Starting phenix.real_space_refine
on Thu Mar  5 00:36:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yzp_14393/03_2026/7yzp_14393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yzp_14393/03_2026/7yzp_14393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yzp_14393/03_2026/7yzp_14393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yzp_14393/03_2026/7yzp_14393.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yzp_14393/03_2026/7yzp_14393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yzp_14393/03_2026/7yzp_14393.map"
  }
  resolution = 4.0
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4320 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      63      5.49       5
     Mg      2      5.21       5
     S      38      5.16       5
     C    8650      2.51       5
     N    2499      2.21       5
     O    2851      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14107
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "F"
      Number of atoms: 1211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1211
          Classifications: {'DNA': 59}
          Link IDs: {'rna3p': 58}
    Chain: "A"
      Number of atoms: 3013
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3013
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 20, 'TRANS': 360}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 356, 2819
          Classifications: {'peptide': 356}
          Link IDs: {'PTRANS': 20, 'TRANS': 335}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 3502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3502
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 8, 'TRANS': 439}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 3502
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 8, 'TRANS': 439}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 21
    residue:
      pdb=" N   GLY A 284 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY A 284 " occ=0.50
    residue:
      pdb=" N   ALA A 287 " occ=0.60
      ... (3 atoms not shown)
      pdb=" CB  ALA A 287 " occ=0.60
    residue:
      pdb=" N   THR A 290 " occ=0.70
      ... (5 atoms not shown)
      pdb=" CG2 THR A 290 " occ=0.70
    residue:
      pdb=" N   ALA A 291 " occ=0.60
      ... (3 atoms not shown)
      pdb=" CB  ALA A 291 " occ=0.60
    residue:
      pdb=" N   GLN A 292 " occ=0.70
      ... (7 atoms not shown)
      pdb=" NE2 GLN A 292 " occ=0.70
    residue:
      pdb=" N   LEU A 293 " occ=0.80
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 293 " occ=0.80
    residue:
      pdb=" N   PRO A 303 " occ=0.61
      ... (5 atoms not shown)
      pdb=" CD  PRO A 303 " occ=0.61
    residue:
      pdb=" N   PRO A 304 " occ=0.68
      ... (5 atoms not shown)
      pdb=" CD  PRO A 304 " occ=0.68
    residue:
      pdb=" N   VAL A 305 " occ=0.88
      ... (5 atoms not shown)
      pdb=" CG2 VAL A 305 " occ=0.88
    residue:
      pdb=" N   TRP A 306 " occ=0.97
      ... (12 atoms not shown)
      pdb=" CH2 TRP A 306 " occ=0.97
    residue:
      pdb=" N   LEU A 307 " occ=0.87
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 307 " occ=0.87
    residue:
      pdb=" N   ILE A 309 " occ=0.89
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 309 " occ=0.89
    ... (remaining 9 not shown)
  Time building chain proxies: 3.27, per 1000 atoms: 0.23
  Number of scatterers: 14107
  At special positions: 0
  Unit cell: (100.605, 140.847, 139.788, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      4     24.99
     S      38     16.00
     P      63     15.00
     Mg      2     11.99
     O    2851      8.00
     N    2499      7.00
     C    8650      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.30
  Conformation dependent library (CDL) restraints added in 401.3 milliseconds
  

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3080

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 15 sheets defined
      45.6% alpha, 14.9% beta
      27 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 39
    Processing helix  chain 'A' and resid 56 through 74
      removed outlier: 3.618A  pdb=" N   GLN A  72 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   THR A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 98
      removed outlier: 4.450A  pdb=" N   SER A  93 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASP A  95 " --> pdb=" O   ASN A  91 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ILE A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A  98 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
      removed outlier: 3.744A  pdb=" N   ILE A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 173
      removed outlier: 3.533A  pdb=" N   GLN A 151 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 294
    Processing helix  chain 'A' and resid 295 through 298
      removed outlier: 3.948A  pdb=" N   ASP A 298 " --> pdb=" O   GLN A 295 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 295 through 298'
    Processing helix  chain 'A' and resid 319 through 329
      removed outlier: 3.848A  pdb=" N   GLN A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 361 through 373
      removed outlier: 3.609A  pdb=" N   LEU A 372 " --> pdb=" O   ARG A 368 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLU A 373 " --> pdb=" O   ARG A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 393
      removed outlier: 4.180A  pdb=" N   ARG A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR A 393 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 39
    Processing helix  chain 'B' and resid 56 through 74
      removed outlier: 3.692A  pdb=" N   ARG B  60 " --> pdb=" O   PRO B  56 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN B  72 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   THR B  73 " --> pdb=" O   ASN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 92
