.7481 (p0)
REVERT: B  645 ILE cc_start: 0.9064 (mt) cc_final: 0.8724 (mt)
REVERT: B  648 LYS cc_start: 0.9079 (tppt) cc_final: 0.8755 (mmmt)
REVERT: B  860 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7011 (tm-30)
REVERT: a  196 ASN cc_start: 0.5349 (t0) cc_final: 0.5145 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 374
  average time/residue: 0.3354
  time to fit residues: 178.4772
Evaluate side-chains
  162 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    5.9990
   chunk 144 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 148 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 172 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS
A 157 HIS
A 312 ASN
A 332 HIS
** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 730 HIS
A 762 GLN
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 957 HIS
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
B 332 HIS
B 573 ASN
B 635 ASN
B 752 HIS
B 781 GLN
B 783 ASN
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 828 GLN
a 190 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.081405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.071593 restraints weight = 57894.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.073256 restraints weight = 32068.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.074423 restraints weight = 20640.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  16115  Z= 0.186
  Angle     :  0.707   8.455  21795  Z= 0.367
  Chirality :  0.046   0.153   2352
  Planarity :  0.005   0.058   2815
  Dihedral  :  5.668  20.384   2091
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.87 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.17), residues: 1914
  helix: -1.67 (0.17), residues: 765
  sheet: -1.75 (0.26), residues: 362
  loop : -2.13 (0.19), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 495 
 HIS   0.015   0.001   HIS B 291 
 PHE   0.042   0.002   PHE B 130 
 TYR   0.017   0.002   TYR A 594 
 ARG   0.004   0.001   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04757 (  609)
  hydrogen bonds       : angle       6.04026 ( 1803)
  SS BOND              : bond        0.00342 (    4)
  SS BOND              : angle       2.15109 (    8)
  covalent geometry    : bond        0.00406 (16111)
  covalent geometry    : angle       0.70543 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 170
  time to evaluate  : 1.853 
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  254 MET cc_start: 0.7377 (pmt) cc_final: 0.7055 (pmt)
REVERT: A  371 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7457 (ttt)
REVERT: B  464 ILE cc_start: 0.8964 (mt) cc_final: 0.8709 (mp)
REVERT: B  553 ASP cc_start: 0.8115 (t0) cc_final: 0.7502 (p0)
REVERT: B  648 LYS cc_start: 0.9039 (tppt) cc_final: 0.8717 (mmmt)
REVERT: B  870 MET cc_start: 0.7508 (mmm) cc_final: 0.7100 (tpt)
REVERT: B  896 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8543 (mptt)
REVERT: a  184 SER cc_start: 0.8330 (t) cc_final: 0.8061 (p)
REVERT: a  192 GLU cc_start: 0.7367 (pm20) cc_final: 0.6817 (tp30)
  outliers start: 42
  outliers final: 17
  residues processed: 205
  average time/residue: 0.2697
  time to fit residues: 83.9171
Evaluate side-chains
  155 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  163 ASP
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  684 TYR
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  908 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 126 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 162 optimal weight:    4.9990
   chunk 132 optimal weight:    4.9990
   chunk 181 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0050
   chunk 142 optimal weight:    8.9990
   chunk 153 optimal weight:    0.1980
   overall best weight:    1.6400

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

Flipped N/Q/H residues before XYZ refinement:
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 957 HIS
B 155 HIS
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.078558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.068732 restraints weight = 57962.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.070384 restraints weight = 32096.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071534 restraints weight = 20739.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16115  Z= 0.193
  Angle     :  0.670   8.085  21795  Z= 0.344
  Chirality :  0.045   0.162   2352
  Planarity :  0.005   0.051   2815
  Dihedral  :  5.263  19.597   2091
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.63 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.18), residues: 1914
  helix: -0.78 (0.18), residues: 782
  sheet: -1.57 (0.26), residues: 367
  loop : -1.83 (0.21), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 776 
 HIS   0.009   0.002   HIS B 155 
 PHE   0.036   0.002   PHE B 130 
 TYR   0.016   0.002   TYR A 433 
 ARG   0.021   0.001   ARG B 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  609)
  hydrogen bonds       : angle       5.45196 ( 1803)
  SS BOND              : bond        0.00359 (    4)
  SS BOND              : angle       2.07992 (    8)
  covalent geometry    : bond        0.00431 (16111)
  covalent geometry    : angle       0.66894 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 149
  time to evaluate  : 1.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 MET cc_start: 0.8634 (mmm) cc_final: 0.8383 (mmm)
REVERT: A  254 MET cc_start: 0.7340 (pmt) cc_final: 0.7074 (pmt)
REVERT: A  508 GLU cc_start: 0.5645 (OUTLIER) cc_final: 0.5342 (pt0)
REVERT: A  514 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7037 (pm20)
REVERT: A  577 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7790 (tt0)
REVERT: B  155 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.6549 (t-90)
REVERT: B  502 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7889 (mm-40)
REVERT: B  553 ASP cc_start: 0.8155 (t0) cc_final: 0.7526 (p0)
REVERT: B  648 LYS cc_start: 0.9011 (tppt) cc_final: 0.8671 (mmmt)
REVERT: B  815 ILE cc_start: 0.9028 (pp) cc_final: 0.8800 (pp)
REVERT: a  184 SER cc_start: 0.8528 (t) cc_final: 0.8087 (p)
  outliers start: 49
