Starting phenix.real_space_refine
on Wed Sep 17 17:45:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dhd_46867/09_2025/9dhd_46867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dhd_46867/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dhd_46867/09_2025/9dhd_46867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dhd_46867/09_2025/9dhd_46867.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dhd_46867/09_2025/9dhd_46867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dhd_46867/09_2025/9dhd_46867.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.41, per 1000 atoms: 0.24
  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: 0.76
  Conformation dependent library (CDL) restraints added in 285.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.45
  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: 2.11

  Time building geometry restraints manager: 0.98 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:             8.190
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.270
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.014   0.001   ARG A 198 
 TYR   0.023   0.002   TYR B 225 
 PHE   0.023   0.002   PHE B 343 
 TRP   0.015   0.002   TRP A 953 
 HIS   0.009   0.001   HIS B 341 

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

*********************** 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  : 0.415 
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: 0.6857 (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: 0.6221
  time to fit residues: 59.7074
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  : 0.411 
-------------------------------------------------------------------------------
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 108 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.111929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.079843 restraints weight = 19855.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 3.10
r_work: 0.2980 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.0621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  10263  Z= 0.165
  Angle     :  0.539   7.147  13879  Z= 0.285
  Chirality :  0.045   0.153   1558
  Planarity :  0.003   0.039   1794
  Dihedral  :  6.059  83.204   1383
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.34 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.24), residues: 1233
  helix: -0.73 (0.41), residues: 152
  sheet: -0.16 (0.23), residues: 480
  loop : -0.34 (0.25), residues: 601

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (10262)
  covalent geometry    : angle       0.53852 (13877)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.64979 (    2)
  hydrogen bonds       : bond        0.03779 (  374)
  hydrogen bonds       : angle       5.59421 ( 1032)

*********************** 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
  112 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7984 (ppp-140)
REVERT: B   56 GLU cc_start: 0.7762 (tp30) cc_final: 0.7066 (pm20)
REVERT: B   57 LYS cc_start: 0.8916 (tttm) cc_final: 0.8574 (tmtt)
REVERT: B  105 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5552 (tp)
REVERT: B  241 VAL cc_start: 0.9020 (t) cc_final: 0.8693 (p)
REVERT: B  390 PHE cc_start: 0.8308 (t80) cc_final: 0.7554 (t80)
REVERT: B  448 LEU cc_start: 0.6334 (mt) cc_final: 0.5229 (mt)
REVERT: B  545 MET cc_start: 0.7820 (ptp) cc_final: 0.7338 (ptp)
REVERT: C   11 TYR cc_start: 0.8161 (t80) cc_final: 0.7567 (t80)
  outliers start: 32
  outliers final: 11
  residues processed: 108
  average time/residue: 0.5372
  time to fit residues: 62.9608
Evaluate side-chains
  83 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
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 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 98 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 113 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 106 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0970
   chunk 17 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 101 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 542 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.112769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.080536 restraints weight = 19924.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 3.14
r_work: 0.2996 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.0962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10263  Z= 0.126
  Angle     :  0.506   8.443  13879  Z= 0.268
  Chirality :  0.044   0.179   1558
  Planarity :  0.003   0.037   1794
  Dihedral  :  5.093  55.686   1372
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.25 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.24), residues: 1233
  helix: -0.52 (0.42), residues: 150
  sheet: -0.05 (0.24), residues: 481
  loop : -0.26 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1080 
 TYR   0.010   0.001   TYR A 812 
 PHE   0.014   0.001   PHE A1030 
 TRP   0.012   0.001   TRP A 207 
 HIS   0.005   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10262)
  covalent geometry    : angle       0.50596 (13877)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.67177 (    2)
  hydrogen bonds       : bond        0.03382 (  374)
  hydrogen bonds       : angle       5.25409 ( 1032)

