Starting phenix.real_space_refine
on Thu Jul  2 21:13:07 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sv7_25445/07_2026/7sv7_25445.map"
  }
  resolution = 3.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      47      5.16       5
     C    6345      2.51       5
     N    1585      2.21       5
     O    1685      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9673
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 9334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1173, 9334
          Classifications: {'peptide': 1173}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 32, 'TRANS': 1140}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 48
    Chain: "B"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 85
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'TRANS': 16}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'UNK:plan-1': 17}
          Unresolved non-hydrogen planarities: 17
    Chain: "A"
      Number of atoms: 254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 254
          Unusual residues: {' MG': 2, 'ATP': 2, 'C14': 1, 'CLR': 2, 'CV6': 1, 'D12': 4, 'DD9': 2, 'PJ8': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
  Time building chain proxies: 1.96, per 1000 atoms: 0.20
  Number of scatterers: 9673
  At special positions: 0
  Unit cell: (81.37, 83.43, 145.23, 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)
     S      47     16.00
     P       6     15.00
     Mg      2     11.99
     F       3      9.00
     O    1685      8.00
     N    1585      7.00
     C    6345      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: 1.11
  Conformation dependent library (CDL) restraints added in 236.3 milliseconds
  

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2236

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 5 sheets defined
      70.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 17
    Processing helix  chain 'A' and resid 20 through 30
      removed outlier: 3.582A  pdb=" N   LEU A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ARG A  29 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLN A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 37
      removed outlier: 3.662A  pdb=" N   ILE A  37 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 44
    Processing helix  chain 'A' and resid 45 through 64
    Processing helix  chain 'A' and resid 68 through 75
      removed outlier: 3.644A  pdb=" N   ALA A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG A  75 " --> pdb=" O   ASN A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 97
      removed outlier: 3.960A  pdb=" N   PHE A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 107
      removed outlier: 4.189A  pdb=" N   ARG A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 110
      No H-bonds generated for 'chain 'A' and resid 108 through 110'
    Processing helix  chain 'A' and resid 114 through 118
      removed outlier: 3.532A  pdb=" N   SER A 118 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 165
      removed outlier: 3.688A  pdb=" N   ILE A 125 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   HIS A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
      removed outlier: 3.649A  pdb=" N   LEU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 188
      removed outlier: 3.745A  pdb=" N   LEU A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ASN A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 195
      removed outlier: 3.748A  pdb=" N   GLU A 193 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 199 through 217
      Proline residue:  A 205  - end of helix
      removed outlier: 3.689A  pdb=" N   GLU A 217 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 268
      removed outlier: 3.901A  pdb=" N   GLY A 226 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   PHE A 229 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET A 245 " --> pdb=" O   GLY A 241 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LYS A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG A 251 " --> pdb=" O   TYR A 247 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLY A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   LYS A 254 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN A 268 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 276
    Processing helix  chain 'A' and resid 277 through 309
      removed outlier: 4.089A  pdb=" N   THR A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL A 302 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   PHE A 305 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 312
      No H-bonds generated for 'chain 'A' and resid 310 through 312'
    Processing helix  chain 'A' and resid 313 through 329
      Proline residue:  A 324  - end of helix
      removed outlier: 3.826A  pdb=" N   ILE A 328 " --> pdb=" O   PRO A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 352
      removed outlier: 4.462A  pdb=" N   VAL A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   MET A 348 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 375
    Processing helix  chain 'A' and resid 402 through 409
    Processing helix  chain 'A' and resid 464 through 472
    Processing helix  chain 'A' and resid 501 through 508
    Processing helix  chain 'A' and resid 513 through 525
    Processing helix  chain 'A' and resid 526 through 531
    Processing helix  chain 'A' and resid 549 through 564
      removed outlier: 3.579A  pdb=" N   LYS A 564 " --> pdb=" O   ARG A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 591
    Processing helix  chain 'A' and resid 606 through 612
      removed outlier: 3.850A  pdb=" N   LEU A 610 " --> pdb=" O   LYS A 606 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LYS A 612 " --> pdb=" O   GLU A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 636
    Processing helix  chain 'A' and resid 848 through 855
    Processing helix  chain 'A' and resid 856 through 886
      removed outlier: 4.368A  pdb=" N   ILE A 860 " --> pdb=" O   HIS A 856 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   PHE A 861 " --> pdb=" O   LYS A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 927
      removed outlier: 3.818A  pdb=" N   TYR A 917 " --> pdb=" O   TYR A 913 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY A 921 " --> pdb=" O   TYR A 917 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   ASP A 924 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   THR A 925 " --> pdb=" O   GLY A 921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 958
      removed outlier: 3.525A  pdb=" N   ILE A 942 " --> pdb=" O   VAL A 938 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR A 943 " --> pdb=" O   HIS A 939 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER A 945 " --> pdb=" O   LEU A 941 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLN A 958 " --> pdb=" O   HIS A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 967
      removed outlier: 3.701A  pdb=" N   THR A 966 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A 967 " --> pdb=" O   THR A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 986
