Starting phenix.real_space_refine
on Mon Jun  9 02:08:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dhd_46867/06_2025/9dhd_46867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dhd_46867/06_2025/9dhd_46867.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dhd_46867/06_2025/9dhd_46867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dhd_46867/06_2025/9dhd_46867.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dhd_46867/06_2025/9dhd_46867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dhd_46867/06_2025/9dhd_46867.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    6399      2.51       5
     N    1718      2.21       5
     O    1895      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10063
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 817, 6431
          Classifications: {'peptide': 817}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 790}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3183
          Classifications: {'peptide': 389}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 376}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 449
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Chain breaks: 1
  Time building chain proxies: 8.90, per 1000 atoms: 0.88
  Number of scatterers: 10063
  At special positions: 0
  Unit cell: (93.936, 106.296, 98.056, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1895      8.00
     N    1718      7.00
     C    6399      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A 313 " 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: 3.59
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2360

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 24 sheets defined
      13.8% alpha, 41.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 250 through 256
      removed outlier: 3.533A  pdb=" N   LYS A 254 " --> pdb=" O   PRO A 251 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLN A 255 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 384
    Processing helix  chain 'A' and resid 987 through 990
    Processing helix  chain 'A' and resid 1016 through 1022
      removed outlier: 3.769A  pdb=" N   THR A1020 " --> pdb=" O   LEU A1017 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   SER A1021 " --> pdb=" O   GLY A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1062
      removed outlier: 3.702A  pdb=" N   LYS A1060 " --> pdb=" O   ASN A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1075
    Processing helix  chain 'A' and resid 1091 through 1097
      removed outlier: 3.561A  pdb=" N   PHE A1097 " --> pdb=" O   LEU A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1100
      No H-bonds generated for 'chain 'A' and resid 1098 through 1100'
    Processing helix  chain 'A' and resid 1101 through 1110
    Processing helix  chain 'A' and resid 1125 through 1137
    Processing helix  chain 'B' and resid 17 through 28
      removed outlier: 3.520A  pdb=" N   ARG B  21 " --> pdb=" O   ASN B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 42 through 45
    Processing helix  chain 'B' and resid 93 through 98
      removed outlier: 3.803A  pdb=" N   GLN B  98 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 124
      removed outlier: 5.063A  pdb=" N   PHE B 121 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   GLU B 122 " --> pdb=" O   GLY B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 220
      removed outlier: 3.557A  pdb=" N   ASN B 219 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 399
      removed outlier: 6.130A  pdb=" N   ASP B 395 " --> pdb=" O   GLU B 391 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   LEU B 396 " --> pdb=" O   ASN B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 425
    Processing helix  chain 'B' and resid 458 through 462
    Processing helix  chain 'C' and resid 53 through 64
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009
      removed outlier: 4.161A  pdb=" N   SER A1027 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL A1040 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   LEU A1029 " --> pdb=" O   GLY A1038 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLY A1038 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ILE A1037 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21
      removed outlier: 6.463A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLU A  54 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ILE A  41 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67
      removed outlier: 4.155A  pdb=" N   ASN A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ALA A  86 " --> pdb=" O   HIS A 105 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   HIS A 105 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ILE A  88 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   SER A  97 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 10.268A  pdb=" N   GLN C  45 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ARG A 103 " --> pdb=" O   GLN C  45 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   ILE C  47 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   HIS A 105 " --> pdb=" O   ILE C  47 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   THR C  49 " --> pdb=" O   HIS A 105 " (cutoff:3.500A)
      removed outlier: 8.896A  pdb=" N   ASN A 107 " --> pdb=" O   THR C  49 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   LYS A 153 " --> pdb=" O   PRO A 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 169
      removed outlier: 6.571A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   CYS A 179 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   PHE A 169 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   THR A 177 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169
