Starting phenix.real_space_refine
on Thu May 15 03:17:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cma_45745/05_2025/9cma_45745_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cma_45745/05_2025/9cma_45745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cma_45745/05_2025/9cma_45745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cma_45745/05_2025/9cma_45745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cma_45745/05_2025/9cma_45745_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cma_45745/05_2025/9cma_45745_neut.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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: 5
    Type Number    sf(0)   Gaussians
     P      86      5.49       5
     S      74      5.16       5
     C    7755      2.51       5
     N    2189      2.21       5
     O    2622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12726
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4936
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 22, 'TRANS': 591}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "C"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "D"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "E"
      Number of atoms: 949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 949
          Classifications: {'DNA': 46}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 45}
    Chain: "F"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 817
          Classifications: {'DNA': 40}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 39}
  Time building chain proxies: 7.51, per 1000 atoms: 0.59
  Number of scatterers: 12726
  At special positions: 0
  Unit cell: (98.53, 111.89, 148.63, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      74     16.00
     P      86     15.00
     O    2622      8.00
     N    2189      7.00
     C    7755      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 135 " - pdb=" SG  CYS D 162 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.82
  Conformation dependent library (CDL) restraints added in 5.4 seconds
  

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2646

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 14 sheets defined
      39.7% alpha, 16.5% beta
      23 base pairs and 67 stacking pairs defined.
    Time for finding SS restraints: 4.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 372 through 388
      removed outlier: 3.549A  pdb=" N   LEU A 376 " --> pdb=" O   HIS A 372 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   GLU A 388 " --> pdb=" O   LYS A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 397 through 409
    Processing helix  chain 'A' and resid 411 through 423
      removed outlier: 4.054A  pdb=" N   LYS A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   LEU A 417 " --> pdb=" O   THR A 413 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   TYR A 418 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 453
    Processing helix  chain 'A' and resid 464 through 472
    Processing helix  chain 'A' and resid 473 through 484
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 509 through 513
      removed outlier: 4.240A  pdb=" N   GLY A 513 " --> pdb=" O   CYS A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 532
    Processing helix  chain 'A' and resid 538 through 554
      removed outlier: 3.749A  pdb=" N   ARG A 542 " --> pdb=" O   CYS A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 620
      removed outlier: 3.540A  pdb=" N   LEU A 602 " --> pdb=" O   ASP A 598 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 603 " --> pdb=" O   ARG A 599 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 604 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 605 " --> pdb=" O   ASP A 601 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A 620 " --> pdb=" O   SER A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 642
      removed outlier: 3.935A  pdb=" N   ALA A 627 " --> pdb=" O   ASN A 623 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLU A 629 " --> pdb=" O   GLU A 625 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 630 " --> pdb=" O   GLU A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 653
    Processing helix  chain 'A' and resid 661 through 680
      removed outlier: 3.590A  pdb=" N   GLU A 675 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 696
      removed outlier: 3.667A  pdb=" N   GLN A 696 " --> pdb=" O   SER A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 718
      removed outlier: 4.123A  pdb=" N   HIS A 718 " --> pdb=" O   ASN A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 735
      removed outlier: 3.666A  pdb=" N   LYS A 727 " --> pdb=" O   GLU A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 756
      removed outlier: 4.313A  pdb=" N   LEU A 746 " --> pdb=" O   HIS A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 766
      removed outlier: 3.853A  pdb=" N   LYS A 763 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   HIS A 764 " --> pdb=" O   LYS A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 824
      removed outlier: 4.203A  pdb=" N   LEU A 817 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 818 " --> pdb=" O   VAL A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 851
      removed outlier: 3.641A  pdb=" N   LEU A 845 " --> pdb=" O   LEU A 841 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   ASP A 848 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   ILE A 849 " --> pdb=" O   LEU A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 879
    Processing helix  chain 'A' and resid 879 through 893
    Processing helix  chain 'A' and resid 894 through 909
      removed outlier: 3.570A  pdb=" N   TRP A 901 " --> pdb=" O   SER A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 922
    Processing helix  chain 'A' and resid 924 through 935
    Processing helix  chain 'A' and resid 937 through 950
      removed outlier: 4.589A  pdb=" N   VAL A 943 " --> pdb=" O   VAL A 939 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   HIS A 946 " --> pdb=" O   GLY A 942 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ALA A 949 " --> pdb=" O   ARG A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 997
      removed outlier: 3.556A  pdb=" N   TRP A 990 " --> pdb=" O   LYS A 986 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU A 993 " --> pdb=" O   ILE A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1017
    Processing helix  chain 'B' and resid 8 through 21
      removed outlier: 3.800A  pdb=" N   LEU B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B  16 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLU B  17 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   ALA B  18 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU B  19 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASP B  21 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 57
      No H-bonds generated for 'chain 'B' and resid 55 through 57'
    Processing helix  chain 'B' and resid 74 through 82
      removed outlier: 3.635A  pdb=" N   ILE B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA B  82 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 153