      removed outlier: 4.143A  pdb=" N   ASP A 979 " --> pdb=" O   ARG A 975 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ILE A 980 " --> pdb=" O   PHE A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 1012
      removed outlier: 3.565A  pdb=" N   VAL A1008 " --> pdb=" O   ALA A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1047
      Proline residue:  A1021  - end of helix
      removed outlier: 3.618A  pdb=" N   ALA A1025 " --> pdb=" O   PRO A1021 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLN A1035 " --> pdb=" O   ALA A1031 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   THR A1036 " --> pdb=" O   TYR A1032 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   GLN A1039 " --> pdb=" O   GLN A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1061
      removed outlier: 3.509A  pdb=" N   PHE A1052 " --> pdb=" O   ARG A1048 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1061 through 1069
      removed outlier: 3.524A  pdb=" N   ALA A1067 " --> pdb=" O   TRP A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1122
      removed outlier: 3.512A  pdb=" N   ALA A1081 " --> pdb=" O   LEU A1077 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASN A1088 " --> pdb=" O   LEU A1084 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A1107 " --> pdb=" O   ILE A1103 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A1116 " --> pdb=" O   ILE A1112 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE A1117 " --> pdb=" O   ALA A1113 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR A1122 " --> pdb=" O   SER A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1168
      removed outlier: 3.783A  pdb=" N   LEU A1135 " --> pdb=" O   ILE A1131 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A1139 " --> pdb=" O   LEU A1135 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   MET A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   SER A1141 " --> pdb=" O   MET A1137 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   THR A1142 " --> pdb=" O   ASN A1138 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   TRP A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG A1158 " --> pdb=" O   ASP A1154 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   SER A1159 " --> pdb=" O   SER A1155 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL A1160 " --> pdb=" O   LEU A1156 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   PHE A1166 " --> pdb=" O   ARG A1162 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE A1167 " --> pdb=" O   VAL A1163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1249 through 1259
      removed outlier: 4.039A  pdb=" N   LEU A1258 " --> pdb=" O   LEU A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1278 through 1284
    Processing helix  chain 'A' and resid 1299 through 1305
    Processing helix  chain 'A' and resid 1311 through 1322
      removed outlier: 3.648A  pdb=" N   GLU A1321 " --> pdb=" O   LYS A1317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1324 through 1331
      removed outlier: 4.106A  pdb=" N   PHE A1331 " --> pdb=" O   VAL A1327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1362
    Processing helix  chain 'A' and resid 1377 through 1391
      removed outlier: 3.549A  pdb=" N   GLN A1382 " --> pdb=" O   PRO A1378 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ILE A1383 " --> pdb=" O   VAL A1379 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE A1384 " --> pdb=" O   THR A1380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1403 through 1409
      removed outlier: 3.616A  pdb=" N   LEU A1408 " --> pdb=" O   GLU A1405 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A1409 " --> pdb=" O   ALA A1406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1426 through 1434
      removed outlier: 3.563A  pdb=" N   ARG A1434 " --> pdb=" O   LEU A1430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1434 through 1440
      removed outlier: 3.632A  pdb=" N   ALA A1440 " --> pdb=" O   LEU A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1442 through 1450
      removed outlier: 3.558A  pdb=" N   LYS A1448 " --> pdb=" O   SER A1444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 17
    Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332
      removed outlier: 6.292A  pdb=" N   ILE A 331 " --> pdb=" O   ILE A 906 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 448
      removed outlier: 6.847A  pdb=" N   LYS A 442 " --> pdb=" O   THR A 398 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   THR A 398 " --> pdb=" O   LYS A 442 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   ILE A 444 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   VAL A 397 " --> pdb=" O   GLU A 479 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   GLU A 479 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 491
      removed outlier: 3.548A  pdb=" N   LEU A 454 " --> pdb=" O   ARG A 600 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   LEU A 453 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   LEU A 617 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ALA A 455 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   LEU A 619 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA A 457 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   HIS A 620 " --> pdb=" O   SER A 624 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   SER A 624 " --> pdb=" O   HIS A 620 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1234
      removed outlier: 5.554A  pdb=" N   GLU A1228 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ALA A1217 " --> pdb=" O   GLU A1228 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   PHE A1232 " --> pdb=" O   LYS A1213 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   LYS A1213 " --> pdb=" O   PHE A1232 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   ILE A1234 " --> pdb=" O   THR A1211 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   THR A1211 " --> pdb=" O   ILE A1234 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   VAL A1212 " --> pdb=" O   GLN A1268 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   GLN A1268 " --> pdb=" O   VAL A1212 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   ASP A1214 " --> pdb=" O   GLU A1266 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   GLU A1266 " --> pdb=" O   ASP A1214 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1286 through 1289
      removed outlier: 6.261A  pdb=" N   GLY A1287 " --> pdb=" O   LEU A1368 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   ASP A1370 " --> pdb=" O   GLY A1287 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ILE A1289 " --> pdb=" O   ASP A1370 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU A1367 " --> pdb=" O   ILE A1398 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   CYS A1400 " --> pdb=" O   LEU A1367 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU A1369 " --> pdb=" O   CYS A1400 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN A1412 " --> pdb=" O   ARG A1239 " (cutoff:3.500A)

    554 hydrogen bonds defined for protein.