*********************** 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
  113 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8341 (ptm160) cc_final: 0.7915 (ppp-140)
REVERT: A 1106 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7617 (mp10)
REVERT: B   56 GLU cc_start: 0.7819 (tp30) cc_final: 0.7178 (pm20)
REVERT: B   57 LYS cc_start: 0.8948 (tttm) cc_final: 0.8663 (tmtt)
REVERT: B   63 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7588 (tpt-90)
REVERT: B  238 THR cc_start: 0.6381 (m) cc_final: 0.6135 (m)
REVERT: B  241 VAL cc_start: 0.9013 (t) cc_final: 0.8681 (p)
REVERT: B  390 PHE cc_start: 0.8305 (t80) cc_final: 0.7562 (t80)
REVERT: B  395 ASP cc_start: 0.8918 (t0) cc_final: 0.8236 (m-30)
REVERT: B  448 LEU cc_start: 0.6429 (mt) cc_final: 0.5038 (mt)
REVERT: B  545 MET cc_start: 0.7845 (ptp) cc_final: 0.7175 (pmm)
REVERT: C   11 TYR cc_start: 0.8173 (t80) cc_final: 0.7653 (t80)
REVERT: C   54 ILE cc_start: 0.8876 (tp) cc_final: 0.8636 (tp)
REVERT: C   58 TYR cc_start: 0.8433 (t80) cc_final: 0.8048 (t80)
  outliers start: 33
  outliers final: 12
  residues processed: 109
  average time/residue: 0.5570
  time to fit residues: 65.6334
Evaluate side-chains
  84 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  112 ILE
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 A residue 1106 GLN
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 89 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   chunk 113 optimal weight:    8.9990
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 99 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A   1 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 = 0.3623 r_free = 0.3623 target = 0.109155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.077325 restraints weight = 20109.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 3.06
r_work: 0.2930 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.0966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054  10263  Z= 0.345
  Angle     :  0.651  11.040  13879  Z= 0.337
  Chirality :  0.048   0.199   1558
  Planarity :  0.004   0.044   1794
  Dihedral  :  5.366  57.383   1369
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.07 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.24), residues: 1233
  helix: -0.89 (0.40), residues: 154
  sheet: -0.19 (0.24), residues: 481
  loop : -0.44 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  18 
 TYR   0.017   0.002   TYR A 812 
 PHE   0.022   0.002   PHE A 998 
 TRP   0.012   0.002   TRP A1073 
 HIS   0.007   0.001   HIS A 711 

Details of bonding type rmsd
  covalent geometry    : bond        0.00803 (10262)
  covalent geometry    : angle       0.65116 (13877)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       1.07723 (    2)
  hydrogen bonds       : bond        0.04252 (  374)
  hydrogen bonds       : angle       5.56626 ( 1032)

*********************** 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
  117 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 74
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8382 (ptm160) cc_final: 0.7966 (ppp-140)
REVERT: A  150 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8791 (tptt)
REVERT: A  298 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8526 (tttm)
REVERT: A 1106 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7616 (mp10)
REVERT: B   56 GLU cc_start: 0.7915 (tp30) cc_final: 0.7216 (pm20)
REVERT: B   63 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7638 (tpt-90)
REVERT: B  241 VAL cc_start: 0.9112 (t) cc_final: 0.8785 (p)
REVERT: B  335 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7061 (tm-30)
REVERT: B  390 PHE cc_start: 0.8240 (t80) cc_final: 0.7493 (t80)
REVERT: B  448 LEU cc_start: 0.6404 (mt) cc_final: 0.5346 (mt)
REVERT: B  545 MET cc_start: 0.7988 (ptp) cc_final: 0.7403 (ptp)
REVERT: C   11 TYR cc_start: 0.8282 (t80) cc_final: 0.7746 (t80)
  outliers start: 43
  outliers final: 19
  residues processed: 110
  average time/residue: 0.6051
  time to fit residues: 71.8265
Evaluate side-chains
  92 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
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  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 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  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  521 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain C residue   20 HIS
Chi-restraints excluded: chain C residue   49 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 110 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0020
   chunk 119 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.5988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.112112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.080161 restraints weight = 19986.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 3.15
r_work: 0.2988 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10263  Z= 0.122
  Angle     :  0.531   8.093  13879  Z= 0.275
  Chirality :  0.044   0.166   1558
  Planarity :  0.003   0.046   1794
  Dihedral  :  4.980  55.725   1368
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 18.52 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.24), residues: 1233
  helix: -0.52 (0.41), residues: 150
  sheet: -0.10 (0.24), residues: 481
  loop : -0.31 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 147 
 TYR   0.013   0.001   TYR B 225 
 PHE   0.014   0.001   PHE A1030 
 TRP   0.014   0.001   TRP A 207 
 HIS   0.005   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10262)
  covalent geometry    : angle       0.53123 (13877)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       0.64197 (    2)
  hydrogen bonds       : bond        0.03302 (  374)
  hydrogen bonds       : angle       5.21775 ( 1032)