      removed outlier: 6.571A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   CYS A 179 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   PHE A 169 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   THR A 177 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221
    Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263
      removed outlier: 3.929A  pdb=" N   ARG A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU A 280 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP A 299 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
      removed outlier: 5.483A  pdb=" N   GLU A 288 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   LEU A 297 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 318
      removed outlier: 6.575A  pdb=" N   VAL A 321 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   SER A 331 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   THR A 352 " --> pdb=" O   SER A 331 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU A 333 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 365
      removed outlier: 3.822A  pdb=" N   ASP A 361 " --> pdb=" O   CYS A 378 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 720 through 727
      removed outlier: 6.525A  pdb=" N   SER A 738 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LYS A 723 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 720 through 727
      removed outlier: 6.525A  pdb=" N   SER A 738 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LYS A 723 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ASP A 795 " --> pdb=" O   VAL A 801 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL A 801 " --> pdb=" O   ASP A 795 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   SER A 762 " --> pdb=" O   ALA A 804 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   GLN A 806 " --> pdb=" O   SER A 762 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   SER A 764 " --> pdb=" O   GLN A 806 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 811 through 820
      removed outlier: 5.405A  pdb=" N   ALA A 813 " --> pdb=" O   ALA A 834 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA A 834 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   THR A 827 " --> pdb=" O   TYR A 853 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   TYR A 853 " --> pdb=" O   THR A 827 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ARG A 847 " --> pdb=" O   THR A 833 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLN A 852 " --> pdb=" O   THR A 860 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   THR A 860 " --> pdb=" O   GLN A 852 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   SER A 854 " --> pdb=" O   LEU A 858 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   LEU A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 874 through 876
      removed outlier: 6.596A  pdb=" N   VAL A 888 " --> pdb=" O   ASN A 904 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   ASN A 904 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU A 890 " --> pdb=" O   GLU A 902 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 911 through 917
      removed outlier: 6.444A  pdb=" N   ALA A 934 " --> pdb=" O   GLU A 944 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   GLU A 944 " --> pdb=" O   ALA A 934 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 954 through 959
      removed outlier: 6.801A  pdb=" N   ALA A 968 " --> pdb=" O   SER A 955 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   VAL A 957 " --> pdb=" O   LEU A 966 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   LEU A 966 " --> pdb=" O   VAL A 957 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ILE A 959 " --> pdb=" O   ASN A 964 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   ASN A 964 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ASN A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   GLN A 978 " --> pdb=" O   GLU A 994 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   GLU A 994 " --> pdb=" O   GLN A 978 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1077
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1113 through 1115
    Processing sheet with id=AB9, first strand: chain 'B' and resid 104 through 105
      removed outlier: 7.062A  pdb=" N   THR B  51 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 60 through 65
      removed outlier: 6.876A  pdb=" N   ILE B  73 " --> pdb=" O   ARG B  63 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   PHE B  65 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   TYR B  71 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   SER B  81 " --> pdb=" O   SER B  76 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   LEU B  82 " --> pdb=" O   ILE B 130 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE B 130 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ILE B  84 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 139 through 140
    Processing sheet with id=AC3, first strand: chain 'B' and resid 139 through 140
      removed outlier: 7.022A  pdb=" N   GLU B 189 " --> pdb=" O   CYS B 211 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   CYS B 211 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP B 205 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ASP B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   LEU B 203 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 222 through 225
      removed outlier: 3.615A  pdb=" N   ARG B 254 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   GLN B 243 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   ASP B 252 " --> pdb=" O   GLN B 243 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 330 through 338