      removed outlier: 3.883A  pdb=" N   LEU B  90 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU B  92 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 100
    Processing helix  chain 'B' and resid 152 through 173
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 285 through 294
      removed outlier: 3.574A  pdb=" N   GLU B 294 " --> pdb=" O   THR B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 297
      No H-bonds generated for 'chain 'B' and resid 295 through 297'
    Processing helix  chain 'B' and resid 316 through 329
      removed outlier: 4.091A  pdb=" N   ARG B 322 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU B 327 " --> pdb=" O   LYS B 323 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLU B 329 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 370
    Processing helix  chain 'B' and resid 371 through 373
      No H-bonds generated for 'chain 'B' and resid 371 through 373'
    Processing helix  chain 'B' and resid 378 through 395
      removed outlier: 4.138A  pdb=" N   ALA B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 56
      removed outlier: 4.461A  pdb=" N   ILE C  50 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   CYS C  51 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 104
    Processing helix  chain 'C' and resid 128 through 141
      removed outlier: 4.247A  pdb=" N   GLU C 134 " --> pdb=" O   LYS C 130 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ALA C 137 " --> pdb=" O   LEU C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 149
      removed outlier: 3.913A  pdb=" N   ARG C 149 " --> pdb=" O   GLY C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 164
    Processing helix  chain 'C' and resid 165 through 177
    Processing helix  chain 'C' and resid 180 through 201
      removed outlier: 3.691A  pdb=" N   PHE C 190 " --> pdb=" O   SER C 186 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLU C 191 " --> pdb=" O   ALA C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 210
      removed outlier: 3.584A  pdb=" N   VAL C 210 " --> pdb=" O   GLN C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 235
      removed outlier: 4.108A  pdb=" N   GLU C 231 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLU C 232 " --> pdb=" O   LEU C 228 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS C 233 " --> pdb=" O   THR C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 836 through 887
      removed outlier: 3.588A  pdb=" N   GLN C 875 " --> pdb=" O   ALA C 871 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLU C 878 " --> pdb=" O   THR C 874 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASP C 879 " --> pdb=" O   GLN C 875 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   TRP C 880 " --> pdb=" O   GLN C 876 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR C 882 " --> pdb=" O   GLU C 878 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LEU C 883 " --> pdb=" O   ASP C 879 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 893 through 900
    Processing helix  chain 'C' and resid 900 through 917
      removed outlier: 3.843A  pdb=" N   ASN C 906 " --> pdb=" O   LEU C 902 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ARG C 917 " --> pdb=" O   GLN C 913 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 952 through 971
      removed outlier: 3.982A  pdb=" N   VAL C 971 " --> pdb=" O   LEU C 967 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 985 through 989
      removed outlier: 3.962A  pdb=" N   THR C 988 " --> pdb=" O   GLY C 985 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LEU C 989 " --> pdb=" O   PHE C 986 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 985 through 989'
    Processing helix  chain 'C' and resid 990 through 1005
    Processing helix  chain 'C' and resid 1017 through 1024
    Processing helix  chain 'D' and resid 24 through 29
    Processing helix  chain 'D' and resid 44 through 56
      removed outlier: 4.908A  pdb=" N   ILE D  50 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   CYS D  51 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 141
    Processing helix  chain 'D' and resid 143 through 148
    Processing helix  chain 'D' and resid 165 through 176
      removed outlier: 4.292A  pdb=" N   GLU D 171 " --> pdb=" O   LYS D 167 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU D 172 " --> pdb=" O   GLU D 168 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU D 173 " --> pdb=" O   ARG D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 208
      removed outlier: 3.916A  pdb=" N   GLN D 184 " --> pdb=" O   GLU D 180 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU D 200 " --> pdb=" O   ALA D 196 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS D 202 " --> pdb=" O   THR D 198 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU D 203 " --> pdb=" O   GLU D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 234
    Processing helix  chain 'D' and resid 836 through 885
      removed outlier: 3.760A  pdb=" N   ARG D 840 " --> pdb=" O   HIS D 836 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN D 875 " --> pdb=" O   ALA D 871 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLN D 876 " --> pdb=" O   GLN D 872 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASP D 879 " --> pdb=" O   GLN D 875 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 895 through 919
      removed outlier: 4.733A  pdb=" N   LEU D 902 " --> pdb=" O   PHE D 898 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   THR D 903 " --> pdb=" O   ALA D 899 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN D 913 " --> pdb=" O   HIS D 909 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG D 917 " --> pdb=" O   GLN D 913 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 949 through 951
      No H-bonds generated for 'chain 'D' and resid 949 through 951'
    Processing helix  chain 'D' and resid 952 through 971
