Starting phenix.real_space_refine
on Wed Jul 30 07:02:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bly_7113/07_2025/6bly_7113.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bly_7113/07_2025/6bly_7113.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bly_7113/07_2025/6bly_7113.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bly_7113/07_2025/6bly_7113.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bly_7113/07_2025/6bly_7113.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bly_7113/07_2025/6bly_7113.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      74      5.16       5
     C    7853      2.51       5
     N    2132      2.21       5
     O    2204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12263
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1177, 9337
          Classifications: {'peptide': 1177}
          Link IDs: {'PTRANS': 66, 'TRANS': 1110}
          Chain breaks: 12
    Chain: "B"
      Number of atoms: 2926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2926
          Classifications: {'peptide': 363}
          Link IDs: {'PTRANS': 15, 'TRANS': 347}
  Time building chain proxies: 7.42, per 1000 atoms: 0.61
  Number of scatterers: 12263
  At special positions: 0
  Unit cell: (88.81, 136.96, 102.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      74     16.00
     O    2204      8.00
     N    2132      7.00
     C    7853      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: 3.52
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2884

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 35 sheets defined
      6.4% alpha, 35.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 487 through 491
      removed outlier: 3.747A  pdb=" N   GLN A 491 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 509
    Processing helix  chain 'A' and resid 1154 through 1156
      No H-bonds generated for 'chain 'A' and resid 1154 through 1156'
    Processing helix  chain 'A' and resid 1352 through 1369
      removed outlier: 3.863A  pdb=" N   ARG A1358 " --> pdb=" O   LYS A1354 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A1359 " --> pdb=" O   THR A1355 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   MET A1361 " --> pdb=" O   ARG A1357 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A1362 " --> pdb=" O   ARG A1358 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA A1365 " --> pdb=" O   MET A1361 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR A1368 " --> pdb=" O   ASN A1364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1372 through 1376
      removed outlier: 3.518A  pdb=" N   GLY A1375 " --> pdb=" O   HIS A1372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1382
      removed outlier: 3.677A  pdb=" N   ARG A1382 " --> pdb=" O   PRO A1378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1403 through 1408
      removed outlier: 3.529A  pdb=" N   LEU A1408 " --> pdb=" O   ASN A1405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1423
      removed outlier: 3.588A  pdb=" N   SER A1416 " --> pdb=" O   THR A1412 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU A1418 " --> pdb=" O   GLU A1414 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA A1419 " --> pdb=" O   ARG A1415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1425 through 1439
      removed outlier: 3.577A  pdb=" N   ILE A1429 " --> pdb=" O   THR A1425 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP A1431 " --> pdb=" O   ASP A1427 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLU A1435 " --> pdb=" O   ASP A1431 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   THR A1436 " --> pdb=" O   ASP A1432 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP A1437 " --> pdb=" O   LEU A1433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 70
      removed outlier: 3.734A  pdb=" N   LYS B  65 " --> pdb=" O   PRO B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
      removed outlier: 3.835A  pdb=" N   LEU B  92 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 106
      removed outlier: 3.607A  pdb=" N   ASN B 104 " --> pdb=" O   ASN B 101 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL B 106 " --> pdb=" O   MET B 103 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1312 through 1314
      removed outlier: 6.187A  pdb=" N   ILE A1345 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20
      removed outlier: 3.888A  pdb=" N   GLN A  37 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LEU A  38 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   SER A  71 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   VAL A  40 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84
      removed outlier: 3.637A  pdb=" N   ALA A  93 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS A 102 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU A 103 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   LEU A 120 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL A 105 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143
      removed outlier: 3.602A  pdb=" N   ARG A 140 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR A 189 " --> pdb=" O   VAL A 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 208
      removed outlier: 5.392A  pdb=" N   ILE A 203 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   GLU A 222 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASP A 205 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   CYS A 238 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER A 260 " --> pdb=" O   CYS A 238 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA A 242 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   TRP A 256 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   SER A 244 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   VAL A 254 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270
      removed outlier: 4.644A  pdb=" N   GLN A 267 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A 285 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   GLY A 297 " --> pdb=" O   ARG A 313 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329
      removed outlier: 6.880A  pdb=" N   THR A 348 " --> pdb=" O   PHE A 360 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   PHE A 360 " --> pdb=" O   THR A 348 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   ILE A 350 " --> pdb=" O   ARG A 358 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 329
      removed outlier: 4.666A  pdb=" N   ILE A 344 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 376
      removed outlier: 3.641A  pdb=" N   LEU A 392 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481
    Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 526
      removed outlier: 5.368A  pdb=" N   VAL A 523 " --> pdb=" O   VAL A1000 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   VAL A1000 " --> pdb=" O   VAL A 523 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR A 525 " --> pdb=" O   ILE A 998 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR A 989 " --> pdb=" O   ARG A 997 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539
      removed outlier: 3.666A  pdb=" N   ASP A 534 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER A 578 " --> pdb=" O   ASP A 534 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 612