    1641 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 1.26 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: 2955
        1.34 -     1.46: 1602
        1.46 -     1.58: 5226
        1.58 -     1.69: 10
        1.69 -     1.81: 79
  Bond restraints: 9872
  Sorted by residual:
  bond pdb=" O5' ATP A1503 "
       pdb=" PA  ATP A1503 "
    ideal  model  delta    sigma   weight residual
    1.579  1.641 -0.062 1.10e-02 8.26e+03 3.17e+01
  bond pdb=" O5' ATP A1504 "
       pdb=" PA  ATP A1504 "
    ideal  model  delta    sigma   weight residual
    1.579  1.638 -0.059 1.10e-02 8.26e+03 2.84e+01
  bond pdb=" O2A ATP A1503 "
       pdb=" PA  ATP A1503 "
    ideal  model  delta    sigma   weight residual
    1.529  1.567 -0.038 2.20e-02 2.07e+03 2.99e+00
  bond pdb=" C25 CV6 A1515 "
       pdb=" F1  CV6 A1515 "
    ideal  model  delta    sigma   weight residual
    1.348  1.317  0.031 2.00e-02 2.50e+03 2.38e+00
  bond pdb=" C16 CV6 A1515 "
       pdb=" C19 CV6 A1515 "
    ideal  model  delta    sigma   weight residual
    1.498  1.528 -0.030 2.00e-02 2.50e+03 2.23e+00
  ... (remaining 9867 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.40: 13337
        8.40 -    16.79: 5
       16.79 -    25.19: 2
       25.19 -    33.58: 0
       33.58 -    41.98: 4
  Bond angle restraints: 13348
  Sorted by residual:
  angle pdb=" O1A ATP A1504 "
        pdb=" PA  ATP A1504 "
        pdb=" O2A ATP A1504 "
      ideal   model   delta    sigma   weight residual
     114.42   72.44   41.98 3.53e+00 8.04e-02 1.42e+02
  angle pdb=" O1A ATP A1503 "
        pdb=" PA  ATP A1503 "
        pdb=" O5' ATP A1503 "
      ideal   model   delta    sigma   weight residual
     110.65   69.89   40.76 3.49e+00 8.21e-02 1.36e+02
  angle pdb=" O1A ATP A1503 "
        pdb=" PA  ATP A1503 "
        pdb=" O2A ATP A1503 "
      ideal   model   delta    sigma   weight residual
     114.42   74.33   40.09 3.53e+00 8.04e-02 1.29e+02
  angle pdb=" O1A ATP A1504 "
        pdb=" PA  ATP A1504 "
        pdb=" O5' ATP A1504 "
      ideal   model   delta    sigma   weight residual
     110.65   71.66   38.99 3.49e+00 8.21e-02 1.25e+02
  angle pdb=" PB  ATP A1504 "
        pdb=" O3B ATP A1504 "
        pdb=" PG  ATP A1504 "
      ideal   model   delta    sigma   weight residual
     139.87  130.34    9.53 1.00e+00 1.00e+00 9.09e+01
  ... (remaining 13343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 5463
       18.00 -    36.00: 316
       36.00 -    53.99: 59
       53.99 -    71.99: 13
       71.99 -    89.99: 6
  Dihedral angle restraints: 5857
    sinusoidal: 2401
      harmonic: 3456
  Sorted by residual:
  dihedral pdb=" CA  LYS A 536 "
           pdb=" C   LYS A 536 "
           pdb=" N   ASP A 537 "
           pdb=" CA  ASP A 537 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.41   16.59     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  ASN A1432 "
           pdb=" CB  ASN A1432 "
           pdb=" CG  ASN A1432 "
           pdb=" OD1 ASN A1432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -173.28  -66.72     2      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CA  GLU A 267 "
           pdb=" CB  GLU A 267 "
           pdb=" CG  GLU A 267 "
           pdb=" CD  GLU A 267 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.04  -57.04     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 5854 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 992
       0.033 -    0.066: 431
       0.066 -    0.099: 75
       0.099 -    0.133: 37
       0.133 -    0.166: 1
  Chirality restraints: 1536
  Sorted by residual:
  chirality pdb=" C16 CV6 A1515 "
            pdb=" C15 CV6 A1515 "
            pdb=" C17 CV6 A1515 "
            pdb=" C19 CV6 A1515 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       1.48    1.64   -0.17 2.00e-01 2.50e+01 6.87e-01
  chirality pdb=" CA  ILE A 448 "
            pdb=" N   ILE A 448 "
            pdb=" C   ILE A 448 "
            pdb=" CB  ILE A 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE A1366 "
            pdb=" N   ILE A1366 "
            pdb=" C   ILE A1366 "
            pdb=" CB  ILE A1366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1533 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C16 CV6 A1515 "    0.072 2.00e-02 2.50e+03   1.16e-01 3.05e+02
        pdb=" C19 CV6 A1515 "    0.028 2.00e-02 2.50e+03
        pdb=" C20 CV6 A1515 "   -0.094 2.00e-02 2.50e+03
        pdb=" C21 CV6 A1515 "   -0.187 2.00e-02 2.50e+03
        pdb=" C22 CV6 A1515 "   -0.156 2.00e-02 2.50e+03
        pdb=" C23 CV6 A1515 "   -0.022 2.00e-02 2.50e+03
        pdb=" C24 CV6 A1515 "    0.069 2.00e-02 2.50e+03
        pdb=" O4  CV6 A1515 "    0.126 2.00e-02 2.50e+03
        pdb=" O5  CV6 A1515 "    0.163 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   CV6 A1515 "   -0.026 2.00e-02 2.50e+03   6.31e-02 1.29e+02
        pdb=" C1  CV6 A1515 "    0.155 2.00e-02 2.50e+03
        pdb=" C10 CV6 A1515 "    0.015 2.00e-02 2.50e+03
        pdb=" C11 CV6 A1515 "   -0.026 2.00e-02 2.50e+03
        pdb=" C12 CV6 A1515 "   -0.108 2.00e-02 2.50e+03
        pdb=" C4  CV6 A1515 "    0.001 2.00e-02 2.50e+03
        pdb=" C5  CV6 A1515 "   -0.033 2.00e-02 2.50e+03
        pdb=" C6  CV6 A1515 "   -0.042 2.00e-02 2.50e+03
        pdb=" C7  CV6 A1515 "   -0.041 2.00e-02 2.50e+03
        pdb=" C8  CV6 A1515 "   -0.005 2.00e-02 2.50e+03
        pdb=" C9  CV6 A1515 "    0.032 2.00e-02 2.50e+03
        pdb=" F   CV6 A1515 "    0.093 2.00e-02 2.50e+03
        pdb=" N1  CV6 A1515 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C15 CV6 A1515 "   -0.003 2.00e-02 2.50e+03   1.35e-02 2.29e+00
        pdb=" C16 CV6 A1515 "    0.011 2.00e-02 2.50e+03
        pdb=" C8  CV6 A1515 "    0.016 2.00e-02 2.50e+03
        pdb=" N1  CV6 A1515 "   -0.023 2.00e-02 2.50e+03
        pdb=" O3  CV6 A1515 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 18
        2.58 -     3.16: 7888
        3.16 -     3.74: 14182
        3.74 -     4.32: 19601
        4.32 -     4.90: 32726
  Nonbonded interactions: 74415
  Sorted by model distance:
  nonbonded pdb="MG    MG A1502 "
            pdb=" O3G ATP A1504 "
     model   vdw
     2.003 2.170
  nonbonded pdb=" OE1 GLN A 493 "
            pdb="MG    MG A1501 "
     model   vdw
     2.026 2.170
  nonbonded pdb="MG    MG A1501 "
            pdb=" O2B ATP A1503 "
     model   vdw