      removed outlier: 5.691A  pdb=" N   MET B 331 " --> pdb=" O   THR B 347 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   THR B 347 " --> pdb=" O   MET B 331 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   LYS B 333 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   HIS B 341 " --> pdb=" O   LEU B 337 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   PHE B 365 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL B 378 " --> pdb=" O   PHE B 365 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL B 367 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 466 through 468
      removed outlier: 6.771A  pdb=" N   ILE B 487 " --> pdb=" O   GLU B 500 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   GLU B 500 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   PHE B 489 " --> pdb=" O   LYS B 498 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.03

  Time building geometry restraints manager: 4.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3331
        1.34 -     1.46: 2033
        1.46 -     1.58: 4823
        1.58 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 10262
  Sorted by residual:
  bond pdb=" CB  GLN A 343 "
       pdb=" CG  GLN A 343 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 2.01e+00
  bond pdb=" CB  ASP B 469 "
       pdb=" CG  ASP B 469 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.84e+00
  bond pdb=" C   GLN B 243 "
       pdb=" N   VAL B 244 "
    ideal  model  delta    sigma   weight residual
    1.330  1.305  0.025 1.97e-02 2.58e+03 1.65e+00
  bond pdb=" CG  ARG A 198 "
       pdb=" CD  ARG A 198 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.48e+00
  bond pdb=" C   PHE A1030 "
       pdb=" N   GLY A1031 "
    ideal  model  delta    sigma   weight residual
    1.330  1.320  0.010 8.50e-03 1.38e+04 1.39e+00
  ... (remaining 10257 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 13694
        2.39 -     4.78: 159
        4.78 -     7.17: 18
        7.17 -     9.56: 4
        9.56 -    11.95: 2
  Bond angle restraints: 13877
  Sorted by residual:
  angle pdb=" CA  MET B 331 "
        pdb=" CB  MET B 331 "
        pdb=" CG  MET B 331 "
      ideal   model   delta    sigma   weight residual
     114.10  122.60   -8.50 2.00e+00 2.50e-01 1.80e+01
  angle pdb=" CB  ARG A 198 "
        pdb=" CG  ARG A 198 "
        pdb=" CD  ARG A 198 "
      ideal   model   delta    sigma   weight residual
     111.30  120.76   -9.46 2.30e+00 1.89e-01 1.69e+01
  angle pdb=" CB  MET A1014 "
        pdb=" CG  MET A1014 "
        pdb=" SD  MET A1014 "
      ideal   model   delta    sigma   weight residual
     112.70  124.65  -11.95 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" N   VAL B 371 "
        pdb=" CA  VAL B 371 "
        pdb=" C   VAL B 371 "
      ideal   model   delta    sigma   weight residual
     111.45  108.27    3.18 9.30e-01 1.16e+00 1.17e+01
  angle pdb=" CB  MET A 291 "
        pdb=" CG  MET A 291 "
        pdb=" SD  MET A 291 "
      ideal   model   delta    sigma   weight residual
     112.70  122.70  -10.00 3.00e+00 1.11e-01 1.11e+01
  ... (remaining 13872 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 5380
       17.87 -    35.74: 570
       35.74 -    53.60: 147
       53.60 -    71.47: 27
       71.47 -    89.34: 17
  Dihedral angle restraints: 6141
    sinusoidal: 2489
      harmonic: 3652
  Sorted by residual:
  dihedral pdb=" CB  CYS A  18 "
           pdb=" SG  CYS A  18 "
           pdb=" SG  CYS A 313 "
           pdb=" CB  CYS A 313 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.77  -44.77     1      1.00e+01 1.00e-02 2.79e+01
  dihedral pdb=" CA  PHE B 242 "
           pdb=" C   PHE B 242 "
           pdb=" N   GLN B 243 "
           pdb=" CA  GLN B 243 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.57   21.43     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  TYR A 828 "
           pdb=" C   TYR A 828 "
           pdb=" N   PHE A 829 "
           pdb=" CA  PHE A 829 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.00   20.00     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 6138 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 919
       0.036 -    0.071: 436
       0.071 -    0.107: 149
       0.107 -    0.142: 53
       0.142 -    0.178: 1
  Chirality restraints: 1558
  Sorted by residual:
  chirality pdb=" CB  ILE B 239 "
            pdb=" CA  ILE B 239 "
            pdb=" CG1 ILE B 239 "
            pdb=" CG2 ILE B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" CA  ILE A 794 "
            pdb=" N   ILE A 794 "
            pdb=" C   ILE A 794 "
            pdb=" CB  ILE A 794 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CA  TYR A  84 "
            pdb=" N   TYR A  84 "
            pdb=" C   TYR A  84 "
            pdb=" CB  TYR A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1555 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  47 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO B  48 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  48 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  48 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 198 "   -0.119 9.50e-02 1.11e+02   5.40e-02 2.41e+00
        pdb=" NE  ARG A 198 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 198 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 198 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 198 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 523 "   -0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO B 524 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 524 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 524 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 4323