      removed outlier: 3.762A  pdb=" N   VAL D 971 " --> pdb=" O   LEU D 967 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 990 through 1006
      removed outlier: 3.528A  pdb=" N   ASP D 995 " --> pdb=" O   SER D 991 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   THR D 996 " --> pdb=" O   GLU D 992 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1017 through 1021
      removed outlier: 4.118A  pdb=" N   MET D1020 " --> pdb=" O   VAL D1017 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1043 through 1046
    Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104
      removed outlier: 6.208A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ARG A   2 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   ILE A  44 " --> pdb=" O   ARG A   2 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   LEU A   4 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A   3 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A 255 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   ASN A 270 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU A 257 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   VAL A 268 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   THR A 259 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15
    Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116
      removed outlier: 8.331A  pdb=" N   ILE A 180 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL A 125 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   THR A 182 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   CYS A 127 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   ALA A 219 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ALA A 181 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ARG A 236 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 283
      removed outlier: 6.819A  pdb=" N   ALA A 280 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   GLU A 310 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU A 282 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104
      removed outlier: 6.364A  pdb=" N   LEU B  77 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ARG B   2 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ILE B  44 " --> pdb=" O   ARG B   2 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   LEU B   4 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   HIS B 256 " --> pdb=" O   HIS B   5 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   SER B 261 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   LEU B 265 " --> pdb=" O   SER B 261 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 116
      removed outlier: 3.671A  pdb=" N   GLN B 113 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 8.950A  pdb=" N   ILE B 180 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL B 125 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   THR B 182 " --> pdb=" O   VAL B 125 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   CYS B 127 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ILE B 179 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   ALA B 219 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ALA B 181 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE B 218 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 279 through 284
      removed outlier: 6.214A  pdb=" N   VAL B 305 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   VAL B 335 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LEU B 307 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU B 337 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 3
      removed outlier: 3.639A  pdb=" N   LEU C  80 " --> pdb=" O   LYS C   9 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLU C  84 " --> pdb=" O   SER C   5 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3
      removed outlier: 3.631A  pdb=" N   GLU C 115 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU C 116 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 979 through 982
      removed outlier: 6.305A  pdb=" N   LEU C 980 " --> pdb=" O   GLY C1012 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   ILE C1014 " --> pdb=" O   LEU C 980 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LEU C 982 " --> pdb=" O   ILE C1014 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   PHE C  33 " --> pdb=" O   VAL C1013 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 922 through 926
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1031 through 1032
    Processing sheet with id=AB4, first strand: chain 'D' and resid 18 through 21
      removed outlier: 6.272A  pdb=" N   ILE D   3 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   GLU D  86 " --> pdb=" O   ILE D   3 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU D 116 " --> pdb=" O   ALA D 126 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ARG D 118 " --> pdb=" O   ILE D 124 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE D 124 " --> pdb=" O   ARG D 118 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 152 through 153
      removed outlier: 6.722A  pdb=" N   LEU D 980 " --> pdb=" O   GLY D1012 " (cutoff:3.500A)
      removed outlier: 8.155A  pdb=" N   ILE D1014 " --> pdb=" O   LEU D 980 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU D 982 " --> pdb=" O   ILE D1014 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   PHE D  33 " --> pdb=" O   VAL D1013 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   ALA D  34 " --> pdb=" O   ILE D1028 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   VAL D1030 " --> pdb=" O   ALA D  34 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   THR D  36 " --> pdb=" O   VAL D1030 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   LYS D1032 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 922 through 926
      removed outlier: 3.510A  pdb=" N   ARG D 946 " --> pdb=" O   VAL D 936 " (cutoff:3.500A)

    589 hydrogen bonds defined for protein.