      removed outlier: 4.162A  pdb=" N   ARG B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG B 149 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   HIS B 153 " --> pdb=" O   ARG B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 216
      removed outlier: 3.660A  pdb=" N   LEU B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 222
      Proline residue:  B 220  - end of helix
      No H-bonds generated for 'chain 'B' and resid 217 through 222'
    Processing helix  chain 'B' and resid 255 through 261
      removed outlier: 4.259A  pdb=" N   GLU B 259 " --> pdb=" O   ILE B 255 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLY B 260 " --> pdb=" O   GLU B 256 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER B 261 " --> pdb=" O   ASP B 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 255 through 261'
    Processing helix  chain 'C' and resid 8 through 23
      removed outlier: 4.080A  pdb=" N   LEU C  12 " --> pdb=" O   GLN C   8 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU C  16 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU C  17 " --> pdb=" O   LYS C  13 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU C  19 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ASP C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU C  22 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 80
      removed outlier: 3.501A  pdb=" N   ILE C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 155
      removed outlier: 3.551A  pdb=" N   SER C 152 " --> pdb=" O   CYS C 148 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY C 155 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 216
    Processing helix  chain 'C' and resid 217 through 219
      No H-bonds generated for 'chain 'C' and resid 217 through 219'
    Processing helix  chain 'D' and resid 8 through 21
      removed outlier: 3.834A  pdb=" N   LEU D  12 " --> pdb=" O   GLN D   8 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL D  15 " --> pdb=" O   ILE D  11 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LEU D  16 " --> pdb=" O   LEU D  12 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   GLU D  17 " --> pdb=" O   LYS D  13 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ALA D  18 " --> pdb=" O   LYS D  14 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU D  19 " --> pdb=" O   VAL D  15 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ASP D  21 " --> pdb=" O   GLU D  17 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 57
      No H-bonds generated for 'chain 'D' and resid 55 through 57'
    Processing helix  chain 'D' and resid 72 through 81
      removed outlier: 3.610A  pdb=" N   LYS D  77 " --> pdb=" O   THR D  73 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   CYS D  81 " --> pdb=" O   LYS D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 153
      removed outlier: 3.511A  pdb=" N   ARG D 149 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASP D 150 " --> pdb=" O   ARG D 146 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   HIS D 153 " --> pdb=" O   ARG D 149 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 216
    Processing helix  chain 'D' and resid 217 through 222
      Proline residue:  D 220  - end of helix
      No H-bonds generated for 'chain 'D' and resid 217 through 222'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 456 through 458
    Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 61
      removed outlier: 3.522A  pdb=" N   ILE B  87 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLU B 104 " --> pdb=" O   ILE B  87 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR B  89 " --> pdb=" O   VAL B 102 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   VAL B 102 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG B  91 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 71
      removed outlier: 3.877A  pdb=" N   ALA B  26 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   GLU B  25 " --> pdb=" O   MET B  40 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   MET B  40 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 199
      removed outlier: 3.618A  pdb=" N   VAL B 136 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 140
    Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161
    Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 61
      removed outlier: 3.532A  pdb=" N   ARG C  61 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL C 102 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER C 112 " --> pdb=" O   PHE C 103 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 52 through 53
      removed outlier: 3.906A  pdb=" N   ALA C  26 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 38 through 40
      removed outlier: 3.777A  pdb=" N   SER C  39 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   VAL C  48 " --> pdb=" O   SER C  39 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL C 236 " --> pdb=" O   SER C 228 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER C 228 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   LYS C 240 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR C 224 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 181
      removed outlier: 3.597A  pdb=" N   SER C 161 " --> pdb=" O   LYS C 168 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER C 170 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 59 through 61
      removed outlier: 3.704A  pdb=" N   GLU D   3 " --> pdb=" O   ARG D  61 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 69 through 71
      removed outlier: 3.656A  pdb=" N   VAL D  70 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ALA D  26 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   GLU D  25 " --> pdb=" O   MET D  40 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   MET D  40 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   CYS D  27 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLN D  38 " --> pdb=" O   CYS D  27 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL D  48 " --> pdb=" O   SER D  39 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN D  49 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS D 248 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR D  51 " --> pdb=" O   HIS D 246 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   HIS D 246 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL D 236 " --> pdb=" O   SER D 228 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   LYS D 240 " --> pdb=" O   THR D 224 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   THR D 224 " --> pdb=" O   LYS D 240 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL D 136 " --> pdb=" O   GLU D 198 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 100
    Processing sheet with id=AB5, first strand: chain 'D' and resid 177 through 181
      removed outlier: 3.676A  pdb=" N   GLY D 166 " --> pdb=" O   ALA D 163 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   SER D 161 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER D 170 " --> pdb=" O   VAL D 159 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   SER D 172 " --> pdb=" O   ALA D 157 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   ALA D 157 " --> pdb=" O   SER D 172 " (cutoff:3.500A)