        2.93 -     3.42: 9312
        3.42 -     3.91: 16738
        3.91 -     4.41: 19602
        4.41 -     4.90: 33589
  Nonbonded interactions: 83564
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 469 "
            pdb=" OD1 ASP B 469 "
     model   vdw
     2.433 3.040
  nonbonded pdb=" N   GLN A 343 "
            pdb=" OE1 GLN A 343 "
     model   vdw
     2.491 3.120
  nonbonded pdb=" OG  SER A  25 "
            pdb=" OD1 ASP A  28 "
     model   vdw
     2.518 3.040
  nonbonded pdb=" O   GLU A1079 "
            pdb=" OE1 GLU A1079 "
     model   vdw
     2.521 3.040
  nonbonded pdb=" C   SER A 815 "
            pdb=" OG  SER A 815 "
     model   vdw
     2.551 2.616
  ... (remaining 83559 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             7.380
  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:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     31.300
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
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      :  0.006   0.043  10263  Z= 0.279
  Angle     :  0.687  11.954  13879  Z= 0.365
  Chirality :  0.047   0.178   1558
  Planarity :  0.004   0.054   1794
  Dihedral  : 16.293  89.341   3778
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.30 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.24), residues: 1233
  helix: -1.00 (0.41), residues: 152
  sheet: -0.40 (0.23), residues: 497
  loop : -0.41 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 953 
 HIS   0.009   0.001   HIS B 341 
 PHE   0.023   0.002   PHE B 343 
 TYR   0.023   0.002   TYR B 225 
 ARG   0.014   0.001   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13277 (  374)
  hydrogen bonds       : angle       6.99150 ( 1032)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       1.10266 (    2)
  covalent geometry    : bond        0.00640 (10262)
  covalent geometry    : angle       0.68718 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8417 (tttm)
REVERT: B   56 GLU cc_start: 0.7813 (tp30) cc_final: 0.6874 (pp20)
REVERT: B  190 ASP cc_start: 0.8329 (t0) cc_final: 0.8124 (m-30)
REVERT: B  241 VAL cc_start: 0.9049 (t) cc_final: 0.8714 (p)
REVERT: B  243 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7986 (pm20)
REVERT: B  370 MET cc_start: 0.8221 (pmm) cc_final: 0.8001 (pmm)
REVERT: B  390 PHE cc_start: 0.8249 (t80) cc_final: 0.7465 (t80)
REVERT: B  395 ASP cc_start: 0.8965 (t0) cc_final: 0.8656 (t0)
REVERT: B  448 LEU cc_start: 0.6327 (mt) cc_final: 0.4685 (mt)
REVERT: B  545 MET cc_start: 0.7789 (ptp) cc_final: 0.7292 (ptp)
REVERT: C   11 TYR cc_start: 0.8266 (t80) cc_final: 0.7555 (t80)
  outliers start: 21
  outliers final: 11
  residues processed: 89
  average time/residue: 1.2590
  time to fit residues: 121.5917
Evaluate side-chains
  78 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  243 GLN
Chi-restraints excluded: chain B residue  381 ASN
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 97 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 542 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.112325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.080082 restraints weight = 19731.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 3.11
r_work: 0.2988 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.0676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10263  Z= 0.145
  Angle     :  0.528   7.190  13879  Z= 0.280
  Chirality :  0.044   0.150   1558
  Planarity :  0.003   0.038   1794
  Dihedral  :  6.008  83.383   1383
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.43 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.24), residues: 1233
  helix: -0.70 (0.41), residues: 152
  sheet: -0.17 (0.23), residues: 482
  loop : -0.32 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 207 
 HIS   0.006   0.001   HIS B 341 
 PHE   0.016   0.001   PHE A1030 
 TYR   0.012   0.001   TYR A 812 
 ARG   0.006   0.000   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  374)
  hydrogen bonds       : angle       5.54654 ( 1032)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.54020 (    2)
  covalent geometry    : bond        0.00329 (10262)
  covalent geometry    : angle       0.52760 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8374 (ptm160) cc_final: 0.7952 (ppp-140)
REVERT: B   56 GLU cc_start: 0.7758 (tp30) cc_final: 0.7030 (pm20)
REVERT: B   57 LYS cc_start: 0.8945 (tttm) cc_final: 0.8644 (tmtt)
REVERT: B  105 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5517 (tp)
REVERT: B  190 ASP cc_start: 0.8139 (t0) cc_final: 0.7937 (t0)
REVERT: B  241 VAL cc_start: 0.9019 (t) cc_final: 0.8693 (p)
REVERT: B  390 PHE cc_start: 0.8307 (t80) cc_final: 0.7562 (t80)
REVERT: B  448 LEU cc_start: 0.6357 (mt) cc_final: 0.5294 (mt)
REVERT: B  545 MET cc_start: 0.7838 (ptp) cc_final: 0.7356 (ptp)
REVERT: C   11 TYR cc_start: 0.8151 (t80) cc_final: 0.7550 (t80)
  outliers start: 31
  outliers final: 12
  residues processed: 107
  average time/residue: 1.1057
  time to fit residues: 130.0288
Evaluate side-chains
  84 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  815 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  381 ASN
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  521 THR
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 81 optimal weight:    0.1980
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 106 optimal weight:    7.9990
   chunk 96 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 93 optimal weight:    8.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 797 HIS
B 341 HIS
B 542 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.112202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.079862 restraints weight = 20020.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.14