    1707 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      67 hydrogen bonds
      134 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 1.69 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: 4471
        1.34 -     1.46: 2318
        1.46 -     1.58: 7491
        1.58 -     1.70: 123
        1.70 -     1.82: 60
  Bond restraints: 14463
  Sorted by residual:
  bond pdb=" C4  ADP D1101 "
       pdb=" C5  ADP D1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C4  ADP C1101 "
       pdb=" C5  ADP C1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" C5  ADP D1101 "
       pdb=" C6  ADP D1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" C5  ADP C1101 "
       pdb=" C6  ADP C1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.408  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" N   ASP A  85 "
       pdb=" CA  ASP A  85 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.14e-02 7.69e+03 9.25e+00
  ... (remaining 14458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 19707
        2.80 -     5.59: 126
        5.59 -     8.39: 19
        8.39 -    11.19: 8
       11.19 -    13.99: 1
  Bond angle restraints: 19861
  Sorted by residual:
  angle pdb=" PA  ADP D1101 "
        pdb=" O3A ADP D1101 "
        pdb=" PB  ADP D1101 "
      ideal   model   delta    sigma   weight residual
     120.50  134.49  -13.99 3.00e+00 1.11e-01 2.17e+01
  angle pdb=" C   ASN D  12 "
        pdb=" CA  ASN D  12 "
        pdb=" CB  ASN D  12 "
      ideal   model   delta    sigma   weight residual
     116.63  111.67    4.96 1.16e+00 7.43e-01 1.83e+01
  angle pdb=" N   ASN A  83 "
        pdb=" CA  ASN A  83 "
        pdb=" C   ASN A  83 "
      ideal   model   delta    sigma   weight residual
     113.12  107.86    5.26 1.25e+00 6.40e-01 1.77e+01
  angle pdb=" N   VAL C 971 "
        pdb=" CA  VAL C 971 "
        pdb=" C   VAL C 971 "
      ideal   model   delta    sigma   weight residual
     112.29  108.37    3.92 9.40e-01 1.13e+00 1.74e+01
  angle pdb=" PA  ADP C1101 "
        pdb=" O3A ADP C1101 "
        pdb=" PB  ADP C1101 "
      ideal   model   delta    sigma   weight residual
     120.50  131.68  -11.18 3.00e+00 1.11e-01 1.39e+01
  ... (remaining 19856 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.90: 7984
       28.90 -    57.80: 570
       57.80 -    86.70: 46
       86.70 -   115.60: 3
      115.60 -   144.50: 1
  Dihedral angle restraints: 8604
    sinusoidal: 3868
      harmonic: 4736
  Sorted by residual:
  dihedral pdb=" C   ASP B 376 "
           pdb=" N   ASP B 376 "
           pdb=" CA  ASP B 376 "
           pdb=" CB  ASP B 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.45   12.85     0      2.50e+00 1.60e-01 2.64e+01
  dihedral pdb=" N   ASP B 376 "
           pdb=" C   ASP B 376 "
           pdb=" CA  ASP B 376 "
           pdb=" CB  ASP B 376 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.54  -10.74     0      2.50e+00 1.60e-01 1.85e+01
  dihedral pdb=" C4'  DG F  34 "
           pdb=" C3'  DG F  34 "
           pdb=" O3'  DG F  34 "
           pdb=" P    DT F  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.50  144.50     1      3.50e+01 8.16e-04 1.42e+01
  ... (remaining 8601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 2128
       0.079 -    0.159: 160
       0.159 -    0.238: 5
       0.238 -    0.318: 0
       0.318 -    0.397: 1
  Chirality restraints: 2294
  Sorted by residual:
  chirality pdb=" CA  ASP B 376 "
            pdb=" N   ASP B 376 "
            pdb=" C   ASP B 376 "
            pdb=" CB  ASP B 376 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" C3' ADP D1101 "
            pdb=" C2' ADP D1101 "
            pdb=" C4' ADP D1101 "
            pdb=" O3' ADP D1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.72    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ASP A  85 "
            pdb=" N   ASP A  85 "
            pdb=" C   ASP A  85 "
            pdb=" CB  ASP A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.85e-01
  ... (remaining 2291 not shown)

  Planarity restraints: 2364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 895 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   PHE D 895 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   PHE D 895 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG D 896 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C1034 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.74e+00
        pdb=" C   ASN C1034 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASN C1034 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY C1035 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  87 "    0.007 2.00e-02 2.50e+03   1.43e-02 2.04e+00
        pdb=" C   VAL D  87 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   VAL D  87 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LYS D  88 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2361 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.25: 20
        2.25 -     2.92: 5542
        2.92 -     3.58: 21296
        3.58 -     4.24: 31935
        4.24 -     4.90: 52744
  Nonbonded interactions: 111537
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  83 "
            pdb="MN    MN A 502 "
     model   vdw
     1.593 2.320
  nonbonded pdb=" N   ASN B  83 "
            pdb="MN    MN B 502 "
     model   vdw
     2.004 2.400
  nonbonded pdb=" OD1 ASP B   8 "
            pdb="MN    MN B 501 "
     model   vdw
     2.006 2.320
  nonbonded pdb=" OD1 ASN B  83 "
            pdb="MN    MN B 502 "
     model   vdw
     2.023 2.320
  nonbonded pdb=" CD2 HIS A 222 "
            pdb="MN    MN A 502 "
     model   vdw
     2.051 2.540