     2.133 2.170
  nonbonded pdb=" OG  SER A1251 "
            pdb="MG    MG A1502 "
     model   vdw
     2.261 2.170
  nonbonded pdb="MG    MG A1501 "
            pdb=" O3G ATP A1503 "
     model   vdw
     2.277 2.170
  ... (remaining 74410 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.860
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
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   0.062   9872  Z= 0.154
  Angle     :  0.939  41.979  13348  Z= 0.386
  Chirality :  0.038   0.166   1536
  Planarity :  0.004   0.116   1608
  Dihedral  : 12.193  89.990   3621
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  3.56 %
    Favored  : 95.74 %
  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: -0.82 (0.23), residues: 1163
  helix: -0.21 (0.18), residues: 746
  sheet: -1.41 (0.51), residues: 79
  loop : -0.73 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1048 
 TYR   0.011   0.001   TYR A 517 
 PHE   0.010   0.001   PHE A 931 
 TRP   0.009   0.001   TRP A1274 
 HIS   0.002   0.001   HIS A1085 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.15 ( 9872)
  covalent geometry    : angle       0.93933 /  0.39 (13348)
  hydrogen bonds       : bond        0.21443 / 14.08 (  554)
  hydrogen bonds       : angle       6.55825 /  4.68 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 218
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A    3 ARG cc_start: 0.7250 (ptt90) cc_final: 0.7008 (ptt180)
REVERT: A  190 LYS cc_start: 0.9011 (ttpt) cc_final: 0.7948 (mttt)
REVERT: A  216 TRP cc_start: 0.8646 (t60) cc_final: 0.8441 (t60)
REVERT: A  503 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8023 (ttmm)
REVERT: A  525 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7559 (mp10)
REVERT: A  529 ASP cc_start: 0.8635 (m-30) cc_final: 0.8352 (m-30)
REVERT: A  606 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8604 (mmmm)
REVERT: A  611 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7517 (tttm)
REVERT: A  629 THR cc_start: 0.7366 (m) cc_final: 0.6884 (p)
REVERT: A 1045 SER cc_start: 0.8904 (t) cc_final: 0.8612 (p)
REVERT: A 1063 TRP cc_start: 0.8681 (m-10) cc_final: 0.8476 (m-90)
REVERT: A 1103 ILE cc_start: 0.9417 (tp) cc_final: 0.9043 (tp)
REVERT: A 1145 TRP cc_start: 0.8412 (t60) cc_final: 0.8202 (t60)
REVERT: A 1213 LYS cc_start: 0.8124 (mttt) cc_final: 0.7380 (tptt)
REVERT: A 1219 TYR cc_start: 0.8314 (m-80) cc_final: 0.7914 (m-80)
REVERT: A 1243 LEU cc_start: 0.8166 (pp) cc_final: 0.7444 (mp)
REVERT: A 1273 SER cc_start: 0.8870 (t) cc_final: 0.8412 (m)
REVERT: A 1317 LYS cc_start: 0.8546 (tptt) cc_final: 0.7982 (tptt)
REVERT: A 1401 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: A 1407 MET cc_start: 0.8162 (mmp) cc_final: 0.7713 (mtp)
REVERT: A 1423 GLN cc_start: 0.7654 (pt0) cc_final: 0.7428 (pp30)
REVERT: A 1439 GLN cc_start: 0.7022 (mm110) cc_final: 0.6214 (pp30)
  outliers start: 7
  outliers final: 1
  residues processed: 223
  average time/residue: 0.0867
  time to fit residues: 27.0259
Evaluate side-chains
  139 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue 1114 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0670
   chunk 117 optimal weight:   10.0000
   overall best weight:    1.1524

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 ASN
A 268 ASN
A 287 ASN
A 290 GLN
A 372 GLN
A 378 GLN
A 525 GLN
A 609 HIS
A1035 GLN
A1039 GLN
A1054 HIS
A1100 GLN
A1148 ASN
A1281 GLN
A1412 GLN
A1419 ASN
A1423 GLN
A1432 ASN
A1439 GLN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.133698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.117160 restraints weight = 14367.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.120663 restraints weight = 7346.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.122219 restraints weight = 4305.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124383 restraints weight = 3038.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.124615 restraints weight = 2156.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9872  Z= 0.147
  Angle     :  0.563   7.449  13348  Z= 0.290
  Chirality :  0.041   0.178   1536
  Planarity :  0.004   0.031   1608
  Dihedral  :  6.253  79.087   1419
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.29 %
    Favored  : 86.83 %
  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:  0.04 (0.24), residues: 1163
  helix:  0.61 (0.19), residues: 758
  sheet: -1.38 (0.51), residues: 79
  loop : -0.76 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1403 
 TYR   0.020   0.001   TYR A 380 
 PHE   0.023   0.002   PHE A 236 
 TRP   0.013   0.001   TRP A1274 
 HIS   0.003   0.001   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.15 ( 9872)
  covalent geometry    : angle       0.56257 /  0.29 (13348)
  hydrogen bonds       : bond        0.05726 /  3.76 (  554)
  hydrogen bonds       : angle       4.34297 /  3.13 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  125 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8018 (mt)
REVERT: A  129 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7793 (mp)
REVERT: A  145 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7900 (mp)
REVERT: A  190 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8096 (mttt)
REVERT: A  265 MET cc_start: 0.8329 (tmm) cc_final: 0.8087 (tmm)
REVERT: A  503 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7893 (ttmm)
REVERT: A  525 GLN cc_start: 0.7969 (mp10) cc_final: 0.7684 (mp10)
REVERT: A  629 THR cc_start: 0.7792 (m) cc_final: 0.7411 (p)
REVERT: A 1213 LYS cc_start: 0.8094 (mttt) cc_final: 0.7406 (tptt)
REVERT: A 1273 SER cc_start: 0.8806 (t) cc_final: 0.8483 (m)
REVERT: A 1377 ASP cc_start: 0.7309 (p0) cc_final: 0.6982 (p0)
REVERT: A 1401 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7675 (tp30)
REVERT: A 1439 GLN cc_start: 0.6896 (mm-40) cc_final: 0.6352 (pp30)
  outliers start: 19
  outliers final: 8
  residues processed: 157
  average time/residue: 0.0896
  time to fit residues: 20.4172
Evaluate side-chains
  131 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1084 LEU
Chi-restraints excluded: chain A residue 1114 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 112 optimal weight:    0.8980
   chunk 87 optimal weight:    7.9990
   overall best weight:    0.9580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 187 ASN
A 207 GLN
A 268 ASN
A 376 GLN