r_work: 0.2978 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10263  Z= 0.148
  Angle     :  0.518   8.708  13879  Z= 0.274
  Chirality :  0.044   0.179   1558
  Planarity :  0.003   0.037   1794
  Dihedral  :  5.126  56.106   1372
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.16 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.24), residues: 1233
  helix: -0.60 (0.41), residues: 152
  sheet: -0.07 (0.24), residues: 481
  loop : -0.28 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1073 
 HIS   0.005   0.001   HIS B 341 
 PHE   0.014   0.001   PHE A1030 
 TYR   0.011   0.001   TYR A 812 
 ARG   0.003   0.000   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03482 (  374)
  hydrogen bonds       : angle       5.26785 ( 1032)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.72407 (    2)
  covalent geometry    : bond        0.00339 (10262)
  covalent geometry    : angle       0.51828 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 80
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8378 (ptm160) cc_final: 0.7935 (ppp-140)
REVERT: A 1107 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: B   56 GLU cc_start: 0.7813 (tp30) cc_final: 0.7006 (pp20)
REVERT: B   57 LYS cc_start: 0.8936 (tttm) cc_final: 0.8555 (tmtt)
REVERT: B   63 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7558 (tpt-90)
REVERT: B  238 THR cc_start: 0.6335 (m) cc_final: 0.6106 (m)
REVERT: B  241 VAL cc_start: 0.9039 (t) cc_final: 0.8707 (p)
REVERT: B  390 PHE cc_start: 0.8308 (t80) cc_final: 0.7561 (t80)
REVERT: B  395 ASP cc_start: 0.8928 (t0) cc_final: 0.8245 (m-30)
REVERT: B  448 LEU cc_start: 0.6435 (mt) cc_final: 0.5002 (mt)
REVERT: B  545 MET cc_start: 0.7859 (ptp) cc_final: 0.7157 (pmm)
REVERT: C   11 TYR cc_start: 0.8177 (t80) cc_final: 0.7625 (t80)
REVERT: C   58 TYR cc_start: 0.8442 (t80) cc_final: 0.8049 (t80)
  outliers start: 34
  outliers final: 12
  residues processed: 110
  average time/residue: 1.5401
  time to fit residues: 187.3103
Evaluate side-chains
  85 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  767 SER
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  815 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 82 optimal weight:    0.3980
   chunk 92 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B  14 GLN
B 542 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.112082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.079925 restraints weight = 19792.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 3.11
r_work: 0.2985 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10263  Z= 0.159
  Angle     :  0.534   8.297  13879  Z= 0.276
  Chirality :  0.044   0.165   1558
  Planarity :  0.003   0.037   1794
  Dihedral  :  4.913  55.952   1370
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.80 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1233
  helix: -0.48 (0.41), residues: 150
  sheet: -0.04 (0.24), residues: 481
  loop : -0.25 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1073 
 HIS   0.003   0.001   HIS B 523 
 PHE   0.015   0.001   PHE A1030 
 TYR   0.013   0.001   TYR A 812 
 ARG   0.003   0.000   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 (  374)
  hydrogen bonds       : angle       5.18171 ( 1032)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.66690 (    2)
  covalent geometry    : bond        0.00366 (10262)
  covalent geometry    : angle       0.53383 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 80
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8342 (ptm160) cc_final: 0.7926 (ppp-140)
REVERT: A  298 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8496 (tttm)
REVERT: A  759 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8120 (mp10)
REVERT: A 1106 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7615 (mp10)
REVERT: B   56 GLU cc_start: 0.7840 (tp30) cc_final: 0.7024 (pp20)
REVERT: B   57 LYS cc_start: 0.8919 (tttm) cc_final: 0.8555 (tmtt)
REVERT: B   63 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7539 (tpt-90)
REVERT: B  119 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7751 (ttp-170)
REVERT: B  238 THR cc_start: 0.6296 (m) cc_final: 0.6044 (m)
REVERT: B  241 VAL cc_start: 0.9036 (t) cc_final: 0.8714 (p)
REVERT: B  335 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6959 (tm-30)
REVERT: B  390 PHE cc_start: 0.8291 (t80) cc_final: 0.7570 (t80)
REVERT: B  448 LEU cc_start: 0.6345 (mt) cc_final: 0.5370 (mt)
REVERT: B  545 MET cc_start: 0.7877 (ptp) cc_final: 0.7161 (pmm)
REVERT: C   11 TYR cc_start: 0.8182 (t80) cc_final: 0.7632 (t80)
  outliers start: 38
  outliers final: 14
  residues processed: 114
  average time/residue: 1.3193
  time to fit residues: 162.2514
Evaluate side-chains
  91 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  767 SER
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  815 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1098 LEU
Chi-restraints excluded: chain A residue 1106 GLN
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0770
   chunk 24 optimal weight:    0.4980
   chunk 83 optimal weight:    0.0980
   chunk 68 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
A1106 GLN
B 542 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.115625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.083081 restraints weight = 19422.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 3.12
r_work: 0.3061 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10263  Z= 0.103
  Angle     :  0.512   7.195  13879  Z= 0.264
  Chirality :  0.044   0.146   1558
  Planarity :  0.003   0.041   1794
  Dihedral  :  4.692  55.508   1369