    455 hydrogen bonds defined for protein.
    1257 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      54 hydrogen bonds
      100 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      67 stacking parallelities
  Total time for adding SS restraints: 5.42

  Time building geometry restraints manager: 3.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3574
        1.33 -     1.46: 2677
        1.46 -     1.58: 6590
        1.58 -     1.70: 170
        1.70 -     1.82: 114
  Bond restraints: 13125
  Sorted by residual:
  bond pdb=" CA  GLU A 737 "
       pdb=" C   GLU A 737 "
    ideal  model  delta    sigma   weight residual
    1.522  1.495  0.027 1.38e-02 5.25e+03 3.92e+00
  bond pdb=" C   GLN A 506 "
       pdb=" O   GLN A 506 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.012 7.30e-03 1.88e+04 2.60e+00
  bond pdb=" CA  ASN D  95 "
       pdb=" CB  ASN D  95 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.017 1.22e-02 6.72e+03 1.98e+00
  bond pdb=" CA  PRO D 220 "
       pdb=" C   PRO D 220 "
    ideal  model  delta    sigma   weight residual
    1.520  1.536 -0.016 1.42e-02 4.96e+03 1.34e+00
  bond pdb=" N   ILE C 241 "
       pdb=" CA  ILE C 241 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.017 1.57e-02 4.06e+03 1.21e+00
  ... (remaining 13120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 17370
        1.60 -     3.21: 641
        3.21 -     4.81: 75
        4.81 -     6.42: 24
        6.42 -     8.02: 4
  Bond angle restraints: 18114
  Sorted by residual:
  angle pdb=" C   ASP B  94 "
        pdb=" CA  ASP B  94 "
        pdb=" CB  ASP B  94 "
      ideal   model   delta    sigma   weight residual
     116.54  109.38    7.16 1.15e+00 7.56e-01 3.87e+01
  angle pdb=" N   VAL A 509 "
        pdb=" CA  VAL A 509 "
        pdb=" C   VAL A 509 "
      ideal   model   delta    sigma   weight residual
     113.42  108.31    5.11 1.17e+00 7.31e-01 1.91e+01
  angle pdb=" C   THR A 588 "
        pdb=" CA  THR A 588 "
        pdb=" CB  THR A 588 "
      ideal   model   delta    sigma   weight residual
     117.23  111.67    5.56 1.36e+00 5.41e-01 1.67e+01
  angle pdb=" N   SER A 508 "
        pdb=" CA  SER A 508 "
        pdb=" C   SER A 508 "
      ideal   model   delta    sigma   weight residual
     114.56  109.38    5.18 1.27e+00 6.20e-01 1.67e+01
  angle pdb=" N   ASP B  94 "
        pdb=" CA  ASP B  94 "
        pdb=" C   ASP B  94 "
      ideal   model   delta    sigma   weight residual
     108.31  114.11   -5.80 1.52e+00 4.33e-01 1.46e+01
  ... (remaining 18109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6519
       17.91 -    35.83: 782
       35.83 -    53.74: 350
       53.74 -    71.65: 100
       71.65 -    89.57: 13
  Dihedral angle restraints: 7764
    sinusoidal: 3693
      harmonic: 4071
  Sorted by residual:
  dihedral pdb=" CB  CYS D 135 "
           pdb=" SG  CYS D 135 "
           pdb=" SG  CYS D 162 "
           pdb=" CB  CYS D 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.98   58.02     1      1.00e+01 1.00e-02 4.52e+01
  dihedral pdb=" CA  GLN A 775 "
           pdb=" C   GLN A 775 "
           pdb=" N   ASP A 776 "
           pdb=" CA  ASP A 776 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.62  -22.38     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  GLU A 459 "
           pdb=" C   GLU A 459 "
           pdb=" N   SER A 460 "
           pdb=" CA  SER A 460 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.50   21.50     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 7761 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1649
       0.049 -    0.098: 358
       0.098 -    0.147: 65
       0.147 -    0.196: 1
       0.196 -    0.245: 1
  Chirality restraints: 2074
  Sorted by residual:
  chirality pdb=" CG  LEU D 221 "
            pdb=" CB  LEU D 221 "
            pdb=" CD1 LEU D 221 "
            pdb=" CD2 LEU D 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CG  LEU A 958 "
            pdb=" CB  LEU A 958 "
            pdb=" CD1 LEU A 958 "
            pdb=" CD2 LEU A 958 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CG  LEU A 450 "
            pdb=" CB  LEU A 450 "
            pdb=" CD1 LEU A 450 "
            pdb=" CD2 LEU A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.32e-01
  ... (remaining 2071 not shown)

  Planarity restraints: 2020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 937 "    0.036 5.00e-02 4.00e+02   5.44e-02 4.73e+00
        pdb=" N   PRO A 938 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 938 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 938 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 495 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.04e+00
        pdb=" CD  GLN A 495 "    0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 495 "   -0.013 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 495 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 723 "   -0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A 724 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 724 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 724 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 2017 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 418
        2.68 -     3.24: 13160
        3.24 -     3.79: 21548
        3.79 -     4.35: 28119
        4.35 -     4.90: 41674
  Nonbonded interactions: 104919
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  41 "
            pdb=" OG  SER B  43 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OE1 GLN A 492 "
            pdb=" NZ  LYS A 493 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" OG  SER D  43 "
            pdb=" OH  TYR D 211 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" O   GLY A 826 "
            pdb=" ND2 ASN A 965 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" O   ARG C 149 "
            pdb=" OG  SER C 152 "
     model   vdw
     2.192 3.040
  ... (remaining 104914 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 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.150
  Process input model:                     33.510
  Find NCS groups from input model:        0.260
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
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      :  0.003   0.028  13128  Z= 0.166
  Angle     :  0.715   8.024  18120  Z= 0.425
  Chirality :  0.042   0.245   2074
  Planarity :  0.005   0.062   2020
  Dihedral  : 19.095  89.568   5109
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 22.26
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.28 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -1.47 (0.22), residues: 1385
  helix: -0.40 (0.26), residues: 387
  sheet: -0.90 (0.31), residues: 295
  loop : -1.28 (0.23), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 990 
 HIS   0.006   0.001   HIS A 485 
 PHE   0.019   0.002   PHE A 407 
 TYR   0.014   0.002   TYR D  60 
 ARG   0.008   0.001   ARG D  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30393 (  509)
  hydrogen bonds       : angle       9.89567 ( 1357)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       1.04745 (    6)
  covalent geometry    : bond        0.00322 (13125)