  outliers final: 25
  residues processed: 189
  average time/residue: 0.2501
  time to fit residues: 73.8812
Evaluate side-chains
  150 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 1.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  698 ASP
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  908 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 133 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9980
   chunk 137 optimal weight:    4.9990
   chunk 184 optimal weight:    5.9990
   chunk 173 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 139 optimal weight:    3.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 HIS
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a   3 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.076315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.066583 restraints weight = 58830.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.068187 restraints weight = 32603.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.069299 restraints weight = 21083.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  16115  Z= 0.262
  Angle     :  0.690  10.178  21795  Z= 0.354
  Chirality :  0.046   0.165   2352
  Planarity :  0.005   0.054   2815
  Dihedral  :  5.295  22.664   2091
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.75 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.18), residues: 1914
  helix: -0.49 (0.18), residues: 786
  sheet: -1.52 (0.26), residues: 366
  loop : -1.77 (0.21), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 355 
 HIS   0.018   0.002   HIS B 155 
 PHE   0.026   0.002   PHE B 130 
 TYR   0.021   0.002   TYR A 433 
 ARG   0.006   0.001   ARG B 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04307 (  609)
  hydrogen bonds       : angle       5.42642 ( 1803)
  SS BOND              : bond        0.00372 (    4)
  SS BOND              : angle       1.75937 (    8)
  covalent geometry    : bond        0.00581 (16111)
  covalent geometry    : angle       0.68881 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 129
  time to evaluate  : 1.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 MET cc_start: 0.7488 (pmt) cc_final: 0.7264 (pmt)
REVERT: A  288 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6299 (p90)
REVERT: A  508 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5438 (pt0)
REVERT: A  514 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7301 (pm20)
REVERT: A  577 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7873 (tt0)
REVERT: A  638 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8157 (mp10)
REVERT: B   62 ARG cc_start: 0.7396 (mpp-170) cc_final: 0.6991 (mtm-85)
REVERT: B  502 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8013 (mm-40)
REVERT: B  553 ASP cc_start: 0.8164 (t0) cc_final: 0.7758 (p0)
REVERT: B  815 ILE cc_start: 0.9118 (pp) cc_final: 0.8909 (pp)
  outliers start: 55
  outliers final: 29
  residues processed: 175
  average time/residue: 0.2618
  time to fit residues: 71.1667
Evaluate side-chains
  153 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 1.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  521 LYS
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  867 LEU
Chi-restraints excluded: chain a residue    3 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 164 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   chunk 169 optimal weight:    0.0570
   chunk 160 optimal weight:    0.9990
   chunk 155 optimal weight:    0.8980
   chunk 187 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 HIS
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.078406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.068699 restraints weight = 58672.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.070351 restraints weight = 32092.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.071497 restraints weight = 20447.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16115  Z= 0.120
  Angle     :  0.606   9.500  21795  Z= 0.304
  Chirality :  0.043   0.159   2352
  Planarity :  0.004   0.041   2815
  Dihedral  :  4.971  19.722   2091
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.68 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.19), residues: 1914
  helix: -0.09 (0.19), residues: 785
  sheet: -1.36 (0.26), residues: 362
  loop : -1.54 (0.22), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 776 
 HIS   0.005   0.001   HIS B 332 
 PHE   0.027   0.001   PHE B 130 
 TYR   0.024   0.001   TYR B 325 
 ARG   0.004   0.000   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  609)
  hydrogen bonds       : angle       5.00234 ( 1803)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       1.23960 (    8)
  covalent geometry    : bond        0.00266 (16111)
  covalent geometry    : angle       0.60547 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 143
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8647 (mt)
REVERT: A  288 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6600 (p90)
REVERT: A  514 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7366 (pm20)
REVERT: A  577 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7859 (tt0)
REVERT: A  638 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8111 (mp10)
REVERT: B  146 HIS cc_start: 0.8379 (m-70) cc_final: 0.7600 (m90)
REVERT: B  248 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6609 (t80)
REVERT: B  249 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.5902 (t80)
REVERT: B  502 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7953 (mm-40)
REVERT: B  550 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7499 (tt)
REVERT: B  860 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: B  995 MET cc_start: 0.7211 (mmm) cc_final: 0.6741 (tpp)
REVERT: a  184 SER cc_start: 0.8837 (t) cc_final: 0.8403 (m)
  outliers start: 44
  outliers final: 26
  residues processed: 175
  average time/residue: 0.2490
  time to fit residues: 67.7344
Evaluate side-chains
  154 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 1.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  521 LYS
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  248 TYR