  ... (remaining 111532 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 105 or resid 109 through 137 or resid 151 throug \ 
h 188 or resid 205 through 342 or resid 354 through 502))
  selection = (chain 'B' and (resid 1 through 188 or resid 205 through 502))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.28 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.520
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109  14463  Z= 0.176
  Angle     :  0.619  13.986  19861  Z= 0.316
  Chirality :  0.040   0.397   2294
  Planarity :  0.003   0.036   2364
  Dihedral  : 17.725 144.499   5524
  Min Nonbonded Distance : 1.593

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.73 (0.22), residues: 1611
  helix:  1.67 (0.21), residues: 686
  sheet:  0.15 (0.35), residues: 225
  loop : -0.56 (0.25), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 347 
 TYR   0.013   0.001   TYR B  63 
 PHE   0.013   0.001   PHE A 366 
 TRP   0.019   0.001   TRP B  30 
 HIS   0.008   0.001   HIS D  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (14463)
  covalent geometry    : angle       0.61871 (19861)
  hydrogen bonds       : bond        0.16883 (  654)
  hydrogen bonds       : angle       5.73899 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.574 
Fit side-chains
REVERT: C 1020 MET cc_start: 0.7360 (ttp) cc_final: 0.6408 (ttp)
REVERT: D   13 SER cc_start: 0.8825 (t) cc_final: 0.8415 (p)
REVERT: D  990 ASP cc_start: 0.7422 (p0) cc_final: 0.7162 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0862
  time to fit residues: 20.9134
Evaluate side-chains
  94 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 98 optimal weight:    0.0670
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0770
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.8080

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 192 GLN
D 842 ASN
D1027 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.096212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.080145 restraints weight = 40522.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.081092 restraints weight = 28622.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.082448 restraints weight = 22928.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.082570 restraints weight = 16676.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.082656 restraints weight = 15722.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3403
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14463  Z= 0.131
  Angle     :  0.582   7.744  19861  Z= 0.294
  Chirality :  0.040   0.170   2294
  Planarity :  0.003   0.032   2364
  Dihedral  : 17.573 144.337   2417
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.42 %
    Favored  : 91.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.22), residues: 1611
  helix:  1.65 (0.20), residues: 683
  sheet:  0.20 (0.34), residues: 243
  loop : -0.45 (0.25), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.024   0.001   TYR C 144 
 PHE   0.014   0.001   PHE C 147 
 TRP   0.028   0.001   TRP B  30 
 HIS   0.008   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (14463)
  covalent geometry    : angle       0.58187 (19861)
  hydrogen bonds       : bond        0.04220 (  654)
  hydrogen bonds       : angle       4.46295 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: B   30 TRP cc_start: 0.8522 (t60) cc_final: 0.8189 (t60)
REVERT: C  188 MET cc_start: 0.7720 (tmm) cc_final: 0.7466 (tmm)
REVERT: D   13 SER cc_start: 0.8923 (t) cc_final: 0.8496 (p)
REVERT: D  992 GLU cc_start: 0.7531 (mp0) cc_final: 0.7253 (mp0)
  outliers start: 14
  outliers final: 11
  residues processed: 115
  average time/residue: 0.0827
  time to fit residues: 15.5443
Evaluate side-chains
  102 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  851 GLN
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 101 optimal weight:    0.0870
   chunk 148 optimal weight:    3.9990
   chunk 163 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 154 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9990
   overall best weight:    1.3164

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 ASN
C 864 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 ASN
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.093345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.076845 restraints weight = 40821.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.077898 restraints weight = 28235.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.079500 restraints weight = 21577.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.079606 restraints weight = 16087.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.079747 restraints weight = 14362.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14463  Z= 0.159
  Angle     :  0.586   9.503  19861  Z= 0.295
  Chirality :  0.040   0.162   2294
  Planarity :  0.003   0.038   2364
  Dihedral  : 17.670 144.983   2417
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.06 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.74 (0.22), residues: 1611
  helix:  1.65 (0.21), residues: 683
  sheet:  0.03 (0.33), residues: 253
  loop : -0.48 (0.26), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 347 
 TYR   0.018   0.001   TYR B 217 
 PHE   0.016   0.001   PHE C 147 
 TRP   0.017   0.001   TRP B  30 
 HIS   0.006   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (14463)
  covalent geometry    : angle       0.58569 (19861)
  hydrogen bonds       : bond        0.03981 (  654)
  hydrogen bonds       : angle       4.38868 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8793 (t80) cc_final: 0.8381 (t80)
REVERT: C  188 MET cc_start: 0.7926 (tmm) cc_final: 0.7555 (tmm)
REVERT: C  992 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7110 (tm-30)