  covalent geometry    : angle       0.71484 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  988 MET cc_start: 0.9101 (ttt) cc_final: 0.8770 (ttm)
REVERT: B   75 MET cc_start: 0.8401 (mmp) cc_final: 0.8146 (mmm)
REVERT: B  229 MET cc_start: 0.7368 (tpt) cc_final: 0.6484 (tpp)
REVERT: B  239 TYR cc_start: 0.9256 (m-80) cc_final: 0.8764 (m-80)
REVERT: C   23 ILE cc_start: 0.4249 (mm) cc_final: 0.3813 (mm)
REVERT: C   68 MET cc_start: 0.8187 (tpt) cc_final: 0.7739 (tpp)
REVERT: C  144 PHE cc_start: 0.9423 (t80) cc_final: 0.9008 (t80)
REVERT: C  169 PHE cc_start: 0.9455 (m-80) cc_final: 0.9086 (m-80)
REVERT: C  235 LEU cc_start: 0.9117 (tp) cc_final: 0.8845 (tp)
REVERT: D   40 MET cc_start: 0.4892 (tpt) cc_final: 0.4429 (tpt)
REVERT: D   68 MET cc_start: 0.9123 (tmm) cc_final: 0.8680 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2964
  time to fit residues: 62.8555
Evaluate side-chains
  117 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    9.9990
   chunk 111 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 133 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 372 HIS
** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 GLN
A 716 HIS
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 748 GLN
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 821 HIS
A 929 GLN
A 970 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.078622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.059290 restraints weight = 108400.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.060580 restraints weight = 85118.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.061480 restraints weight = 71163.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13128  Z= 0.191
  Angle     :  0.705   7.500  18120  Z= 0.381
  Chirality :  0.044   0.155   2074
  Planarity :  0.005   0.050   2020
  Dihedral  : 21.891  89.613   2439
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 18.97
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.79 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.10 %
    Favored  : 90.00 %
  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: -1.41 (0.22), residues: 1385
  helix: -0.15 (0.23), residues: 442
  sheet: -0.96 (0.30), residues: 297
  loop : -1.40 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 624 
 HIS   0.009   0.001   HIS A 644 
 PHE   0.028   0.002   PHE D 144 
 TYR   0.020   0.002   TYR A 747 
 ARG   0.007   0.001   ARG A 721 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06639 (  509)
  hydrogen bonds       : angle       6.70568 ( 1357)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       1.04752 (    6)
  covalent geometry    : bond        0.00388 (13125)
  covalent geometry    : angle       0.70529 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  664 TRP cc_start: 0.7829 (t60) cc_final: 0.7354 (t60)
REVERT: A  988 MET cc_start: 0.8920 (ttt) cc_final: 0.8595 (ttm)
REVERT: B   75 MET cc_start: 0.8412 (mmp) cc_final: 0.8098 (mmp)
REVERT: B  229 MET cc_start: 0.7726 (tpt) cc_final: 0.7176 (tpp)
REVERT: B  239 TYR cc_start: 0.9289 (m-80) cc_final: 0.8894 (m-80)
REVERT: C   23 ILE cc_start: 0.4826 (mm) cc_final: 0.3969 (mm)
REVERT: C   68 MET cc_start: 0.8292 (tpt) cc_final: 0.7933 (tpp)
REVERT: C   72 LEU cc_start: 0.8733 (mm) cc_final: 0.8446 (mm)
REVERT: C  116 MET cc_start: 0.7095 (tpt) cc_final: 0.6422 (tpt)
REVERT: C  144 PHE cc_start: 0.9398 (t80) cc_final: 0.9041 (t80)
REVERT: C  169 PHE cc_start: 0.9430 (m-80) cc_final: 0.9196 (m-80)
REVERT: D  119 MET cc_start: 0.7151 (ppp) cc_final: 0.6947 (ppp)
  outliers start: 11
  outliers final: 7
  residues processed: 131
  average time/residue: 0.2835
  time to fit residues: 52.1225
Evaluate side-chains
  120 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue  133 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 111 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 134 optimal weight:   20.0000
   chunk 72 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN
** C 246 HIS ** 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 = 0.4121 r_free = 0.4121 target = 0.076487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.057051 restraints weight = 110708.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.058355 restraints weight = 86312.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.059236 restraints weight = 71706.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13128  Z= 0.182
  Angle     :  0.687   9.575  18120  Z= 0.365
  Chirality :  0.043   0.208   2074
  Planarity :  0.004   0.050   2020
  Dihedral  : 21.863  87.225   2439
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 20.19
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.86 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.62 %
    Favored  : 86.15 %
  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: -1.32 (0.22), residues: 1385
  helix: -0.07 (0.23), residues: 444
  sheet: -0.86 (0.30), residues: 300
  loop : -1.39 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  28 
 HIS   0.007   0.001   HIS A 485 
 PHE   0.036   0.002   PHE B 214 
 TYR   0.020   0.002   TYR D 250 
 ARG   0.007   0.001   ARG A 721 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06155 (  509)
  hydrogen bonds       : angle       6.23280 ( 1357)
  SS BOND              : bond        0.00325 (    3)
  SS BOND              : angle       0.86044 (    6)
  covalent geometry    : bond        0.00386 (13125)
  covalent geometry    : angle       0.68708 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 1.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  448 GLU cc_start: 0.9412 (tp30) cc_final: 0.9102 (mm-30)
REVERT: A  946 HIS cc_start: 0.9331 (OUTLIER) cc_final: 0.9054 (p90)
REVERT: A  988 MET cc_start: 0.8828 (ttt) cc_final: 0.8457 (ttt)
REVERT: B   75 MET cc_start: 0.8583 (mmp) cc_final: 0.8329 (mmp)
REVERT: B  229 MET cc_start: 0.7821 (tpt) cc_final: 0.7379 (tpp)
REVERT: B  239 TYR cc_start: 0.9256 (m-80) cc_final: 0.8915 (m-80)
REVERT: C   68 MET cc_start: 0.8370 (tpt) cc_final: 0.8035 (tpp)
REVERT: C   72 LEU cc_start: 0.8780 (mm) cc_final: 0.8524 (mm)
REVERT: C  144 PHE cc_start: 0.9421 (t80) cc_final: 0.9090 (t80)
REVERT: D  119 MET cc_start: 0.7329 (ppp) cc_final: 0.7081 (ppp)
REVERT: D  139 MET cc_start: 0.9796 (OUTLIER) cc_final: 0.9520 (pmm)
REVERT: D  144 PHE cc_start: 0.9637 (t80) cc_final: 0.9433 (t80)
REVERT: D  244 MET cc_start: 0.9099 (tpt) cc_final: 0.8897 (tpt)
  outliers start: 15
  outliers final: 8
  residues processed: 123
  average time/residue: 0.2851
  time to fit residues: 49.4858
Evaluate side-chains
  115 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain D residue  139 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 144 optimal weight:   10.0000
   chunk 145 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 125 optimal weight:   20.0000
   chunk 52 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 140 optimal weight:    7.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 644 HIS
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 946 HIS
C  44 HIS
** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.071954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.052240 restraints weight = 114323.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.053385 restraints weight = 89919.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.054216 restraints weight = 75916.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  13128  Z= 0.237
  Angle     :  0.733   9.437  18120  Z= 0.393
  Chirality :  0.045   0.206   2074
  Planarity :  0.005   0.074   2020
  Dihedral  : 22.036  85.361   2439
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 26.15
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.44 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.43 %
    Favored  : 82.95 %
  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: -1.53 (0.22), residues: 1385
  helix: -0.31 (0.23), residues: 444
  sheet: -0.90 (0.28), residues: 321
  loop : -1.51 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B  28 
 HIS   0.009   0.002   HIS A 485 
 PHE   0.053   0.003   PHE A 407 
 TYR   0.026   0.003   TYR D 250 
 ARG   0.005   0.001   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06634 (  509)
  hydrogen bonds       : angle       6.22911 ( 1357)
  SS BOND              : bond        0.00349 (    3)
  SS BOND              : angle       0.96515 (    6)
  covalent geometry    : bond        0.00503 (13125)
  covalent geometry    : angle       0.73245 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  682 MET cc_start: 0.9101 (mmp) cc_final: 0.8872 (mmm)
REVERT: A  744 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7336 (mp)
REVERT: A  988 MET cc_start: 0.8907 (ttt) cc_final: 0.8706 (ttt)
REVERT: B    1 MET cc_start: 0.9231 (tpp) cc_final: 0.8744 (tpt)
REVERT: B   28 TRP cc_start: 0.7017 (OUTLIER) cc_final: 0.6721 (m-90)
REVERT: B  199 MET cc_start: 0.7806 (mmm) cc_final: 0.7351 (tpp)
REVERT: B  239 TYR cc_start: 0.9195 (m-80) cc_final: 0.8790 (m-80)
REVERT: C   28 TRP cc_start: 0.9164 (t-100) cc_final: 0.8421 (t-100)
REVERT: C   68 MET cc_start: 0.8560 (tpt) cc_final: 0.8290 (tpp)
REVERT: C  144 PHE cc_start: 0.9400 (t80) cc_final: 0.9063 (t80)
REVERT: C  229 MET cc_start: 0.6744 (mmm) cc_final: 0.6020 (mmm)
REVERT: D   40 MET cc_start: 0.4938 (tpp) cc_final: 0.4649 (tpp)
REVERT: D  119 MET cc_start: 0.7668 (ppp) cc_final: 0.7300 (ppp)
REVERT: D  139 MET cc_start: 0.9820 (OUTLIER) cc_final: 0.9524 (pmm)
REVERT: D  144 PHE cc_start: 0.9689 (t80) cc_final: 0.9385 (t80)
REVERT: D  244 MET cc_start: 0.9190 (tpt) cc_final: 0.8626 (tpt)
  outliers start: 32
  outliers final: 15
  residues processed: 137
  average time/residue: 0.2857
  time to fit residues: 54.6806
Evaluate side-chains
  118 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 ARG
Chi-restraints excluded: chain A residue  946 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  139 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 68 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 79 optimal weight:   20.0000
   chunk 80 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    4.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 246 HIS
D 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.073719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.054264 restraints weight = 115255.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.055500 restraints weight = 90383.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.056343 restraints weight = 75888.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  13128  Z= 0.177
  Angle     :  0.682  10.239  18120  Z= 0.358
  Chirality :  0.043   0.218   2074
  Planarity :  0.004   0.049   2020
  Dihedral  : 21.969  86.292   2439
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 21.73
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.00 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.05 %
    Favored  : 80.41 %
  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 (0.22), residues: 1385
  helix: -0.10 (0.23), residues: 442
  sheet: -0.91 (0.28), residues: 320
  loop : -1.54 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  28 
 HIS   0.007   0.002   HIS A 485 
 PHE   0.049   0.002   PHE A 407 
 TYR   0.021   0.002   TYR C 249 
 ARG   0.015   0.001   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05404 (  509)
  hydrogen bonds       : angle       5.93893 ( 1357)
  SS BOND              : bond        0.00327 (    3)
  SS BOND              : angle       0.92498 (    6)
  covalent geometry    : bond        0.00384 (13125)
  covalent geometry    : angle       0.68175 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.9001 (m-10)
REVERT: A  682 MET cc_start: 0.9098 (mmp) cc_final: 0.8855 (mmm)
REVERT: B   28 TRP cc_start: 0.6950 (OUTLIER) cc_final: 0.6506 (m-90)
REVERT: B   75 MET cc_start: 0.8896 (mmp) cc_final: 0.8678 (mmp)
REVERT: B  199 MET cc_start: 0.7676 (mmm) cc_final: 0.7344 (tpp)
REVERT: B  229 MET cc_start: 0.8359 (mmm) cc_final: 0.7385 (ptt)
REVERT: B  239 TYR cc_start: 0.9192 (m-80) cc_final: 0.8864 (m-80)
REVERT: C   28 TRP cc_start: 0.9201 (t-100) cc_final: 0.8479 (t-100)
REVERT: C   68 MET cc_start: 0.8534 (tpt) cc_final: 0.8262 (tpp)
REVERT: C  116 MET cc_start: 0.7512 (tpt) cc_final: 0.6761 (tpt)
REVERT: C  144 PHE cc_start: 0.9412 (t80) cc_final: 0.9012 (t80)
REVERT: C  195 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8535 (t)
REVERT: C  229 MET cc_start: 0.7141 (mmm) cc_final: 0.6611 (mmm)
REVERT: C  235 LEU cc_start: 0.9392 (tp) cc_final: 0.8862 (pp)
REVERT: D    2 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7207 (t80)
REVERT: D   40 MET cc_start: 0.5100 (tpp) cc_final: 0.4831 (tpp)
REVERT: D   61 ARG cc_start: 0.9330 (ttp80) cc_final: 0.9042 (ttp80)
REVERT: D   68 MET cc_start: 0.9181 (tmm) cc_final: 0.8894 (tmm)
REVERT: D  119 MET cc_start: 0.7713 (ppp) cc_final: 0.7319 (ppp)
REVERT: D  139 MET cc_start: 0.9829 (OUTLIER) cc_final: 0.9593 (pmm)
REVERT: D  144 PHE cc_start: 0.9692 (t80) cc_final: 0.9378 (t80)
  outliers start: 31
  outliers final: 14
  residues processed: 130
  average time/residue: 0.2619
  time to fit residues: 48.6221
Evaluate side-chains
  119 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  953 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  249 TYR
Chi-restraints excluded: chain D residue    2 PHE
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  139 MET
Chi-restraints excluded: chain D residue  197 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 145 optimal weight:    7.9990
   chunk 90 optimal weight:   30.0000
   chunk 42 optimal weight:   30.0000
   chunk 101 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 72 optimal weight:   20.0000
   chunk 85 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 134 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 246 HIS ** 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 = 0.3984 r_free = 0.3984 target = 0.071021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.051930 restraints weight = 118304.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.053120 restraints weight = 92447.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.053858 restraints weight = 77722.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.4840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13128  Z= 0.221
  Angle     :  0.729  13.400  18120  Z= 0.387
  Chirality :  0.045   0.273   2074
  Planarity :  0.005   0.074   2020
  Dihedral  : 22.003  85.114   2439