*********************** 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
  113 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 77
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8353 (ptm160) cc_final: 0.7910 (ppp-140)
REVERT: A  150 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8774 (tptt)
REVERT: A  298 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8452 (tttm)
REVERT: A  759 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8021 (mp10)
REVERT: A  896 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8548 (pm20)
REVERT: A 1106 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7522 (mp10)
REVERT: B   63 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7454 (tpt-90)
REVERT: B  119 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7661 (ttp-170)
REVERT: B  241 VAL cc_start: 0.9013 (t) cc_final: 0.8689 (p)
REVERT: B  335 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6892 (tm-30)
REVERT: B  390 PHE cc_start: 0.8174 (t80) cc_final: 0.7434 (t80)
REVERT: B  395 ASP cc_start: 0.8918 (t0) cc_final: 0.8647 (t0)
REVERT: B  448 LEU cc_start: 0.6387 (mt) cc_final: 0.5350 (mt)
REVERT: B  545 MET cc_start: 0.7695 (ptp) cc_final: 0.7233 (ptp)
REVERT: C   11 TYR cc_start: 0.8216 (t80) cc_final: 0.7635 (t80)
REVERT: C   39 ARG cc_start: 0.7705 (mpp-170) cc_final: 0.7435 (mpp-170)
  outliers start: 36
  outliers final: 11
  residues processed: 109
  average time/residue: 0.5707
  time to fit residues: 67.2194
Evaluate side-chains
  87 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  786 VAL
Chi-restraints excluded: chain A residue  896 GLU
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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 108 optimal weight:    9.9990
   chunk 95 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.113217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.081024 restraints weight = 19786.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 3.08
r_work: 0.3016 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1227

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= 0.139
  Angle     :  0.539   8.929  13879  Z= 0.277
  Chirality :  0.044   0.134   1558
  Planarity :  0.003   0.039   1794
  Dihedral  :  4.848  55.989   1368
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.24), residues: 1233
  helix: -0.45 (0.41), residues: 150
  sheet: -0.07 (0.24), residues: 482
  loop : -0.27 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 198 
 TYR   0.015   0.001   TYR B 225 
 PHE   0.014   0.001   PHE A1030 
 TRP   0.011   0.001   TRP A1073 
 HIS   0.005   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10262)
  covalent geometry    : angle       0.53860 (13877)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.62332 (    2)
  hydrogen bonds       : bond        0.03282 (  374)
  hydrogen bonds       : angle       5.10838 ( 1032)