Chi-restraints excluded: chain B residue  249 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  698 ASP
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  733 ILE
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  849 ILE
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  908 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 122 optimal weight:    4.9990
   chunk 156 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0980
   chunk 2 optimal weight:    6.9990
   chunk 114 optimal weight:   10.0000
   chunk 169 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.077374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.067537 restraints weight = 58784.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.069188 restraints weight = 32489.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.070303 restraints weight = 20893.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16115  Z= 0.161
  Angle     :  0.626  14.428  21795  Z= 0.314
  Chirality :  0.043   0.140   2352
  Planarity :  0.004   0.047   2815
  Dihedral  :  4.850  18.631   2091
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.03 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.19), residues: 1914
  helix:  0.08 (0.19), residues: 789
  sheet: -1.31 (0.26), residues: 363
  loop : -1.49 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 495 
 HIS   0.005   0.001   HIS B 730 
 PHE   0.021   0.002   PHE B 130 
 TYR   0.022   0.001   TYR B 628 
 ARG   0.004   0.000   ARG B 687 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  609)
  hydrogen bonds       : angle       4.93035 ( 1803)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       1.41194 (    8)
  covalent geometry    : bond        0.00362 (16111)
  covalent geometry    : angle       0.62546 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 127
  time to evaluate  : 2.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6304 (p90)
REVERT: A  514 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7464 (pm20)
REVERT: A  577 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7877 (tt0)
REVERT: A  638 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8115 (mt0)
REVERT: B  146 HIS cc_start: 0.8371 (m-70) cc_final: 0.7589 (m90)
REVERT: B  249 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5974 (t80)
REVERT: B  502 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7910 (mm-40)
REVERT: B  995 MET cc_start: 0.7279 (mmm) cc_final: 0.7049 (tpp)
  outliers start: 56
  outliers final: 35
  residues processed: 171
  average time/residue: 0.2517
  time to fit residues: 68.3212
Evaluate side-chains
  161 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 122
  time to evaluate  : 2.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  647 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  249 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  733 ILE
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  849 ILE
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  867 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 183 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9990
   chunk 164 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0980
   chunk 143 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 514 GLN
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a   3 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.077781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.067699 restraints weight = 58474.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.069445 restraints weight = 31261.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.070624 restraints weight = 19707.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16115  Z= 0.141
  Angle     :  0.609  10.889  21795  Z= 0.306
  Chirality :  0.043   0.143   2352
  Planarity :  0.004   0.040   2815
  Dihedral  :  4.766  18.351   2091
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.09 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.19), residues: 1914
  helix:  0.27 (0.19), residues: 784
  sheet: -1.22 (0.26), residues: 357
  loop : -1.44 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 495 
 HIS   0.005   0.001   HIS B 332 
 PHE   0.020   0.001   PHE B 130 
 TYR   0.019   0.001   TYR B 628 
 ARG   0.005   0.000   ARG B 687 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  609)
  hydrogen bonds       : angle       4.81769 ( 1803)
  SS BOND              : bond        0.00266 (    4)
  SS BOND              : angle       1.23111 (    8)
  covalent geometry    : bond        0.00319 (16111)
  covalent geometry    : angle       0.60877 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 136
  time to evaluate  : 1.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6211 (p90)
REVERT: A  577 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7931 (tt0)
REVERT: A  638 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8164 (mt0)
REVERT: B  249 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6115 (t80)
REVERT: B  303 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7672 (mttt)
REVERT: B  502 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7975 (mm-40)
REVERT: B  550 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7766 (tt)
REVERT: B  860 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: B  995 MET cc_start: 0.7551 (mmm) cc_final: 0.7256 (tpp)
REVERT: a  191 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8654 (tt)
  outliers start: 53
  outliers final: 35
  residues processed: 177
  average time/residue: 0.2544
  time to fit residues: 70.8049
Evaluate side-chains
  164 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 1.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  647 GLU
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  249 TYR
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  698 ASP
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  733 ILE
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  849 ILE
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  867 LEU
Chi-restraints excluded: chain a residue    3 ASN