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 26.39
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.29 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.52 %
    Favored  : 78.93 %
  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: -1.64 (0.22), residues: 1385
  helix: -0.30 (0.23), residues: 443
  sheet: -1.05 (0.28), residues: 310
  loop : -1.61 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  28 
 HIS   0.024   0.002   HIS A 946 
 PHE   0.029   0.002   PHE B 214 
 TYR   0.028   0.003   TYR A 408 
 ARG   0.009   0.001   ARG A 969 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06374 (  509)
  hydrogen bonds       : angle       6.01387 ( 1357)
  SS BOND              : bond        0.00421 (    3)
  SS BOND              : angle       1.08118 (    6)
  covalent geometry    : bond        0.00472 (13125)
  covalent geometry    : angle       0.72876 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  484 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8916 (m-80)
REVERT: A  500 PHE cc_start: 0.9533 (m-80) cc_final: 0.9204 (m-80)
REVERT: A  664 TRP cc_start: 0.8324 (t60) cc_final: 0.7556 (t60)
REVERT: A  682 MET cc_start: 0.9206 (mmp) cc_final: 0.8957 (mmm)
REVERT: A  834 GLU cc_start: 0.3400 (OUTLIER) cc_final: 0.1947 (tt0)
REVERT: A  988 MET cc_start: 0.8828 (ttt) cc_final: 0.8598 (tmm)
REVERT: B   28 TRP cc_start: 0.6948 (OUTLIER) cc_final: 0.6244 (m-90)
REVERT: B   75 MET cc_start: 0.9081 (mmp) cc_final: 0.8858 (mmp)
REVERT: B  211 TYR cc_start: 0.9682 (m-80) cc_final: 0.9457 (m-80)
REVERT: B  239 TYR cc_start: 0.9222 (m-80) cc_final: 0.8931 (m-80)
REVERT: C   28 TRP cc_start: 0.9229 (t-100) cc_final: 0.8659 (t-100)
REVERT: C  116 MET cc_start: 0.7628 (tpt) cc_final: 0.6893 (tpt)
REVERT: C  121 LEU cc_start: 0.3615 (OUTLIER) cc_final: 0.2864 (mm)
REVERT: C  144 PHE cc_start: 0.9429 (t80) cc_final: 0.9098 (t80)
REVERT: D    2 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7219 (t80)
REVERT: D   40 MET cc_start: 0.5155 (tpp) cc_final: 0.4868 (tpp)
REVERT: D   61 ARG cc_start: 0.9232 (ttp80) cc_final: 0.8878 (ttp80)
REVERT: D  119 MET cc_start: 0.7819 (ppp) cc_final: 0.7409 (ppp)
REVERT: D  139 MET cc_start: 0.9848 (OUTLIER) cc_final: 0.9625 (pmm)
REVERT: D  144 PHE cc_start: 0.9708 (t80) cc_final: 0.9396 (t80)
REVERT: D  244 MET cc_start: 0.8960 (tpt) cc_final: 0.7849 (tpt)
  outliers start: 31
  outliers final: 20
  residues processed: 130
  average time/residue: 0.2666
  time to fit residues: 49.3977
Evaluate side-chains
  128 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  760 LYS
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue  945 ARG
Chi-restraints excluded: chain A residue  953 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  249 TYR
Chi-restraints excluded: chain D residue    2 PHE
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  103 PHE
Chi-restraints excluded: chain D residue  139 MET
Chi-restraints excluded: chain D residue  197 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 138 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 139 optimal weight:    8.9990
   chunk 60 optimal weight:   30.0000
   chunk 102 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 131 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 HIS ** 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 = 0.3997 r_free = 0.3997 target = 0.071749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.052564 restraints weight = 114756.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.053756 restraints weight = 89063.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.054602 restraints weight = 74512.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.5124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13128  Z= 0.171
  Angle     :  0.705  12.728  18120  Z= 0.367
  Chirality :  0.044   0.225   2074
  Planarity :  0.004   0.053   2020
  Dihedral  : 21.980  85.042   2439
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 22.82
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.79 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.16 %
    Favored  : 77.46 %
  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: -1.48 (0.22), residues: 1385
  helix: -0.12 (0.24), residues: 453
  sheet: -0.99 (0.28), residues: 318
  loop : -1.56 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  28 
 HIS   0.010   0.001   HIS A 946 
 PHE   0.027   0.002   PHE B 214 
 TYR   0.025   0.002   TYR A 408 
 ARG   0.007   0.001   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05208 (  509)
  hydrogen bonds       : angle       5.79440 ( 1357)
  SS BOND              : bond        0.00399 (    3)
  SS BOND              : angle       0.82714 (    6)
  covalent geometry    : bond        0.00369 (13125)
  covalent geometry    : angle       0.70502 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 1.385 
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: A  484 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8964 (m-80)
REVERT: A  500 PHE cc_start: 0.9551 (m-80) cc_final: 0.9233 (m-80)
REVERT: A  682 MET cc_start: 0.9188 (mmp) cc_final: 0.8944 (mmm)
REVERT: B   28 TRP cc_start: 0.6873 (OUTLIER) cc_final: 0.6380 (m-90)
REVERT: B   75 MET cc_start: 0.8955 (mmp) cc_final: 0.8707 (mmp)
REVERT: B  229 MET cc_start: 0.8477 (mmm) cc_final: 0.7746 (ttt)
REVERT: C   28 TRP cc_start: 0.9311 (t-100) cc_final: 0.8585 (t-100)
REVERT: C  116 MET cc_start: 0.7561 (tpt) cc_final: 0.6818 (tpt)
REVERT: C  121 LEU cc_start: 0.3692 (OUTLIER) cc_final: 0.2872 (mm)
REVERT: C  144 PHE cc_start: 0.9464 (t80) cc_final: 0.9068 (t80)
REVERT: C  229 MET cc_start: 0.7136 (mmm) cc_final: 0.6444 (mmm)
REVERT: C  235 LEU cc_start: 0.9459 (tp) cc_final: 0.8948 (pp)
REVERT: D    2 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7094 (t80)
REVERT: D   40 MET cc_start: 0.5035 (tpp) cc_final: 0.4742 (tpp)
REVERT: D   61 ARG cc_start: 0.9219 (ttp80) cc_final: 0.8835 (ttp80)
REVERT: D  116 MET cc_start: 0.7973 (tpp) cc_final: 0.6827 (tmm)
REVERT: D  119 MET cc_start: 0.7903 (ppp) cc_final: 0.7508 (ppp)
REVERT: D  139 MET cc_start: 0.9855 (OUTLIER) cc_final: 0.9624 (pmm)
REVERT: D  144 PHE cc_start: 0.9717 (t80) cc_final: 0.9368 (t80)
REVERT: D  229 MET cc_start: 0.7687 (tpt) cc_final: 0.6915 (tpp)
  outliers start: 29
  outliers final: 19
  residues processed: 127
  average time/residue: 0.2713
  time to fit residues: 49.5680
Evaluate side-chains
  126 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 ARG
Chi-restraints excluded: chain A residue  953 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  249 TYR
Chi-restraints excluded: chain D residue    2 PHE
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  103 PHE
Chi-restraints excluded: chain D residue  139 MET
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  197 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 100 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 142 optimal weight:   10.0000
   chunk 120 optimal weight:    6.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.070132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.051113 restraints weight = 118377.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.052290 restraints weight = 91703.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.053141 restraints weight = 76753.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.5650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13128  Z= 0.193