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 18.07 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.24), residues: 1233
  helix: -0.40 (0.41), residues: 150
  sheet:  0.02 (0.24), residues: 481
  loop : -0.21 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 207 
 HIS   0.003   0.000   HIS B 523 
 PHE   0.014   0.001   PHE A 851 
 TYR   0.015   0.001   TYR B 225 
 ARG   0.014   0.000   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03058 (  374)
  hydrogen bonds       : angle       4.99901 ( 1032)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.56369 (    2)
  covalent geometry    : bond        0.00228 (10262)
  covalent geometry    : angle       0.51198 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 80
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8261 (ptm160) cc_final: 0.7864 (ppp-140)
REVERT: A  298 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8548 (tttm)
REVERT: A  759 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8163 (mp10)
REVERT: A 1106 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7515 (mp-120)
REVERT: B   57 LYS cc_start: 0.8918 (tttm) cc_final: 0.8684 (tttm)
REVERT: B   63 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7461 (tpt-90)
REVERT: B  238 THR cc_start: 0.6283 (m) cc_final: 0.6042 (m)
REVERT: B  241 VAL cc_start: 0.9020 (t) cc_final: 0.8694 (p)
REVERT: B  335 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7024 (tm-30)
REVERT: B  390 PHE cc_start: 0.8301 (t80) cc_final: 0.7514 (t80)
REVERT: B  397 PHE cc_start: 0.7696 (m-80) cc_final: 0.7430 (m-80)
REVERT: B  448 LEU cc_start: 0.6422 (mt) cc_final: 0.5517 (mt)
REVERT: B  545 MET cc_start: 0.7885 (ptp) cc_final: 0.7291 (pmm)
REVERT: C   11 TYR cc_start: 0.8086 (t80) cc_final: 0.7598 (t80)
REVERT: C   52 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7944 (t)
REVERT: C   58 TYR cc_start: 0.8413 (t80) cc_final: 0.8069 (t80)
  outliers start: 36
  outliers final: 12
  residues processed: 110
  average time/residue: 1.3296
  time to fit residues: 157.5096
Evaluate side-chains
  90 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  929 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1106 GLN
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 22 optimal weight:    0.0670
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 109 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
B 542 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.081750 restraints weight = 19648.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 3.14
r_work: 0.3029 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10263  Z= 0.155
  Angle     :  0.542   9.493  13879  Z= 0.277
  Chirality :  0.044   0.137   1558
  Planarity :  0.003   0.063   1794
  Dihedral  :  4.681  55.942   1366
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.78 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.24), residues: 1233
  helix: -0.41 (0.41), residues: 150
  sheet:  0.04 (0.24), residues: 481
  loop : -0.18 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1073 
 HIS   0.003   0.001   HIS A 711 
 PHE   0.012   0.001   PHE A 851 
 TYR   0.015   0.001   TYR B 225 
 ARG   0.016   0.001   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  374)
  hydrogen bonds       : angle       5.01284 ( 1032)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.64232 (    2)
  covalent geometry    : bond        0.00357 (10262)
  covalent geometry    : angle       0.54205 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 71
  time to evaluate  : 1.179 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8293 (ptm160) cc_final: 0.7890 (ppp-140)
REVERT: A  298 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8558 (tttm)
REVERT: A  759 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8171 (mp10)
REVERT: B   63 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7495 (tpt-90)
REVERT: B  235 GLN cc_start: 0.8638 (tp40) cc_final: 0.8149 (pt0)
REVERT: B  238 THR cc_start: 0.6329 (m) cc_final: 0.6098 (m)
REVERT: B  241 VAL cc_start: 0.9051 (t) cc_final: 0.8714 (p)
REVERT: B  390 PHE cc_start: 0.8279 (t80) cc_final: 0.7507 (t80)
REVERT: B  397 PHE cc_start: 0.7741 (m-80) cc_final: 0.7490 (m-80)
REVERT: B  448 LEU cc_start: 0.6446 (mt) cc_final: 0.5520 (mt)
REVERT: B  545 MET cc_start: 0.7970 (ptp) cc_final: 0.7332 (pmm)
REVERT: C   11 TYR cc_start: 0.8141 (t80) cc_final: 0.7607 (t80)
REVERT: C   58 TYR cc_start: 0.8453 (t80) cc_final: 0.8092 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 99
  average time/residue: 1.1083
  time to fit residues: 119.7258
Evaluate side-chains
  91 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  815 SER
Chi-restraints excluded: chain A residue  929 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0030
   chunk 85 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   overall best weight:    0.7992

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

Flipped N/Q/H residues before XYZ refinement:
B 542 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.114529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.081519 restraints weight = 19763.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 3.16
r_work: 0.3039 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10263  Z= 0.137
  Angle     :  0.541   9.812  13879  Z= 0.275
  Chirality :  0.044   0.172   1558
  Planarity :  0.003   0.044   1794
  Dihedral  :  4.632  55.832   1366
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.32 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.24), residues: 1233
  helix: -0.35 (0.41), residues: 150
  sheet:  0.06 (0.24), residues: 481
  loop : -0.17 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 207 
 HIS   0.003   0.001   HIS B 523 
 PHE   0.012   0.001   PHE A 851 