Chi-restraints excluded: chain a residue  191 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 185 optimal weight:    4.9990
   chunk 165 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   chunk 170 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 173 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 147 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 108 HIS
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 GLN
B 475 ASN
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a   3 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.076633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.066555 restraints weight = 58714.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.068260 restraints weight = 31543.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.069411 restraints weight = 20007.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.4664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16115  Z= 0.190
  Angle     :  0.650  12.571  21795  Z= 0.327
  Chirality :  0.044   0.161   2352
  Planarity :  0.004   0.041   2815
  Dihedral  :  4.837  19.226   2091
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.38 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.19), residues: 1914
  helix:  0.31 (0.19), residues: 786
  sheet: -1.22 (0.26), residues: 357
  loop : -1.47 (0.22), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B 495 
 HIS   0.006   0.001   HIS B 730 
 PHE   0.044   0.002   PHE B 215 
 TYR   0.020   0.001   TYR B 628 
 ARG   0.006   0.001   ARG B 687 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03749 (  609)
  hydrogen bonds       : angle       4.91083 ( 1803)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       2.28802 (    8)
  covalent geometry    : bond        0.00430 (16111)
  covalent geometry    : angle       0.64843 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 126
  time to evaluate  : 1.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.6093 (p90)
REVERT: A  508 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5425 (pt0)
REVERT: A  511 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8045 (mmmt)
REVERT: A  577 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7950 (tt0)
REVERT: A  638 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8220 (mp10)
REVERT: A  989 PRO cc_start: 0.6709 (Cg_exo) cc_final: 0.6476 (Cg_endo)
REVERT: B  249 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6217 (t80)
REVERT: B  303 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7649 (mttt)
REVERT: B  431 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7411 (ttt180)
REVERT: B  502 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8006 (mm-40)
REVERT: B  908 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.8132 (t-100)
REVERT: B  995 MET cc_start: 0.7616 (mmm) cc_final: 0.7304 (tpp)
REVERT: a  191 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8728 (tt)
  outliers start: 52
  outliers final: 37
  residues processed: 168
  average time/residue: 0.2607
  time to fit residues: 68.6409
Evaluate side-chains
  164 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 120
  time to evaluate  : 1.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  647 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  886 ILE
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  249 TYR
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  431 ARG
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  733 ILE
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  849 ILE
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  867 LEU
Chi-restraints excluded: chain B residue  908 TRP
Chi-restraints excluded: chain a residue    3 ASN
Chi-restraints excluded: chain a residue  191 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 86 optimal weight:    0.3980
   chunk 84 optimal weight:    4.9990
   chunk 151 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 97 optimal weight:   10.0000
   chunk 112 optimal weight:    0.9980
   chunk 142 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.077794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.067780 restraints weight = 58053.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.069506 restraints weight = 30986.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.070688 restraints weight = 19616.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16115  Z= 0.128
  Angle     :  0.626  13.167  21795  Z= 0.312
  Chirality :  0.043   0.155   2352
  Planarity :  0.004   0.041   2815
  Dihedral  :  4.736  18.255   2091
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.08 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.19), residues: 1914
  helix:  0.40 (0.19), residues: 787
  sheet: -1.14 (0.27), residues: 350
  loop : -1.33 (0.22), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 495 
 HIS   0.004   0.001   HIS B 332 
 PHE   0.040   0.002   PHE A 109 
 TYR   0.022   0.001   TYR B 628 
 ARG   0.006   0.000   ARG B 687 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  609)
  hydrogen bonds       : angle       4.76121 ( 1803)
  SS BOND              : bond        0.00209 (    4)
  SS BOND              : angle       1.85220 (    8)
  covalent geometry    : bond        0.00291 (16111)
  covalent geometry    : angle       0.62480 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 128
  time to evaluate  : 1.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8772 (mt)
REVERT: A  288 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6072 (p90)
REVERT: A  511 LYS cc_start: 0.8338 (mmmt) cc_final: 0.8120 (mmmt)
REVERT: A  577 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7920 (tt0)
REVERT: A  638 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8195 (mt0)
REVERT: A  989 PRO cc_start: 0.6640 (Cg_exo) cc_final: 0.6416 (Cg_endo)
REVERT: B  249 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6138 (t80)
REVERT: B  303 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7669 (mttt)
REVERT: B  502 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7966 (mm-40)
REVERT: B  592 MET cc_start: 0.8253 (ptp) cc_final: 0.7757 (pmm)