A1411 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.134159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.117624 restraints weight = 14356.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.120999 restraints weight = 7458.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.122778 restraints weight = 4417.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.124343 restraints weight = 3053.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.124754 restraints weight = 2307.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9872  Z= 0.127
  Angle     :  0.520   7.050  13348  Z= 0.266
  Chirality :  0.040   0.175   1536
  Planarity :  0.003   0.030   1608
  Dihedral  :  6.109  77.567   1416
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.18 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.47 (0.24), residues: 1163
  helix:  0.97 (0.19), residues: 755
  sheet: -0.93 (0.51), residues: 78
  loop : -0.73 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1259 
 TYR   0.017   0.001   TYR A 380 
 PHE   0.021   0.001   PHE A 236 
 TRP   0.010   0.001   TRP A 865 
 HIS   0.002   0.001   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 9872)
  covalent geometry    : angle       0.51988 /  0.27 (13348)
  hydrogen bonds       : bond        0.04708 /  3.09 (  554)
  hydrogen bonds       : angle       4.01183 /  2.90 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  125 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7967 (mt)
REVERT: A  190 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8045 (mttt)
REVERT: A  265 MET cc_start: 0.8449 (tmm) cc_final: 0.8177 (tmm)
REVERT: A  503 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7906 (ttmm)
REVERT: A  525 GLN cc_start: 0.7959 (mp10) cc_final: 0.7608 (mp10)
REVERT: A  611 LYS cc_start: 0.8138 (tptt) cc_final: 0.7663 (tttm)
REVERT: A  629 THR cc_start: 0.7821 (m) cc_final: 0.7469 (p)
REVERT: A  931 PHE cc_start: 0.7785 (p90) cc_final: 0.7347 (p90)
REVERT: A  958 GLN cc_start: 0.7848 (mm110) cc_final: 0.7646 (mm110)
REVERT: A 1213 LYS cc_start: 0.8120 (mttt) cc_final: 0.7359 (tptt)
REVERT: A 1273 SER cc_start: 0.8859 (t) cc_final: 0.8523 (m)
REVERT: A 1377 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7101 (p0)
REVERT: A 1401 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7336 (mm-30)
REVERT: A 1407 MET cc_start: 0.7866 (mmm) cc_final: 0.7526 (mtt)
REVERT: A 1439 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6380 (pp30)
  outliers start: 28
  outliers final: 16
  residues processed: 159
  average time/residue: 0.0836
  time to fit residues: 19.8155
Evaluate side-chains
  141 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  187 ASN
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1045 SER
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1166 PHE
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 68 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 187 ASN
A 220 GLN
A1054 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.116503 restraints weight = 14593.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.119764 restraints weight = 7675.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.122124 restraints weight = 4383.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.123640 restraints weight = 2893.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.123999 restraints weight = 2176.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9872  Z= 0.139
  Angle     :  0.528   7.983  13348  Z= 0.267
  Chirality :  0.040   0.184   1536
  Planarity :  0.003   0.032   1608
  Dihedral  :  6.165  79.367   1416
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.46 %
    Favored  : 82.77 %
  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:  0.52 (0.25), residues: 1163
  helix:  1.04 (0.19), residues: 758
  sheet: -1.03 (0.51), residues: 78
  loop : -0.78 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1259 
 TYR   0.023   0.001   TYR A1219 
 PHE   0.019   0.001   PHE A1257 
 TRP   0.011   0.001   TRP A1145 
 HIS   0.002   0.001   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 9872)
  covalent geometry    : angle       0.52846 /  0.27 (13348)
  hydrogen bonds       : bond        0.04537 /  2.97 (  554)
  hydrogen bonds       : angle       3.94605 /  2.84 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  125 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7829 (mt)
REVERT: A  190 LYS cc_start: 0.8899 (ttpt) cc_final: 0.7893 (mttt)
REVERT: A  265 MET cc_start: 0.8385 (tmm) cc_final: 0.7994 (tmm)
REVERT: A  503 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7883 (ttmm)
REVERT: A  611 LYS cc_start: 0.8218 (tptt) cc_final: 0.7660 (tttm)
REVERT: A  629 THR cc_start: 0.7791 (m) cc_final: 0.7396 (p)
REVERT: A 1042 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7967 (tp40)
REVERT: A 1213 LYS cc_start: 0.8073 (mttt) cc_final: 0.7248 (tptt)
REVERT: A 1273 SER cc_start: 0.8910 (t) cc_final: 0.8629 (m)
REVERT: A 1377 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7089 (p0)
REVERT: A 1401 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7438 (mm-30)
REVERT: A 1407 MET cc_start: 0.7814 (mmm) cc_final: 0.7435 (mtt)
REVERT: A 1439 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6375 (pp30)
  outliers start: 28
  outliers final: 21
  residues processed: 155
  average time/residue: 0.0825
  time to fit residues: 18.8790
Evaluate side-chains
  147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1042 GLN
Chi-restraints excluded: chain A residue 1045 SER
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1166 PHE
Chi-restraints excluded: chain A residue 1215 LEU
Chi-restraints excluded: chain A residue 1268 GLN
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0060
   chunk 80 optimal weight:    0.5980
   chunk 92 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 110 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.6198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.135702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.119252 restraints weight = 14499.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.122545 restraints weight = 7588.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.124815 restraints weight = 4330.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.126308 restraints weight = 2888.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.126688 restraints weight = 2184.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9872  Z= 0.104