REVERT: D  168 GLU cc_start: 0.7103 (pt0) cc_final: 0.6867 (tt0)
  outliers start: 16
  outliers final: 15
  residues processed: 106
  average time/residue: 0.0921
  time to fit residues: 16.0123
Evaluate side-chains
  107 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain D residue  192 GLN
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 134 optimal weight:    4.9990
   chunk 128 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0370
   chunk 44 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 136 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 ASN
C 851 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.095617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.078825 restraints weight = 40211.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.079863 restraints weight = 26705.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.080910 restraints weight = 20851.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.081147 restraints weight = 16706.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.081652 restraints weight = 15424.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  14463  Z= 0.114
  Angle     :  0.550  10.639  19861  Z= 0.273
  Chirality :  0.039   0.158   2294
  Planarity :  0.003   0.030   2364
  Dihedral  : 17.645 144.825   2417
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.78 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.76 (0.22), residues: 1611
  helix:  1.70 (0.21), residues: 689
  sheet:  0.17 (0.34), residues: 241
  loop : -0.59 (0.25), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.019   0.001   TYR B 217 
 PHE   0.024   0.001   PHE C 986 
 TRP   0.028   0.001   TRP B  30 
 HIS   0.005   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (14463)
  covalent geometry    : angle       0.55043 (19861)
  hydrogen bonds       : bond        0.03480 (  654)
  hydrogen bonds       : angle       4.21907 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: C  188 MET cc_start: 0.7945 (tmm) cc_final: 0.7621 (tmm)
REVERT: C  983 ASP cc_start: 0.7072 (t0) cc_final: 0.6870 (t0)
REVERT: D  168 GLU cc_start: 0.7069 (pt0) cc_final: 0.6794 (tt0)
REVERT: D  188 MET cc_start: 0.7988 (tmm) cc_final: 0.7751 (tmm)
REVERT: D  910 LEU cc_start: 0.7721 (mm) cc_final: 0.7501 (tt)
  outliers start: 22
  outliers final: 16
  residues processed: 120
  average time/residue: 0.0868
  time to fit residues: 17.2806
Evaluate side-chains
  107 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue  192 GLN
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 150 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0980
   chunk 108 optimal weight:    2.9990
   chunk 157 optimal weight:    0.0770
   chunk 137 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0980
   chunk 159 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 129 optimal weight:    4.9990
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
B 277 GLN
C 851 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.095443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.078655 restraints weight = 40203.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.079899 restraints weight = 27311.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.080783 restraints weight = 19851.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.081060 restraints weight = 15698.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.081242 restraints weight = 14626.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3376
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14463  Z= 0.102
  Angle     :  0.551  10.828  19861  Z= 0.271
  Chirality :  0.038   0.161   2294
  Planarity :  0.003   0.028   2364
  Dihedral  : 17.635 144.097   2417
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.06 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.83 (0.22), residues: 1611
  helix:  1.79 (0.21), residues: 689
  sheet:  0.26 (0.34), residues: 241
  loop : -0.61 (0.25), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 347 
 TYR   0.019   0.001   TYR B 217 
 PHE   0.022   0.001   PHE C 986 
 TRP   0.028   0.001   TRP B  30 
 HIS   0.005   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (14463)
  covalent geometry    : angle       0.55143 (19861)
  hydrogen bonds       : bond        0.03263 (  654)
  hydrogen bonds       : angle       4.10106 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.482 
Fit side-chains
REVERT: C  162 LEU cc_start: 0.7939 (mt) cc_final: 0.7665 (tp)
REVERT: C  188 MET cc_start: 0.7901 (tmm) cc_final: 0.7546 (tmm)
REVERT: D  910 LEU cc_start: 0.7762 (mm) cc_final: 0.7512 (tt)
  outliers start: 18
  outliers final: 13
  residues processed: 122
  average time/residue: 0.0936
  time to fit residues: 18.5949
Evaluate side-chains
  110 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain C residue  945 VAL
Chi-restraints excluded: chain D residue  192 GLN
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0030
   chunk 95 optimal weight:    0.4980
   chunk 131 optimal weight:    2.9990
   chunk 114 optimal weight:    0.6980
   chunk 115 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.4388

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.096858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.079809 restraints weight = 40181.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.081292 restraints weight = 27311.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.082219 restraints weight = 19232.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.082378 restraints weight = 15268.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.082539 restraints weight = 14256.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3408
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3408