      removed outlier: 3.539A  pdb=" N   PHE A 608 " --> pdb=" O   VAL A 621 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 651
      removed outlier: 7.583A  pdb=" N   MET A 659 " --> pdb=" O   VAL A 647 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   CYS A 649 " --> pdb=" O   VAL A 657 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL A 657 " --> pdb=" O   CYS A 649 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 670 through 671
    Processing sheet with id=AB7, first strand: chain 'A' and resid 695 through 702
      removed outlier: 3.620A  pdb=" N   THR A 697 " --> pdb=" O   VAL A 788 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   MET A 794 " --> pdb=" O   LEU A 807 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LEU A 807 " --> pdb=" O   MET A 794 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE A 796 " --> pdb=" O   VAL A 805 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 846 through 854
      removed outlier: 6.529A  pdb=" N   HIS A 866 " --> pdb=" O   LYS A 847 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL A 849 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU A 864 " --> pdb=" O   VAL A 849 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   LEU A 851 " --> pdb=" O   TYR A 862 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   TYR A 862 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   ALA A 853 " --> pdb=" O   ARG A 860 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ARG A 860 " --> pdb=" O   ALA A 853 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU A 872 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   ILE A 873 " --> pdb=" O   VAL A 895 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 877 through 878
    Processing sheet with id=AC1, first strand: chain 'A' and resid 931 through 937
      removed outlier: 5.645A  pdb=" N   TYR A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   SER A 941 " --> pdb=" O   VAL A 955 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 955 " --> pdb=" O   SER A 941 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1021 through 1024
      removed outlier: 6.598A  pdb=" N   ALA A1037 " --> pdb=" O   HIS A1023 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1027 through 1028
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1046 through 1050
      removed outlier: 3.544A  pdb=" N   GLU A1056 " --> pdb=" O   ARG A1049 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1098 through 1106
      removed outlier: 6.627A  pdb=" N   GLY A1124 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   MET A1103 " --> pdb=" O   ALA A1122 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ALA A1122 " --> pdb=" O   MET A1103 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   THR A1105 " --> pdb=" O   TYR A1120 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   TYR A1120 " --> pdb=" O   THR A1105 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   GLY A1137 " --> pdb=" O   GLU A1167 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU A1167 " --> pdb=" O   GLY A1137 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE A1139 " --> pdb=" O   GLU A1165 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLU A1165 " --> pdb=" O   ILE A1139 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ILE A1141 " --> pdb=" O   LEU A1163 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1172 through 1177
      removed outlier: 4.104A  pdb=" N   ALA A1174 " --> pdb=" O   ALA A1185 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LEU A1192 " --> pdb=" O   MET A1203 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1212 through 1217
      removed outlier: 3.630A  pdb=" N   GLN A1214 " --> pdb=" O   ALA A1225 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 1232 through 1237
      removed outlier: 7.106A  pdb=" N   LEU A1233 " --> pdb=" O   VAL A1246 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   THR A1242 " --> pdb=" O   GLN A1237 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 1255 through 1258
      removed outlier: 6.802A  pdb=" N   SER A1272 " --> pdb=" O   TYR A1256 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A1258 " --> pdb=" O   LEU A1270 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LEU A1270 " --> pdb=" O   VAL A1258 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'A' and resid 1255 through 1258
      removed outlier: 6.802A  pdb=" N   SER A1272 " --> pdb=" O   TYR A1256 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A1258 " --> pdb=" O   LEU A1270 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LEU A1270 " --> pdb=" O   VAL A1258 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   LEU A1278 " --> pdb=" O   ASP A1301 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   ASP A1301 " --> pdb=" O   LEU A1278 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   VAL A1280 " --> pdb=" O   ARG A1299 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A1297 " --> pdb=" O   MET A1282 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 113
      removed outlier: 6.656A  pdb=" N   PHE B 401 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   THR B 113 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   SER B 399 " --> pdb=" O   THR B 113 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   ILE B 389 " --> pdb=" O   TRP B 383 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   TRP B 383 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   CYS B 391 " --> pdb=" O   LEU B 381 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LEU B 381 " --> pdb=" O   CYS B 391 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   GLY B 393 " --> pdb=" O   TRP B 379 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 122 through 127
      removed outlier: 3.575A  pdb=" N   ARG B 126 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL B 135 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 164 through 169
      removed outlier: 4.072A  pdb=" N   ALA B 166 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   TYR B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR B 187 " --> pdb=" O   LYS B 196 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   LYS B 196 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   GLN B 189 " --> pdb=" O   ASN B 194 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASN B 194 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 205 through 210
      removed outlier: 6.895A  pdb=" N   CYS B 220 " --> pdb=" O   ARG B 206 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ALA B 208 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   PHE B 210 " --> pdb=" O   LYS B 216 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   LYS B 216 " --> pdb=" O   PHE B 210 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL B 226 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   ILE B 239 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ILE B 228 " --> pdb=" O   GLU B 237 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 250 through 252
    Processing sheet with id=AD7, first strand: chain 'B' and resid 291 through 296
    Processing sheet with id=AD8, first strand: chain 'B' and resid 334 through 339
      removed outlier: 3.929A  pdb=" N   ALA B 336 " --> pdb=" O   GLY B 350 " (cutoff:3.500A)

    335 hydrogen bonds defined for protein.