  Angle     :  0.482   6.418  13348  Z= 0.245
  Chirality :  0.039   0.175   1536
  Planarity :  0.003   0.031   1608
  Dihedral  :  5.944  79.521   1416
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.64 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.85 (0.25), residues: 1163
  helix:  1.29 (0.19), residues: 762
  sheet: -0.80 (0.53), residues: 78
  loop : -0.71 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1259 
 TYR   0.015   0.001   TYR A 380 
 PHE   0.020   0.001   PHE A 931 
 TRP   0.013   0.001   TRP A1145 
 HIS   0.002   0.000   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.10 ( 9872)
  covalent geometry    : angle       0.48191 /  0.25 (13348)
  hydrogen bonds       : bond        0.03961 /  2.58 (  554)
  hydrogen bonds       : angle       3.76117 /  2.71 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8397 (tp)
REVERT: A  190 LYS cc_start: 0.8849 (ttpt) cc_final: 0.7922 (mttt)
REVERT: A  212 MET cc_start: 0.7751 (mmm) cc_final: 0.7380 (mmm)
REVERT: A  227 LEU cc_start: 0.7910 (tp) cc_final: 0.7665 (tp)
REVERT: A  265 MET cc_start: 0.8428 (tmm) cc_final: 0.8222 (tmm)
REVERT: A  503 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7887 (ttmm)
REVERT: A  525 GLN cc_start: 0.7901 (mp10) cc_final: 0.7500 (mp10)
REVERT: A  611 LYS cc_start: 0.8187 (tptt) cc_final: 0.7644 (tttm)
REVERT: A  629 THR cc_start: 0.7789 (m) cc_final: 0.7415 (p)
REVERT: A 1042 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8022 (tp40)
REVERT: A 1101 MET cc_start: 0.8089 (tpp) cc_final: 0.7710 (ttm)
REVERT: A 1103 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9197 (tp)
REVERT: A 1213 LYS cc_start: 0.7970 (mttt) cc_final: 0.7179 (tptt)
REVERT: A 1377 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6981 (p0)
REVERT: A 1401 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7490 (mm-30)
REVERT: A 1407 MET cc_start: 0.7667 (mmm) cc_final: 0.7416 (mtt)
REVERT: A 1439 GLN cc_start: 0.7025 (mm-40) cc_final: 0.6387 (pp30)
  outliers start: 25
  outliers final: 15
  residues processed: 153
  average time/residue: 0.0735
  time to fit residues: 16.6971
Evaluate side-chains
  146 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  268 ASN
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1042 GLN
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1215 LEU
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0060
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 268 ASN
A1054 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.135095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.118536 restraints weight = 14429.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.121815 restraints weight = 7543.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.124414 restraints weight = 4316.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.125152 restraints weight = 2813.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.125914 restraints weight = 2318.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9872  Z= 0.116
  Angle     :  0.491   7.138  13348  Z= 0.248
  Chirality :  0.040   0.169   1536
  Planarity :  0.003   0.031   1608
  Dihedral  :  5.924  80.123   1416
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.05 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.95 (0.25), residues: 1163
  helix:  1.38 (0.19), residues: 760
  sheet: -0.75 (0.58), residues: 68
  loop : -0.70 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1066 
 TYR   0.013   0.001   TYR A 380 
 PHE   0.021   0.001   PHE A 931 
 TRP   0.014   0.001   TRP A1145 
 HIS   0.002   0.001   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 9872)
  covalent geometry    : angle       0.49074 /  0.25 (13348)
  hydrogen bonds       : bond        0.04005 /  2.61 (  554)
  hydrogen bonds       : angle       3.74462 /  2.69 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8401 (tp)
REVERT: A  190 LYS cc_start: 0.8860 (ttpt) cc_final: 0.7990 (mttt)
REVERT: A  212 MET cc_start: 0.7841 (mmm) cc_final: 0.7455 (mmm)
REVERT: A  265 MET cc_start: 0.8379 (tmm) cc_final: 0.8090 (tmm)
REVERT: A  503 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7946 (ttmm)
REVERT: A  525 GLN cc_start: 0.7982 (mp10) cc_final: 0.7626 (mp10)
REVERT: A  629 THR cc_start: 0.7844 (m) cc_final: 0.7443 (p)
REVERT: A 1042 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8024 (tp40)
REVERT: A 1101 MET cc_start: 0.8158 (tpp) cc_final: 0.7679 (ttm)
REVERT: A 1103 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9194 (tp)
REVERT: A 1213 LYS cc_start: 0.8045 (mttt) cc_final: 0.7255 (tptt)
REVERT: A 1377 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7074 (p0)
REVERT: A 1401 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7419 (mm-30)
REVERT: A 1407 MET cc_start: 0.7647 (mmm) cc_final: 0.7430 (mtt)
REVERT: A 1439 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6465 (pp30)
  outliers start: 30
  outliers final: 23
  residues processed: 153
  average time/residue: 0.0711
  time to fit residues: 16.2500
Evaluate side-chains
  152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  268 ASN
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1042 GLN
Chi-restraints excluded: chain A residue 1045 SER
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1215 LEU
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0470
   chunk 8 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.6678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 ASN
A 220 GLN
A 268 ASN
A1054 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.136140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.119554 restraints weight = 14405.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.122851 restraints weight = 7587.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.125399 restraints weight = 4415.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.126184 restraints weight = 2894.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.126751 restraints weight = 2391.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9872  Z= 0.109
  Angle     :  0.496   7.470  13348  Z= 0.250
  Chirality :  0.039   0.169   1536
  Planarity :  0.003   0.031   1608
  Dihedral  :  5.851  80.107   1416