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14463  Z= 0.102
  Angle     :  0.560  10.922  19861  Z= 0.271
  Chirality :  0.039   0.183   2294
  Planarity :  0.003   0.035   2364
  Dihedral  : 17.660 143.788   2417
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.92 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.80 (0.22), residues: 1611
  helix:  1.79 (0.21), residues: 691
  sheet:  0.26 (0.34), residues: 241
  loop : -0.66 (0.25), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.020   0.001   TYR B 217 
 PHE   0.012   0.001   PHE C 986 
 TRP   0.026   0.001   TRP B  30 
 HIS   0.004   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (14463)
  covalent geometry    : angle       0.55976 (19861)
  hydrogen bonds       : bond        0.03212 (  654)
  hydrogen bonds       : angle       4.05495 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A  387 PHE cc_start: 0.8752 (t80) cc_final: 0.8347 (t80)
REVERT: C  162 LEU cc_start: 0.7944 (mt) cc_final: 0.7708 (tp)
REVERT: C  188 MET cc_start: 0.7901 (tmm) cc_final: 0.7558 (tmm)
REVERT: D  168 GLU cc_start: 0.6974 (pt0) cc_final: 0.6755 (tt0)
REVERT: D  910 LEU cc_start: 0.7727 (mm) cc_final: 0.7523 (tt)
  outliers start: 20
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0938
  time to fit residues: 18.3364
Evaluate side-chains
  105 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain C residue  945 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 165 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 159 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.094611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.078081 restraints weight = 40093.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.079123 restraints weight = 27662.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.080805 restraints weight = 20936.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.080932 restraints weight = 14974.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.080953 restraints weight = 14468.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14463  Z= 0.120
  Angle     :  0.587  14.573  19861  Z= 0.284
  Chirality :  0.039   0.181   2294
  Planarity :  0.003   0.035   2364
  Dihedral  : 17.707 143.969   2417
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.42 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.84 (0.22), residues: 1611
  helix:  1.85 (0.21), residues: 689
  sheet:  0.08 (0.34), residues: 247
  loop : -0.58 (0.25), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 347 
 TYR   0.020   0.001   TYR B 217 
 PHE   0.014   0.001   PHE C 147 
 TRP   0.022   0.001   TRP B  30 
 HIS   0.004   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (14463)
  covalent geometry    : angle       0.58727 (19861)
  hydrogen bonds       : bond        0.03307 (  654)
  hydrogen bonds       : angle       4.08423 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  387 PHE cc_start: 0.8775 (t80) cc_final: 0.8471 (t80)
REVERT: C  162 LEU cc_start: 0.7964 (mt) cc_final: 0.7711 (tp)
REVERT: C  188 MET cc_start: 0.7964 (tmm) cc_final: 0.7611 (tmm)
REVERT: D  910 LEU cc_start: 0.7763 (mm) cc_final: 0.7532 (tt)
  outliers start: 23
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0897
  time to fit residues: 16.7429
Evaluate side-chains
  113 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain C residue  945 VAL
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue  877 VAL
Chi-restraints excluded: chain D residue  886 LEU
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 144 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 101 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 100 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.095777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.078728 restraints weight = 40074.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.080149 restraints weight = 27235.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.081237 restraints weight = 19198.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.081410 restraints weight = 14568.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.081519 restraints weight = 13927.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14463  Z= 0.117
  Angle     :  0.589  15.224  19861  Z= 0.283
  Chirality :  0.039   0.181   2294
  Planarity :  0.003   0.033   2364
  Dihedral  : 17.727 144.075   2417
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.42 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.84 (0.22), residues: 1611
  helix:  1.83 (0.21), residues: 691
  sheet:  0.07 (0.34), residues: 247
  loop : -0.57 (0.26), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 347 
 TYR   0.020   0.001   TYR B 217 
 PHE   0.013   0.001   PHE C 986 
 TRP   0.029   0.001   TRP B  30 
 HIS   0.004   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (14463)
  covalent geometry    : angle       0.58870 (19861)
  hydrogen bonds       : bond        0.03259 (  654)
  hydrogen bonds       : angle       4.08454 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A  387 PHE cc_start: 0.8770 (t80) cc_final: 0.8514 (t80)
REVERT: C  162 LEU cc_start: 0.7976 (mt) cc_final: 0.7707 (tp)
REVERT: C  188 MET cc_start: 0.7927 (tmm) cc_final: 0.7583 (tmm)
  outliers start: 29
  outliers final: 20
  residues processed: 118
  average time/residue: 0.0851
  time to fit residues: 16.6891
Evaluate side-chains
  113 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue  877 VAL
Chi-restraints excluded: chain D residue  886 LEU
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 143 optimal weight:    4.9990
   chunk 136 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 158 optimal weight:    0.9990