  Angle     :  0.737  16.304  18120  Z= 0.381
  Chirality :  0.044   0.206   2074
  Planarity :  0.004   0.058   2020
  Dihedral  : 21.974  83.828   2439
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 24.73
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.58 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.41 %
    Favored  : 76.64 %
  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: -1.53 (0.22), residues: 1385
  helix: -0.18 (0.24), residues: 449
  sheet: -0.99 (0.28), residues: 326
  loop : -1.59 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  28 
 HIS   0.008   0.002   HIS A 946 
 PHE   0.021   0.002   PHE A 407 
 TYR   0.049   0.003   TYR A 408 
 ARG   0.006   0.001   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05955 (  509)
  hydrogen bonds       : angle       5.90744 ( 1357)
  SS BOND              : bond        0.00521 (    3)
  SS BOND              : angle       1.10418 (    6)
  covalent geometry    : bond        0.00416 (13125)
  covalent geometry    : angle       0.73728 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 1.338 
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: A  682 MET cc_start: 0.9205 (mmp) cc_final: 0.8943 (mmm)
REVERT: A  752 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7807 (mtt90)
REVERT: A  834 GLU cc_start: 0.3771 (OUTLIER) cc_final: 0.2324 (tt0)
REVERT: A  985 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6727 (p90)
REVERT: A  988 MET cc_start: 0.8717 (tmm) cc_final: 0.8196 (mtm)
REVERT: B   28 TRP cc_start: 0.6804 (OUTLIER) cc_final: 0.6381 (m-90)
REVERT: B   75 MET cc_start: 0.9030 (mmp) cc_final: 0.8677 (mmm)
REVERT: B  199 MET cc_start: 0.7547 (mmm) cc_final: 0.7048 (tpt)
REVERT: B  229 MET cc_start: 0.8498 (mmm) cc_final: 0.7864 (ttt)
REVERT: B  239 TYR cc_start: 0.9259 (m-80) cc_final: 0.8403 (m-80)
REVERT: C   28 TRP cc_start: 0.9259 (t-100) cc_final: 0.8550 (t-100)
REVERT: C  116 MET cc_start: 0.7686 (tpt) cc_final: 0.6932 (tpt)
REVERT: C  121 LEU cc_start: 0.3688 (OUTLIER) cc_final: 0.2965 (mm)
REVERT: C  144 PHE cc_start: 0.9495 (t80) cc_final: 0.9114 (t80)
REVERT: C  229 MET cc_start: 0.7651 (mmm) cc_final: 0.7292 (mmm)
REVERT: C  235 LEU cc_start: 0.9471 (tp) cc_final: 0.8975 (pp)
REVERT: D    2 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7275 (t80)
REVERT: D   68 MET cc_start: 0.9052 (tmm) cc_final: 0.8716 (tmm)
REVERT: D  115 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8017 (mp0)
REVERT: D  116 MET cc_start: 0.8030 (tpp) cc_final: 0.6918 (tmm)
REVERT: D  119 MET cc_start: 0.7987 (ppp) cc_final: 0.7571 (ppp)
REVERT: D  139 MET cc_start: 0.9858 (OUTLIER) cc_final: 0.9630 (pmm)
REVERT: D  144 PHE cc_start: 0.9729 (t80) cc_final: 0.9412 (t80)
REVERT: D  229 MET cc_start: 0.7711 (tpt) cc_final: 0.6913 (tpp)
  outliers start: 36
  outliers final: 25
  residues processed: 127
  average time/residue: 0.2673
  time to fit residues: 48.4942
Evaluate side-chains
  133 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  624 TRP
Chi-restraints excluded: chain A residue  637 ASP
Chi-restraints excluded: chain A residue  752 ARG
Chi-restraints excluded: chain A residue  760 LYS
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 ARG
Chi-restraints excluded: chain A residue  953 HIS
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  249 TYR
Chi-restraints excluded: chain D residue    2 PHE
Chi-restraints excluded: chain D residue   75 MET
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  103 PHE
Chi-restraints excluded: chain D residue  115 GLU
Chi-restraints excluded: chain D residue  139 MET
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  197 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 127 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 106 optimal weight:   30.0000
   chunk 108 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 144 optimal weight:   10.0000
   chunk 89 optimal weight:    0.4980
   chunk 131 optimal weight:    5.9990
   overall best weight:    4.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 GLN
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** 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 = 0.3966 r_free = 0.3966 target = 0.070120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.051484 restraints weight = 117032.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.052634 restraints weight = 90884.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.053441 restraints weight = 76400.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.5942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13128  Z= 0.174
  Angle     :  0.730  16.910  18120  Z= 0.376
  Chirality :  0.044   0.212   2074
  Planarity :  0.004   0.056   2020
  Dihedral  : 21.973  83.579   2439
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 23.43
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.71 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.57 %
    Favored  : 76.39 %
  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: -1.46 (0.22), residues: 1385
  helix: -0.10 (0.24), residues: 460
  sheet: -0.99 (0.28), residues: 325
  loop : -1.56 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  28 
 HIS   0.007   0.001   HIS A 485 
 PHE   0.022   0.002   PHE A 407 
 TYR   0.048   0.002   TYR A 408 
 ARG   0.008   0.001   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05225 (  509)
  hydrogen bonds       : angle       5.78835 ( 1357)
  SS BOND              : bond        0.00412 (    3)
  SS BOND              : angle       0.85627 (    6)
  covalent geometry    : bond        0.00381 (13125)
  covalent geometry    : angle       0.72977 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 106
  time to evaluate  : 1.325 
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  659 CYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7945 (p)
REVERT: A  682 MET cc_start: 0.9207 (mmp) cc_final: 0.8927 (mmm)
REVERT: A  985 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6601 (p90)
REVERT: A  988 MET cc_start: 0.8801 (tmm) cc_final: 0.8268 (mtm)
REVERT: B   28 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.6372 (m-90)
REVERT: B   75 MET cc_start: 0.9016 (mmp) cc_final: 0.8675 (mmm)
REVERT: B  199 MET cc_start: 0.7600 (mmm) cc_final: 0.7101 (tpt)
REVERT: B  229 MET cc_start: 0.8605 (mmm) cc_final: 0.8059 (ttt)
REVERT: C   28 TRP cc_start: 0.9244 (t-100) cc_final: 0.8540 (t-100)
REVERT: C  116 MET cc_start: 0.7649 (tpt) cc_final: 0.6914 (tpt)
REVERT: C  121 LEU cc_start: 0.3471 (OUTLIER) cc_final: 0.2806 (mm)
REVERT: C  144 PHE cc_start: 0.9504 (t80) cc_final: 0.9131 (t80)
REVERT: C  229 MET cc_start: 0.7788 (mmm) cc_final: 0.7463 (mmm)
REVERT: C  235 LEU cc_start: 0.9453 (tp) cc_final: 0.8970 (pp)
REVERT: D    2 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7274 (t80)
REVERT: D   40 MET cc_start: 0.5254 (tpp) cc_final: 0.4988 (tpp)
REVERT: D   68 MET cc_start: 0.9042 (tmm) cc_final: 0.8692 (tmm)
REVERT: D  119 MET cc_start: 0.7985 (ppp) cc_final: 0.7551 (ppp)
REVERT: D  139 MET cc_start: 0.9865 (OUTLIER) cc_final: 0.9638 (pmm)