*********************** 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
  111 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 74
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8284 (ptm160) cc_final: 0.7904 (ppp-140)
REVERT: A  150 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8797 (tptm)
REVERT: A  298 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8563 (tttm)
REVERT: A 1106 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7566 (mp10)
REVERT: B   63 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7618 (tpt-90)
REVERT: B  119 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7907 (ttp-170)
REVERT: B  238 THR cc_start: 0.6307 (m) cc_final: 0.6063 (m)
REVERT: B  241 VAL cc_start: 0.9038 (t) cc_final: 0.8704 (p)
REVERT: B  335 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.7017 (tm-30)
REVERT: B  390 PHE cc_start: 0.8295 (t80) cc_final: 0.7510 (t80)
REVERT: B  395 ASP cc_start: 0.8844 (t0) cc_final: 0.8585 (t0)
REVERT: B  397 PHE cc_start: 0.7761 (m-80) cc_final: 0.7545 (m-80)
REVERT: B  448 LEU cc_start: 0.6641 (mt) cc_final: 0.5695 (mt)
REVERT: B  545 MET cc_start: 0.7990 (ptp) cc_final: 0.7355 (pmm)
REVERT: C   11 TYR cc_start: 0.8103 (t80) cc_final: 0.7592 (t80)
REVERT: C   58 TYR cc_start: 0.8465 (t80) cc_final: 0.8209 (t80)
  outliers start: 37
  outliers final: 16
  residues processed: 105
  average time/residue: 0.6121
  time to fit residues: 69.3271
Evaluate side-chains
  91 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  786 VAL
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 121 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 18 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.9584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.112776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.080998 restraints weight = 19689.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 3.05
r_work: 0.3006 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10263  Z= 0.156
  Angle     :  0.553  10.017  13879  Z= 0.284
  Chirality :  0.044   0.134   1558
  Planarity :  0.003   0.040   1794
  Dihedral  :  4.868  56.036   1368
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.32 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.24), residues: 1233
  helix: -0.27 (0.42), residues: 144
  sheet: -0.07 (0.24), residues: 482
  loop : -0.28 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 198 
 TYR   0.019   0.001   TYR B 225 
 PHE   0.015   0.001   PHE A1030 
 TRP   0.011   0.001   TRP A1073 
 HIS   0.006   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10262)
  covalent geometry    : angle       0.55278 (13877)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.67808 (    2)
  hydrogen bonds       : bond        0.03335 (  374)
  hydrogen bonds       : angle       5.08749 ( 1032)

*********************** 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
  110 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 76
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8311 (ptm160) cc_final: 0.7910 (ppp-140)
REVERT: A  150 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8765 (tptm)
REVERT: A  298 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8562 (tttm)
REVERT: A 1106 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7556 (mp10)
REVERT: B   63 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7647 (tpt-90)
REVERT: B  119 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7938 (ttp-170)
REVERT: B  238 THR cc_start: 0.6307 (m) cc_final: 0.6082 (m)
REVERT: B  241 VAL cc_start: 0.9051 (t) cc_final: 0.8695 (p)
REVERT: B  335 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.7023 (tm-30)
REVERT: B  390 PHE cc_start: 0.8237 (t80) cc_final: 0.7451 (t80)
REVERT: B  395 ASP cc_start: 0.8844 (t0) cc_final: 0.8572 (t0)
REVERT: B  397 PHE cc_start: 0.7740 (m-80) cc_final: 0.7518 (m-80)
REVERT: B  448 LEU cc_start: 0.6597 (mt) cc_final: 0.5360 (mt)
REVERT: B  545 MET cc_start: 0.8002 (ptp) cc_final: 0.7352 (pmm)
REVERT: C   11 TYR cc_start: 0.8101 (t80) cc_final: 0.7580 (t80)
REVERT: C   39 ARG cc_start: 0.7853 (mpp-170) cc_final: 0.7506 (mpp-170)
  outliers start: 34
  outliers final: 17
  residues processed: 105
  average time/residue: 0.5861
  time to fit residues: 66.4916
Evaluate side-chains
  94 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0370
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0030
   chunk 74 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0870
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 111 optimal weight:    0.4980
   overall best weight:    0.3246