REVERT: B  860 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: a  191 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8675 (tt)
  outliers start: 49
  outliers final: 35
  residues processed: 169
  average time/residue: 0.2478
  time to fit residues: 66.2195
Evaluate side-chains
  164 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 1.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  521 LYS
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  647 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  249 TYR
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  733 ILE
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  849 ILE
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  867 LEU
Chi-restraints excluded: chain a residue  191 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 121 optimal weight:    0.8980
   chunk 164 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 120 optimal weight:    4.9990
   chunk 146 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 161 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 821 ASN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.077820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.067798 restraints weight = 58251.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.069501 restraints weight = 31052.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.070687 restraints weight = 19672.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16115  Z= 0.128
  Angle     :  0.618  13.168  21795  Z= 0.308
  Chirality :  0.043   0.154   2352
  Planarity :  0.004   0.038   2815
  Dihedral  :  4.678  18.432   2091
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.26 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.19), residues: 1914
  helix:  0.43 (0.19), residues: 786
  sheet: -1.10 (0.27), residues: 351
  loop : -1.28 (0.22), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 495 
 HIS   0.005   0.001   HIS B 332 
 PHE   0.036   0.002   PHE B 215 
 TYR   0.023   0.001   TYR B 628 
 ARG   0.007   0.000   ARG B 687 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  609)
  hydrogen bonds       : angle       4.76948 ( 1803)
  SS BOND              : bond        0.00152 (    4)
  SS BOND              : angle       1.61879 (    8)
  covalent geometry    : bond        0.00291 (16111)
  covalent geometry    : angle       0.61742 (21787)

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

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

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3828 Ramachandran restraints generated.
    1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 1.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6098 (p90)
REVERT: A  511 LYS cc_start: 0.8297 (mmmt) cc_final: 0.8082 (mmmt)
REVERT: A  577 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7903 (tt0)
REVERT: A  638 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8201 (mt0)
REVERT: B  303 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7663 (mttt)
REVERT: B  502 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7962 (mm-40)
REVERT: B  592 MET cc_start: 0.8226 (ptp) cc_final: 0.7670 (pmm)
REVERT: B  768 GLU cc_start: 0.7808 (tp30) cc_final: 0.6754 (tp30)
REVERT: B  860 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: B  995 MET cc_start: 0.7373 (mmm) cc_final: 0.7124 (mmm)
REVERT: a  191 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8720 (tt)
  outliers start: 45
  outliers final: 35
  residues processed: 170
  average time/residue: 0.2421
  time to fit residues: 65.8417
Evaluate side-chains
  161 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 2.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  638 GLN
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  779 TYR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  823 LEU
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  486 GLU
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  630 SER
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  733 ILE
Chi-restraints excluded: chain B residue  821 ASN
Chi-restraints excluded: chain B residue  849 ILE
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  853 GLU
Chi-restraints excluded: chain B residue  867 LEU
Chi-restraints excluded: chain a residue  191 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 142 optimal weight:    6.9990
   chunk 116 optimal weight:    0.0870
   chunk 119 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 146 optimal weight:    2.9990
   chunk 168 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 178 optimal weight:    0.0970
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 821 ASN
A 982 GLN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 515 ASN
** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.078867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.069075 restraints weight = 57827.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.070770 restraints weight = 31413.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071898 restraints weight = 19978.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16115  Z= 0.111
  Angle     :  0.617  12.770  21795  Z= 0.306
  Chirality :  0.043   0.195   2352
  Planarity :  0.003   0.036   2815
  Dihedral  :  4.568  17.427   2091
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.61 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.19), residues: 1914
  helix:  0.52 (0.19), residues: 787
  sheet: -1.02 (0.27), residues: 350
  loop : -1.24 (0.22), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 776 
 HIS   0.004   0.001   HIS B 332 
 PHE   0.034   0.001   PHE B 215 
 TYR   0.023   0.001   TYR B 628 
 ARG   0.006   0.000   ARG B 687 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (  609)
  hydrogen bonds       : angle       4.65961 ( 1803)
  SS BOND              : bond        0.00105 (    4)
  SS BOND              : angle       1.30343 (    8)
  covalent geometry    : bond        0.00251 (16111)
  covalent geometry    : angle       0.61615 (21787)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4513.83 seconds
wall clock time: 79 minutes 32.01 seconds (4772.01 seconds total)