 TYR   0.018   0.001   TYR B 225 
 ARG   0.011   0.000   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  374)
  hydrogen bonds       : angle       4.95998 ( 1032)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.66357 (    2)
  covalent geometry    : bond        0.00316 (10262)
  covalent geometry    : angle       0.54147 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 74
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8292 (ptm160) cc_final: 0.7881 (ppp-140)
REVERT: A  298 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8557 (tttm)
REVERT: A  759 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8195 (mp10)
REVERT: A 1054 MET cc_start: 0.8266 (tpp) cc_final: 0.7908 (tpp)
REVERT: B   63 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7483 (tpt-90)
REVERT: B  235 GLN cc_start: 0.8644 (tp40) cc_final: 0.8165 (pt0)
REVERT: B  238 THR cc_start: 0.6315 (m) cc_final: 0.6064 (m)
REVERT: B  241 VAL cc_start: 0.9047 (t) cc_final: 0.8711 (p)
REVERT: B  390 PHE cc_start: 0.8286 (t80) cc_final: 0.7521 (t80)
REVERT: B  397 PHE cc_start: 0.7758 (m-80) cc_final: 0.7525 (m-80)
REVERT: B  448 LEU cc_start: 0.6499 (mt) cc_final: 0.5170 (mt)
REVERT: B  545 MET cc_start: 0.7938 (ptp) cc_final: 0.7308 (pmm)
REVERT: C   11 TYR cc_start: 0.8130 (t80) cc_final: 0.7633 (t80)
REVERT: C   39 ARG cc_start: 0.7716 (mpp-170) cc_final: 0.7343 (mpp-170)
REVERT: C   58 TYR cc_start: 0.8451 (t80) cc_final: 0.8145 (t80)
  outliers start: 32
  outliers final: 19
  residues processed: 102
  average time/residue: 1.2091
  time to fit residues: 133.7053
Evaluate side-chains
  92 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  929 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1105 MET
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 542 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.114020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.081262 restraints weight = 19834.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 3.13
r_work: 0.3038 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10263  Z= 0.155
  Angle     :  0.562  10.896  13879  Z= 0.286
  Chirality :  0.044   0.194   1558
  Planarity :  0.004   0.066   1794
  Dihedral  :  4.679  56.074   1366
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.68 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.24), residues: 1233
  helix: -0.31 (0.41), residues: 150
  sheet:  0.04 (0.24), residues: 482
  loop : -0.17 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1073 
 HIS   0.003   0.001   HIS A 711 
 PHE   0.012   0.001   PHE A 851 
 TYR   0.020   0.001   TYR B 225 
 ARG   0.017   0.001   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  374)
  hydrogen bonds       : angle       4.97155 ( 1032)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.58629 (    2)
  covalent geometry    : bond        0.00359 (10262)
  covalent geometry    : angle       0.56225 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8289 (ptm160) cc_final: 0.7878 (ppp-140)
REVERT: A  298 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8564 (tttm)
REVERT: A  759 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8195 (mp10)
REVERT: A 1054 MET cc_start: 0.8236 (tpp) cc_final: 0.7902 (tpp)
REVERT: B   63 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7652 (tpt-90)
REVERT: B  235 GLN cc_start: 0.8626 (tp40) cc_final: 0.8142 (pt0)
REVERT: B  238 THR cc_start: 0.6273 (m) cc_final: 0.6052 (m)
REVERT: B  241 VAL cc_start: 0.9043 (t) cc_final: 0.8713 (p)
REVERT: B  343 PHE cc_start: 0.6957 (t80) cc_final: 0.6668 (t80)
REVERT: B  390 PHE cc_start: 0.8257 (t80) cc_final: 0.7488 (t80)
REVERT: B  395 ASP cc_start: 0.8883 (t0) cc_final: 0.8160 (OUTLIER)
REVERT: B  397 PHE cc_start: 0.7793 (m-80) cc_final: 0.7562 (m-80)
REVERT: B  448 LEU cc_start: 0.6235 (mt) cc_final: 0.5191 (mt)
REVERT: B  545 MET cc_start: 0.7962 (ptp) cc_final: 0.7323 (pmm)
REVERT: C   11 TYR cc_start: 0.8115 (t80) cc_final: 0.7614 (t80)
REVERT: C   39 ARG cc_start: 0.7774 (mpp-170) cc_final: 0.7441 (mpp-170)
REVERT: C   58 TYR cc_start: 0.8472 (t80) cc_final: 0.8195 (t80)
  outliers start: 29
  outliers final: 22
  residues processed: 101
  average time/residue: 1.1804
  time to fit residues: 129.9344
Evaluate side-chains
  95 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  815 SER
Chi-restraints excluded: chain A residue  929 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1105 MET
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  381 ASN
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 108 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
B 542 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.112517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.080234 restraints weight = 19779.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 3.08
r_work: 0.2999 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10263  Z= 0.197
  Angle     :  0.595  11.508  13879  Z= 0.302
  Chirality :  0.045   0.194   1558
  Planarity :  0.004   0.067   1794
  Dihedral  :  4.834  56.447   1366
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.32 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.24), residues: 1233
  helix: -0.44 (0.41), residues: 152
  sheet: -0.00 (0.24), residues: 482
  loop : -0.25 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1073 
 HIS   0.004   0.001   HIS A 711 
 PHE   0.015   0.001   PHE A 975 
 TYR   0.025   0.001   TYR B 225 
 ARG   0.016   0.001   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  374)
  hydrogen bonds       : angle       5.07634 ( 1032)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       0.68469 (    2)
  covalent geometry    : bond        0.00459 (10262)