    888 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: 7.93

  Time building geometry restraints manager: 3.58 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3252
        1.33 -     1.45: 2273
        1.45 -     1.57: 6918
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 12563
  Sorted by residual:
  bond pdb=" C   PHE A 811 "
       pdb=" N   PRO A 812 "
    ideal  model  delta    sigma   weight residual
    1.337  1.384 -0.047 9.80e-03 1.04e+04 2.32e+01
  bond pdb=" CA  LEU A 201 "
       pdb=" C   LEU A 201 "
    ideal  model  delta    sigma   weight residual
    1.528  1.505  0.023 8.80e-03 1.29e+04 6.63e+00
  bond pdb=" C   ILE A 873 "
       pdb=" O   ILE A 873 "
    ideal  model  delta    sigma   weight residual
    1.235  1.211  0.024 1.05e-02 9.07e+03 5.24e+00
  bond pdb=" C   LEU B 346 "
       pdb=" O   LEU B 346 "
    ideal  model  delta    sigma   weight residual
    1.236  1.210  0.026 1.20e-02 6.94e+03 4.65e+00
  bond pdb=" C   ALA A 242 "
       pdb=" N   ILE A 243 "
    ideal  model  delta    sigma   weight residual
    1.333  1.308  0.025 1.20e-02 6.94e+03 4.41e+00
  ... (remaining 12558 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 16427
        2.44 -     4.87: 540
        4.87 -     7.31: 60
        7.31 -     9.75: 17
        9.75 -    12.19: 3
  Bond angle restraints: 17047
  Sorted by residual:
  angle pdb=" C   ASP A 653 "
        pdb=" N   PRO A 654 "
        pdb=" CA  PRO A 654 "
      ideal   model   delta    sigma   weight residual
     119.84  131.80  -11.96 1.25e+00 6.40e-01 9.15e+01
  angle pdb=" N   PHE B 210 "
        pdb=" CA  PHE B 210 "
        pdb=" C   PHE B 210 "
      ideal   model   delta    sigma   weight residual
     108.45  115.91   -7.46 1.26e+00 6.30e-01 3.50e+01
  angle pdb=" C   PRO A 272 "
        pdb=" N   LYS A 273 "
        pdb=" CA  LYS A 273 "
      ideal   model   delta    sigma   weight residual
     120.58  128.05   -7.47 1.32e+00 5.74e-01 3.20e+01
  angle pdb=" CA  PHE B 151 "
        pdb=" C   PHE B 151 "
        pdb=" O   PHE B 151 "
      ideal   model   delta    sigma   weight residual
     120.51  113.17    7.34 1.43e+00 4.89e-01 2.64e+01
  angle pdb=" C   LEU A 201 "
        pdb=" CA  LEU A 201 "
        pdb=" CB  LEU A 201 "
      ideal   model   delta    sigma   weight residual
     116.63  111.05    5.58 1.16e+00 7.43e-01 2.31e+01
  ... (remaining 17042 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.79: 7030
       14.79 -    29.58: 376
       29.58 -    44.37: 57
       44.37 -    59.16: 8
       59.16 -    73.95: 7
  Dihedral angle restraints: 7478
    sinusoidal: 3016
      harmonic: 4462
  Sorted by residual:
  dihedral pdb=" C   ASP A 333 "
           pdb=" N   ASP A 333 "
           pdb=" CA  ASP A 333 "
           pdb=" CB  ASP A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.32   14.72     0      2.50e+00 1.60e-01 3.47e+01
  dihedral pdb=" CA  GLY A 211 "
           pdb=" C   GLY A 211 "
           pdb=" N   TYR A 212 "
           pdb=" CA  TYR A 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.32   28.68     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" CA  ASN B 289 "
           pdb=" C   ASN B 289 "
           pdb=" N   THR B 290 "
           pdb=" CA  THR B 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.70   28.30     0      5.00e+00 4.00e-02 3.20e+01
  ... (remaining 7475 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1771
       0.112 -    0.225: 130
       0.225 -    0.337: 2
       0.337 -    0.450: 0
       0.450 -    0.562: 1
  Chirality restraints: 1904
  Sorted by residual:
  chirality pdb=" CA  ASP A 333 "
            pdb=" N   ASP A 333 "
            pdb=" C   ASP A 333 "
            pdb=" CB  ASP A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.89e+00
  chirality pdb=" CA  LEU A 200 "
            pdb=" N   LEU A 200 "
            pdb=" C   LEU A 200 "
            pdb=" CB  LEU A 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CB  ILE A 243 "
            pdb=" CA  ILE A 243 "
            pdb=" CG1 ILE A 243 "
            pdb=" CG2 ILE A 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 1901 not shown)

  Planarity restraints: 2172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1312 "    0.043 2.00e-02 2.50e+03   2.39e-02 1.42e+01
        pdb=" CG  TRP A1312 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1312 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1312 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1312 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1312 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1312 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1312 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1312 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1312 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 653 "    0.060 5.00e-02 4.00e+02   8.91e-02 1.27e+01