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

Flipped N/Q/H residues before XYZ refinement:
A1106 GLN
** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 542 ASN
C  61 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.114795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.082638 restraints weight = 19573.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 3.10
r_work: 0.3043 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10263  Z= 0.101
  Angle     :  0.548  11.157  13879  Z= 0.276
  Chirality :  0.044   0.171   1558
  Planarity :  0.003   0.037   1794
  Dihedral  :  4.637  55.140   1368
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.86 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.24), residues: 1233
  helix: -0.25 (0.42), residues: 144
  sheet:  0.05 (0.24), residues: 491
  loop : -0.22 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 198 
 TYR   0.022   0.001   TYR B 225 
 PHE   0.013   0.001   PHE B 379 
 TRP   0.012   0.001   TRP A 207 
 HIS   0.007   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (10262)
  covalent geometry    : angle       0.54762 (13877)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.43928 (    2)
  hydrogen bonds       : bond        0.03004 (  374)
  hydrogen bonds       : angle       4.92373 ( 1032)

*********************** 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: 25
    poor density    : 80
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7957 (ppp-140)
REVERT: A  150 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8770 (tptm)
REVERT: A  298 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8524 (tttm)
REVERT: A 1106 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7466 (mp-120)
REVERT: B   63 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7464 (tpt-90)
REVERT: B  235 GLN cc_start: 0.8621 (tp40) cc_final: 0.8138 (pt0)
REVERT: B  238 THR cc_start: 0.6331 (m) cc_final: 0.6092 (m)
REVERT: B  241 VAL cc_start: 0.9039 (t) cc_final: 0.8709 (p)
REVERT: B  390 PHE cc_start: 0.8234 (t80) cc_final: 0.7448 (t80)
REVERT: B  395 ASP cc_start: 0.8856 (t0) cc_final: 0.8604 (t0)
REVERT: B  397 PHE cc_start: 0.7674 (m-80) cc_final: 0.7447 (m-80)
REVERT: B  448 LEU cc_start: 0.6319 (mt) cc_final: 0.5269 (mt)
REVERT: B  545 MET cc_start: 0.7903 (ptp) cc_final: 0.7342 (pmm)
REVERT: C   11 TYR cc_start: 0.8090 (t80) cc_final: 0.7654 (t80)
REVERT: C   39 ARG cc_start: 0.7801 (mpp-170) cc_final: 0.7570 (mpp-170)
  outliers start: 25
  outliers final: 11
  residues processed: 100
  average time/residue: 0.6241
  time to fit residues: 67.0373
Evaluate side-chains
  87 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 VAL
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 121 optimal weight:    0.0270
   chunk 22 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 108 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0670
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.9980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.113317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081529 restraints weight = 19631.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 3.06
r_work: 0.3014 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10263  Z= 0.161
  Angle     :  0.580  12.243  13879  Z= 0.293
  Chirality :  0.045   0.184   1558
  Planarity :  0.003   0.061   1794
  Dihedral  :  4.660  55.750   1365
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.66 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.24), residues: 1233
  helix: -0.21 (0.42), residues: 144
  sheet:  0.02 (0.24), residues: 482
  loop : -0.23 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 198 
 TYR   0.025   0.001   TYR B 225 
 PHE   0.012   0.001   PHE A 851 
 TRP   0.009   0.001   TRP A1073 
 HIS   0.007   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10262)
  covalent geometry    : angle       0.57964 (13877)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.61373 (    2)
  hydrogen bonds       : bond        0.03309 (  374)
  hydrogen bonds       : angle       4.97423 ( 1032)

*********************** 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
  98 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  150 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8825 (tptm)
REVERT: A  298 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8553 (tttm)
REVERT: B   63 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7629 (tpt-90)
REVERT: B  235 GLN cc_start: 0.8602 (tp40) cc_final: 0.8122 (pt0)
REVERT: B  238 THR cc_start: 0.6268 (m) cc_final: 0.6057 (m)
REVERT: B  241 VAL cc_start: 0.9045 (t) cc_final: 0.8713 (p)
REVERT: B  390 PHE cc_start: 0.8235 (t80) cc_final: 0.7464 (t80)
REVERT: B  395 ASP cc_start: 0.8885 (t0) cc_final: 0.8624 (t0)
REVERT: B  397 PHE cc_start: 0.7726 (m-80) cc_final: 0.7488 (m-80)
REVERT: B  448 LEU cc_start: 0.6337 (mt) cc_final: 0.5278 (mt)
REVERT: B  545 MET cc_start: 0.7980 (ptp) cc_final: 0.7368 (pmm)
REVERT: C   11 TYR cc_start: 0.8116 (t80) cc_final: 0.7626 (t80)
  outliers start: 25
  outliers final: 13
  residues processed: 92
  average time/residue: 0.5735
  time to fit residues: 57.1943
Evaluate side-chains
  87 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  929 SER
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 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  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 62 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0030
   chunk 58 optimal weight:    0.0870
   chunk 25 optimal weight:    0.9990
   chunk 110 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5970