   chunk 123 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 159 optimal weight:    0.6980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.096138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.079052 restraints weight = 40223.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.080537 restraints weight = 27289.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.081511 restraints weight = 19223.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.081726 restraints weight = 14737.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.081855 restraints weight = 14036.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14463  Z= 0.113
  Angle     :  0.595  15.578  19861  Z= 0.285
  Chirality :  0.039   0.177   2294
  Planarity :  0.003   0.033   2364
  Dihedral  : 17.723 143.921   2417
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.56 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.84 (0.22), residues: 1611
  helix:  1.85 (0.21), residues: 689
  sheet: -0.04 (0.33), residues: 257
  loop : -0.53 (0.26), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 347 
 TYR   0.026   0.001   TYR B 217 
 PHE   0.014   0.001   PHE C 986 
 TRP   0.029   0.001   TRP B  30 
 HIS   0.003   0.001   HIS D 919 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (14463)
  covalent geometry    : angle       0.59526 (19861)
  hydrogen bonds       : bond        0.03240 (  654)
  hydrogen bonds       : angle       4.06361 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.534 
Fit side-chains
REVERT: C  188 MET cc_start: 0.7964 (tmm) cc_final: 0.7617 (tmm)
  outliers start: 22
  outliers final: 20
  residues processed: 117
  average time/residue: 0.0970
  time to fit residues: 18.7095
Evaluate side-chains
  111 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain C residue  932 LEU
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue  877 VAL
Chi-restraints excluded: chain D residue  886 LEU
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 126 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.094032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.077110 restraints weight = 40760.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.078162 restraints weight = 28274.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.079755 restraints weight = 21720.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.079861 restraints weight = 16302.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.079938 restraints weight = 15075.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14463  Z= 0.167
  Angle     :  0.637  15.124  19861  Z= 0.309
  Chirality :  0.040   0.175   2294
  Planarity :  0.003   0.037   2364
  Dihedral  : 17.846 145.079   2417
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.56 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.73 (0.22), residues: 1611
  helix:  1.75 (0.21), residues: 689
  sheet: -0.25 (0.33), residues: 257
  loop : -0.51 (0.26), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 347 
 TYR   0.024   0.002   TYR B 217 
 PHE   0.037   0.002   PHE A 387 
 TRP   0.026   0.001   TRP B  30 
 HIS   0.004   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (14463)
  covalent geometry    : angle       0.63743 (19861)
  hydrogen bonds       : bond        0.03643 (  654)
  hydrogen bonds       : angle       4.21954 ( 1841)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.411 
Fit side-chains
REVERT: C  188 MET cc_start: 0.7962 (tmm) cc_final: 0.7630 (tmm)
REVERT: C  873 MET cc_start: 0.6252 (tpp) cc_final: 0.5782 (tpt)
  outliers start: 22
  outliers final: 18
  residues processed: 108
  average time/residue: 0.0913
  time to fit residues: 16.4070
Evaluate side-chains
  104 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  251 LYS
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  877 VAL
Chi-restraints excluded: chain C residue  893 ASP
Chi-restraints excluded: chain C residue  932 LEU
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue  877 VAL
Chi-restraints excluded: chain D residue  886 LEU
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  905 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 115 optimal weight:    5.9990
   chunk 152 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
C 872 GLN
** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.090752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.074226 restraints weight = 40943.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.075152 restraints weight = 29178.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.076277 restraints weight = 22383.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.076345 restraints weight = 18855.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.076502 restraints weight = 16923.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14463  Z= 0.213
  Angle     :  0.692  15.331  19861  Z= 0.340
  Chirality :  0.042   0.179   2294
  Planarity :  0.004   0.036   2364
  Dihedral  : 18.108 147.983   2417
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.99 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.22), residues: 1611
  helix:  1.51 (0.21), residues: 689
  sheet: -0.63 (0.32), residues: 256
  loop : -0.63 (0.26), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 347 
 TYR   0.024   0.002   TYR B 217 
 PHE   0.052   0.002   PHE A 387 
 TRP   0.033   0.002   TRP B  30 
 HIS   0.007   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (14463)
  covalent geometry    : angle       0.69233 (19861)
  hydrogen bonds       : bond        0.04160 (  654)
  hydrogen bonds       : angle       4.47165 ( 1841)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1886.46 seconds
wall clock time: 33 minutes 36.22 seconds (2016.22 seconds total)