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.94 %
    Favored  : 80.99 %
  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:  1.06 (0.25), residues: 1163
  helix:  1.44 (0.19), residues: 764
  sheet: -0.60 (0.56), residues: 74
  loop : -0.63 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1066 
 TYR   0.012   0.001   TYR A 380 
 PHE   0.021   0.001   PHE A 931 
 TRP   0.014   0.001   TRP A1145 
 HIS   0.002   0.000   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 9872)
  covalent geometry    : angle       0.49552 /  0.25 (13348)
  hydrogen bonds       : bond        0.03824 /  2.49 (  554)
  hydrogen bonds       : angle       3.69022 /  2.64 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8431 (tp)
REVERT: A  190 LYS cc_start: 0.8873 (ttpt) cc_final: 0.7978 (mttt)
REVERT: A  212 MET cc_start: 0.7845 (mmm) cc_final: 0.7502 (mmm)
REVERT: A  265 MET cc_start: 0.8329 (tmm) cc_final: 0.8028 (tmm)
REVERT: A  503 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7969 (ttmm)
REVERT: A  525 GLN cc_start: 0.7967 (mp10) cc_final: 0.7585 (mp10)
REVERT: A  611 LYS cc_start: 0.8291 (tptt) cc_final: 0.7566 (tttm)
REVERT: A  629 THR cc_start: 0.7889 (m) cc_final: 0.7491 (p)
REVERT: A 1042 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8009 (tp40)
REVERT: A 1101 MET cc_start: 0.8219 (tpp) cc_final: 0.7744 (ttm)
REVERT: A 1103 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9174 (tp)
REVERT: A 1213 LYS cc_start: 0.8030 (mttt) cc_final: 0.7227 (tptt)
REVERT: A 1377 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7030 (p0)
REVERT: A 1401 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7439 (mm-30)
REVERT: A 1439 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6479 (pp30)
  outliers start: 31
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0772
  time to fit residues: 17.9172
Evaluate side-chains
  153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  268 ASN
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1042 GLN
Chi-restraints excluded: chain A residue 1045 SER
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1215 LEU
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1410 CYS
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 108 optimal weight:    6.9990
   chunk 102 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 GLN
A1054 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.135785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.119128 restraints weight = 14393.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122490 restraints weight = 7496.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.125069 restraints weight = 4324.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.125832 restraints weight = 2807.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.126455 restraints weight = 2323.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9872  Z= 0.110
  Angle     :  0.495   7.213  13348  Z= 0.250
  Chirality :  0.040   0.216   1536
  Planarity :  0.003   0.031   1608
  Dihedral  :  5.811  80.337   1416
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.35 %
    Favored  : 81.09 %
  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:  1.14 (0.25), residues: 1163
  helix:  1.50 (0.19), residues: 761
  sheet: -0.55 (0.55), residues: 75
  loop : -0.61 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1066 
 TYR   0.012   0.001   TYR A 380 
 PHE   0.022   0.001   PHE A 931 
 TRP   0.010   0.001   TRP A 865 
 HIS   0.003   0.001   HIS A 484 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 9872)
  covalent geometry    : angle       0.49497 /  0.25 (13348)
  hydrogen bonds       : bond        0.03792 /  2.47 (  554)
  hydrogen bonds       : angle       3.67825 /  2.63 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8395 (tp)
REVERT: A  190 LYS cc_start: 0.8856 (ttpt) cc_final: 0.7985 (mttt)
REVERT: A  265 MET cc_start: 0.8243 (tmm) cc_final: 0.7912 (tmm)
REVERT: A  503 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7955 (ttmm)
REVERT: A  525 GLN cc_start: 0.8009 (mp10) cc_final: 0.7617 (mp10)
REVERT: A  611 LYS cc_start: 0.8315 (tptt) cc_final: 0.7580 (tttm)
REVERT: A  629 THR cc_start: 0.7883 (m) cc_final: 0.7487 (p)
REVERT: A 1042 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7988 (tp40)
REVERT: A 1101 MET cc_start: 0.8225 (tpp) cc_final: 0.7738 (ttm)
REVERT: A 1103 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9179 (tp)
REVERT: A 1213 LYS cc_start: 0.8005 (mttt) cc_final: 0.7261 (tptt)
REVERT: A 1377 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7040 (p0)
REVERT: A 1401 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7437 (mm-30)
REVERT: A 1439 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6536 (pp30)
  outliers start: 36
  outliers final: 29
  residues processed: 146
  average time/residue: 0.0666
  time to fit residues: 14.3261
Evaluate side-chains
  154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1042 GLN
Chi-restraints excluded: chain A residue 1045 SER
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1215 LEU
Chi-restraints excluded: chain A residue 1261 LEU
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1410 CYS
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 ASN
A 146 HIS
A 220 GLN
A1054 HIS
A1375 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.133058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.116223 restraints weight = 14387.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119513 restraints weight = 7588.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.121709 restraints weight = 4374.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.123067 restraints weight = 2946.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.123615 restraints weight = 2242.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9872  Z= 0.127
  Angle     :  0.518   7.601  13348  Z= 0.259
  Chirality :  0.040   0.179   1536
  Planarity :  0.003   0.031   1608
  Dihedral  :  5.921  81.127   1416
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.84 %
    Favored  : 80.79 %
  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:  1.11 (0.25), residues: 1163
  helix:  1.47 (0.19), residues: 762
  sheet: -0.53 (0.56), residues: 73
  loop : -0.60 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1066 
 TYR   0.012   0.001   TYR A1381 
 PHE   0.023   0.001   PHE A 931 