REVERT: D  144 PHE cc_start: 0.9725 (t80) cc_final: 0.9405 (t80)
REVERT: D  229 MET cc_start: 0.7829 (tpt) cc_final: 0.7074 (tpp)
  outliers start: 37
  outliers final: 23
  residues processed: 128
  average time/residue: 0.2755
  time to fit residues: 50.4677
Evaluate side-chains
  131 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  624 TRP
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  760 LYS
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 ARG
Chi-restraints excluded: chain A residue  953 HIS
Chi-restraints excluded: chain A residue  976 VAL
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  249 TYR
Chi-restraints excluded: chain D residue    2 PHE
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  103 PHE
Chi-restraints excluded: chain D residue  139 MET
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 146 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 123 optimal weight:    5.9990
   chunk 142 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 117 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 132 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.069315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.050874 restraints weight = 118083.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.052019 restraints weight = 91257.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.052816 restraints weight = 76356.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.6362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13128  Z= 0.180
  Angle     :  0.751  19.241  18120  Z= 0.384
  Chirality :  0.044   0.201   2074
  Planarity :  0.004   0.049   2020
  Dihedral  : 21.960  82.872   2439
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 24.20
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.29 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.82 %
    Favored  : 76.39 %
  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: -1.54 (0.22), residues: 1385
  helix: -0.18 (0.24), residues: 461
  sheet: -0.99 (0.29), residues: 318
  loop : -1.62 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  28 
 HIS   0.008   0.001   HIS A 485 
 PHE   0.024   0.002   PHE A 407 
 TYR   0.051   0.002   TYR A 408 
 ARG   0.007   0.001   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05678 (  509)
  hydrogen bonds       : angle       5.84162 ( 1357)
  SS BOND              : bond        0.00474 (    3)
  SS BOND              : angle       0.94715 (    6)
  covalent geometry    : bond        0.00391 (13125)
  covalent geometry    : angle       0.75118 (18114)

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

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

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2770 Ramachandran restraints generated.
    1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 1.398 
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  484 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8911 (m-80)
REVERT: A  659 CYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8016 (p)
REVERT: A  682 MET cc_start: 0.9207 (mmp) cc_final: 0.8918 (mmm)
REVERT: A  985 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6237 (p90)
REVERT: A  988 MET cc_start: 0.8800 (tmm) cc_final: 0.8296 (mpp)
REVERT: B   28 TRP cc_start: 0.6821 (OUTLIER) cc_final: 0.6420 (m-90)
REVERT: B   75 MET cc_start: 0.9022 (mmp) cc_final: 0.8675 (mmm)
REVERT: B  229 MET cc_start: 0.8606 (mmm) cc_final: 0.8012 (ttt)
REVERT: C   28 TRP cc_start: 0.9212 (t-100) cc_final: 0.8527 (t-100)
REVERT: C  121 LEU cc_start: 0.3514 (OUTLIER) cc_final: 0.2814 (mm)
REVERT: C  144 PHE cc_start: 0.9487 (t80) cc_final: 0.9127 (t80)
REVERT: C  229 MET cc_start: 0.7759 (mmm) cc_final: 0.7434 (mmm)
REVERT: C  235 LEU cc_start: 0.9473 (tp) cc_final: 0.8985 (pp)
REVERT: D    2 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7270 (t80)
REVERT: D  115 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8101 (mp0)
REVERT: D  119 MET cc_start: 0.8039 (ppp) cc_final: 0.7651 (ppp)
REVERT: D  139 MET cc_start: 0.9869 (OUTLIER) cc_final: 0.9636 (pmm)
REVERT: D  144 PHE cc_start: 0.9724 (t80) cc_final: 0.9396 (t80)
REVERT: D  229 MET cc_start: 0.7937 (tpt) cc_final: 0.7226 (tpp)
  outliers start: 34
  outliers final: 25
  residues processed: 126
  average time/residue: 0.2699
  time to fit residues: 48.6357
Evaluate side-chains
  132 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  624 TRP
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  760 LYS
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 ARG
Chi-restraints excluded: chain A residue  953 HIS
Chi-restraints excluded: chain A residue  976 VAL
Chi-restraints excluded: chain A residue  985 HIS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  249 TYR
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  249 TYR
Chi-restraints excluded: chain D residue    2 PHE
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  103 PHE
Chi-restraints excluded: chain D residue  115 GLU
Chi-restraints excluded: chain D residue  139 MET
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 127 optimal weight:    0.9990
   chunk 138 optimal weight:   20.0000
   chunk 70 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0270
   chunk 23 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 69 optimal weight:   30.0000
   chunk 8 optimal weight:    0.0470
   chunk 108 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.4142

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

Flipped N/Q/H residues before XYZ refinement:
A 372 HIS
** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 891 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.070693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.052106 restraints weight = 116057.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.053321 restraints weight = 88671.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.054179 restraints weight = 73567.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.6450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13128  Z= 0.145
  Angle     :  0.742  18.721  18120  Z= 0.376
  Chirality :  0.044   0.220   2074
  Planarity :  0.004   0.050   2020
  Dihedral  : 21.881  83.322   2439
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 20.96
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.06 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.98 %
    Favored  : 75.98 %
  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: -1.43 (0.22), residues: 1385
  helix: -0.05 (0.24), residues: 461
  sheet: -1.07 (0.28), residues: 334
  loop : -1.49 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  28 
 HIS   0.006   0.001   HIS A 485 
 PHE   0.026   0.002   PHE A 407 
 TYR   0.053   0.002   TYR A 408 
 ARG   0.008   0.001   ARG A 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04800 (  509)
  hydrogen bonds       : angle       5.64040 ( 1357)
  SS BOND              : bond        0.00957 (    3)
  SS BOND              : angle       1.81495 (    6)
  covalent geometry    : bond        0.00316 (13125)
  covalent geometry    : angle       0.74176 (18114)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5604.05 seconds
wall clock time: 98 minutes 29.39 seconds (5909.39 seconds total)