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.114599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.082669 restraints weight = 19481.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.08
r_work: 0.3040 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1639

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= 0.121
  Angle     :  0.561  13.299  13879  Z= 0.284
  Chirality :  0.044   0.174   1558
  Planarity :  0.003   0.050   1794
  Dihedral  :  4.553  55.132   1365
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 21.38 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.24), residues: 1233
  helix: -0.17 (0.42), residues: 144
  sheet:  0.12 (0.24), residues: 491
  loop : -0.20 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 198 
 TYR   0.028   0.001   TYR B 225 
 PHE   0.012   0.001   PHE A 851 
 TRP   0.011   0.001   TRP A1073 
 HIS   0.007   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10262)
  covalent geometry    : angle       0.56098 (13877)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.54284 (    2)
  hydrogen bonds       : bond        0.03104 (  374)
  hydrogen bonds       : angle       4.87911 ( 1032)

********************** 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
  89 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8845 (tptm)
REVERT: A  298 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8541 (tttm)
REVERT: A  369 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8393 (tpm-80)
REVERT: B  235 GLN cc_start: 0.8629 (tp40) cc_final: 0.8136 (pt0)
REVERT: B  238 THR cc_start: 0.6339 (m) cc_final: 0.6087 (m)
REVERT: B  241 VAL cc_start: 0.9052 (t) cc_final: 0.8722 (p)
REVERT: B  390 PHE cc_start: 0.8254 (t80) cc_final: 0.7490 (t80)
REVERT: B  395 ASP cc_start: 0.8857 (t0) cc_final: 0.8611 (t0)
REVERT: B  448 LEU cc_start: 0.6272 (mt) cc_final: 0.5022 (mt)
REVERT: B  545 MET cc_start: 0.7936 (ptp) cc_final: 0.7363 (pmm)
REVERT: C   11 TYR cc_start: 0.8091 (t80) cc_final: 0.7640 (t80)
REVERT: C   39 ARG cc_start: 0.7794 (mpp-170) cc_final: 0.7437 (mpp-170)
  outliers start: 16
  outliers final: 10
  residues processed: 87
  average time/residue: 0.5337
  time to fit residues: 50.6830
Evaluate side-chains
  80 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  931 LEU
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain B residue  120 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 94 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0670
   overall best weight:    0.5718

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.114492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.082328 restraints weight = 19685.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 3.09
r_work: 0.3034 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1712

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= 0.122
  Angle     :  0.573  12.809  13879  Z= 0.289
  Chirality :  0.044   0.169   1558
  Planarity :  0.003   0.052   1794
  Dihedral  :  4.545  55.365   1365
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 21.38 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.24), residues: 1233
  helix: -0.04 (0.42), residues: 144
  sheet:  0.12 (0.24), residues: 492
  loop : -0.20 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 198 
 TYR   0.031   0.001   TYR B 225 
 PHE   0.012   0.001   PHE A 851 
 TRP   0.011   0.001   TRP A1073 
 HIS   0.006   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10262)
  covalent geometry    : angle       0.57267 (13877)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.56234 (    2)
  hydrogen bonds       : bond        0.03096 (  374)
  hydrogen bonds       : angle       4.81719 ( 1032)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3056.39 seconds
wall clock time: 53 minutes 8.09 seconds (3188.09 seconds total)