 TRP   0.012   0.001   TRP A1145 
 HIS   0.002   0.001   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 9872)
  covalent geometry    : angle       0.51794 /  0.26 (13348)
  hydrogen bonds       : bond        0.03989 /  2.61 (  554)
  hydrogen bonds       : angle       3.73041 /  2.67 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8419 (tp)
REVERT: A  190 LYS cc_start: 0.8826 (ttpt) cc_final: 0.7994 (mttt)
REVERT: A  265 MET cc_start: 0.8302 (tmm) cc_final: 0.8025 (tmm)
REVERT: A  503 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7900 (ttmm)
REVERT: A  611 LYS cc_start: 0.8281 (tptt) cc_final: 0.7532 (tttm)
REVERT: A  629 THR cc_start: 0.7932 (m) cc_final: 0.7530 (p)
REVERT: A 1042 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8002 (tp40)
REVERT: A 1101 MET cc_start: 0.8248 (tpp) cc_final: 0.7757 (ttm)
REVERT: A 1103 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9169 (tp)
REVERT: A 1166 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.6506 (t80)
REVERT: A 1213 LYS cc_start: 0.8092 (mttt) cc_final: 0.7267 (tptt)
REVERT: A 1377 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7069 (p0)
REVERT: A 1439 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6534 (pp30)
  outliers start: 34
  outliers final: 24
  residues processed: 149
  average time/residue: 0.0744
  time to fit residues: 16.7025
Evaluate side-chains
  152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1042 GLN
Chi-restraints excluded: chain A residue 1045 SER
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1166 PHE
Chi-restraints excluded: chain A residue 1215 LEU
Chi-restraints excluded: chain A residue 1261 LEU
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1410 CYS
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 22 optimal weight:    0.1980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 GLN
A1054 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.135885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.119164 restraints weight = 14524.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122495 restraints weight = 7706.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.124999 restraints weight = 4488.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.125954 restraints weight = 2946.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.126525 restraints weight = 2424.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9872  Z= 0.114
  Angle     :  0.510  10.965  13348  Z= 0.254
  Chirality :  0.040   0.190   1536
  Planarity :  0.003   0.031   1608
  Dihedral  :  5.878  81.418   1416
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.83 %
    Favored  : 80.30 %
  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:  1.15 (0.25), residues: 1163
  helix:  1.46 (0.19), residues: 769
  sheet: -0.54 (0.55), residues: 75
  loop : -0.51 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1066 
 TYR   0.014   0.001   TYR A1381 
 PHE   0.022   0.001   PHE A 931 
 TRP   0.012   0.001   TRP A1145 
 HIS   0.002   0.001   HIS A 199 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.11 ( 9872)
  covalent geometry    : angle       0.51002 /  0.25 (13348)
  hydrogen bonds       : bond        0.03844 /  2.51 (  554)
  hydrogen bonds       : angle       3.72282 /  2.66 ( 1641)

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8374 (tp)
REVERT: A  190 LYS cc_start: 0.8776 (ttpt) cc_final: 0.7909 (mttt)
REVERT: A  265 MET cc_start: 0.8361 (tmm) cc_final: 0.8076 (tmm)
REVERT: A  503 LYS cc_start: 0.8300 (ttpt) cc_final: 0.7910 (ttmm)
REVERT: A  629 THR cc_start: 0.7894 (m) cc_final: 0.7482 (p)
REVERT: A 1042 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7987 (tp40)
REVERT: A 1101 MET cc_start: 0.8232 (tpp) cc_final: 0.7753 (ttm)
REVERT: A 1103 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9158 (tp)
REVERT: A 1213 LYS cc_start: 0.8029 (mttt) cc_final: 0.7281 (tptt)
REVERT: A 1377 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7147 (p0)
REVERT: A 1439 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6533 (pp30)
  outliers start: 29
  outliers final: 24
  residues processed: 146
  average time/residue: 0.0772
  time to fit residues: 16.9821
Evaluate side-chains
  149 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1042 GLN
Chi-restraints excluded: chain A residue 1045 SER
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain A residue 1114 VAL
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1215 LEU
Chi-restraints excluded: chain A residue 1261 LEU
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1377 ASP
Chi-restraints excluded: chain A residue 1410 CYS
Chi-restraints excluded: chain A residue 1435 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 117 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 GLN
A1054 HIS
A1209 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.135392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.118599 restraints weight = 14636.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.121855 restraints weight = 7820.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.124153 restraints weight = 4594.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.125313 restraints weight = 3045.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.125796 restraints weight = 2442.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9872  Z= 0.151
  Angle     :  0.563  11.342  13348  Z= 0.281
  Chirality :  0.042   0.244   1536
  Planarity :  0.003   0.032   1608
  Dihedral  :  6.128  82.588   1416
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.33 %
    Favored  : 79.90 %
  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:  1.01 (0.25), residues: 1163
  helix:  1.38 (0.19), residues: 763
  sheet: -0.33 (0.59), residues: 63
  loop : -0.67 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1066 
 TYR   0.014   0.001   TYR A1381 
 PHE   0.024   0.002   PHE A 931 
 TRP   0.011   0.001   TRP A 865 
 HIS   0.002   0.001   HIS A 484 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 ( 9872)
  covalent geometry    : angle       0.56349 /  0.28 (13348)
  hydrogen bonds       : bond        0.04275 /  2.80 (  554)
  hydrogen bonds       : angle       3.83542 /  2.74 ( 1641)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1357.79 seconds
wall clock time: 24 minutes 15.01 seconds (1455.01 seconds total)