  covalent geometry    : angle       0.59531 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 69
  time to evaluate  : 1.236 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8329 (ptm160) cc_final: 0.7919 (ppp-140)
REVERT: A  298 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8559 (tttm)
REVERT: A  759 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8191 (mp10)
REVERT: B   63 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7693 (tpt-90)
REVERT: B  238 THR cc_start: 0.6435 (m) cc_final: 0.6186 (m)
REVERT: B  241 VAL cc_start: 0.9069 (t) cc_final: 0.8728 (p)
REVERT: B  343 PHE cc_start: 0.6924 (t80) cc_final: 0.6711 (t80)
REVERT: B  390 PHE cc_start: 0.8263 (t80) cc_final: 0.7482 (t80)
REVERT: B  395 ASP cc_start: 0.8869 (t0) cc_final: 0.8119 (OUTLIER)
REVERT: B  448 LEU cc_start: 0.6260 (mt) cc_final: 0.5172 (mt)
REVERT: B  545 MET cc_start: 0.7972 (ptp) cc_final: 0.7528 (ptp)
REVERT: C   11 TYR cc_start: 0.8144 (t80) cc_final: 0.7648 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 93
  average time/residue: 1.1404
  time to fit residues: 115.6985
Evaluate side-chains
  91 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 65
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  767 SER
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  815 SER
Chi-restraints excluded: chain A residue  929 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1105 MET
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  381 ASN
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain C residue   20 HIS
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 120 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 542 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.113712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.081420 restraints weight = 19725.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 3.11
r_work: 0.3019 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10263  Z= 0.139
  Angle     :  0.567  12.172  13879  Z= 0.287
  Chirality :  0.044   0.182   1558
  Planarity :  0.004   0.060   1794
  Dihedral  :  4.704  55.512   1366
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.86 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.24), residues: 1233
  helix: -0.26 (0.42), residues: 150
  sheet:  0.01 (0.24), residues: 482
  loop : -0.23 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1073 
 HIS   0.003   0.001   HIS B 523 
 PHE   0.012   0.001   PHE A 975 
 TYR   0.028   0.001   TYR B 225 
 ARG   0.015   0.001   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03169 (  374)
  hydrogen bonds       : angle       4.94465 ( 1032)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.60359 (    2)
  covalent geometry    : bond        0.00319 (10262)
  covalent geometry    : angle       0.56719 (13877)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 1.194 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8305 (ptm160) cc_final: 0.7889 (ppp-140)
REVERT: A  298 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8532 (tttm)
REVERT: A  369 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8389 (tpm-80)
REVERT: A  759 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8223 (mp10)
REVERT: B   63 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7668 (tpt-90)
REVERT: B  238 THR cc_start: 0.6462 (m) cc_final: 0.6196 (m)
REVERT: B  241 VAL cc_start: 0.9046 (t) cc_final: 0.8712 (p)
REVERT: B  343 PHE cc_start: 0.6880 (t80) cc_final: 0.6633 (t80)
REVERT: B  390 PHE cc_start: 0.8278 (t80) cc_final: 0.7535 (t80)
REVERT: B  395 ASP cc_start: 0.8892 (t0) cc_final: 0.8081 (m-30)
REVERT: B  448 LEU cc_start: 0.6268 (mt) cc_final: 0.5168 (mt)
REVERT: B  545 MET cc_start: 0.7950 (ptp) cc_final: 0.7332 (pmm)
REVERT: C   11 TYR cc_start: 0.8116 (t80) cc_final: 0.7621 (t80)
REVERT: C   39 ARG cc_start: 0.7794 (mpp-170) cc_final: 0.7402 (mpp-170)
REVERT: C   58 TYR cc_start: 0.8482 (t80) cc_final: 0.8213 (t80)
  outliers start: 27
  outliers final: 18
  residues processed: 93
  average time/residue: 1.1502
  time to fit residues: 116.5562
Evaluate side-chains
  88 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  767 SER
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  929 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1108 VAL
Chi-restraints excluded: chain A residue 1130 ILE
Chi-restraints excluded: chain B residue   63 ARG
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  381 ASN
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
B 542 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.110843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.078981 restraints weight = 19925.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.09
r_work: 0.2958 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10263  Z= 0.235
  Angle     :  0.637  13.456  13879  Z= 0.321
  Chirality :  0.045   0.204   1558
  Planarity :  0.004   0.083   1794
  Dihedral  :  4.959  56.550   1366
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.95 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.24), residues: 1233
  helix: -0.46 (0.41), residues: 152
  sheet: -0.05 (0.24), residues: 485
  loop : -0.31 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1073 
 HIS   0.005   0.001   HIS A 711 
 PHE   0.017   0.002   PHE A1030 
 TYR   0.029   0.002   TYR B 225 
 ARG   0.021   0.001   ARG A 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  374)
  hydrogen bonds       : angle       5.14129 ( 1032)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.78628 (    2)
  covalent geometry    : bond        0.00550 (10262)
  covalent geometry    : angle       0.63747 (13877)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6582.52 seconds
wall clock time: 116 minutes 19.41 seconds (6979.41 seconds total)