        pdb=" N   PRO A 654 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A 654 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 654 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1074 "    0.016 2.00e-02 2.50e+03   2.38e-02 9.93e+00
        pdb=" CG  PHE A1074 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1074 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1074 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1074 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1074 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1074 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2169 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1710
        2.76 -     3.29: 10398
        3.29 -     3.83: 19956
        3.83 -     4.36: 23703
        4.36 -     4.90: 42357
  Nonbonded interactions: 98124
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 331 "
            pdb=" N   TYR A 332 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OG  SER A  17 "
            pdb=" OG  SER A 373 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER B 221 "
            pdb=" OD1 ASP B 223 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   GLY A 276 "
            pdb=" OH  TYR A 288 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG1 THR A 583 "
            pdb=" O   GLY A 604 "
     model   vdw
     2.309 3.040
  ... (remaining 98119 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             47.370
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     36.160
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.080
  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:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   87.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
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      :  0.008   0.072  12563  Z= 0.362
  Angle     :  1.040  12.185  17047  Z= 0.582
  Chirality :  0.061   0.562   1904
  Planarity :  0.008   0.089   2172
  Dihedral  :  9.963  73.946   4594
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.66 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  1.49 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (0.18), residues: 1512
  helix: -4.44 (0.26), residues: 80
  sheet: -2.21 (0.19), residues: 603
  loop : -2.84 (0.18), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.004   TRP A1312 
 HIS   0.012   0.003   HIS A   9 
 PHE   0.051   0.005   PHE A1074 
 TYR   0.040   0.004   TYR A   2 
 ARG   0.010   0.001   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24356 (  326)
  hydrogen bonds       : angle       9.90677 (  888)
  covalent geometry    : bond        0.00838 (12563)
  covalent geometry    : angle       1.04050 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 343
  time to evaluate  : 1.440 
Fit side-chains
REVERT: A  320 ILE cc_start: 0.7879 (pp) cc_final: 0.7512 (pt)
REVERT: A 1208 THR cc_start: 0.7905 (t) cc_final: 0.7654 (p)
REVERT: B  176 MET cc_start: 0.8663 (ttp) cc_final: 0.8387 (ttm)
  outliers start: 12
  outliers final: 7
  residues processed: 353
  average time/residue: 0.3280
  time to fit residues: 156.7196
Evaluate side-chains
  166 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  873 ILE
Chi-restraints excluded: chain A residue 1176 CYS
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain B residue  346 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 129 optimal weight:    5.9990
   chunk 115 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 119 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 ASN
** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 680 HIS
A 783 HIS
** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1089 ASN
A1095 GLN
B  69 ASN
B 325 GLN
B 343 HIS
B 405 ASN
B 416 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.127598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.107926 restraints weight = 17426.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.12
r_work: 0.3125 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  12563  Z= 0.180
  Angle     :  0.685   8.680  17047  Z= 0.357
  Chirality :  0.048   0.218   1904
  Planarity :  0.006   0.098   2172
  Dihedral  :  6.733  53.729   1682
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.01 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  8.10 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.19), residues: 1512
  helix: -3.10 (0.44), residues: 79
  sheet: -1.66 (0.19), residues: 614
  loop : -2.50 (0.19), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1312 
 HIS   0.005   0.001   HIS A   9 
 PHE   0.027   0.002   PHE B 210 
 TYR   0.020   0.002   TYR A   2 
 ARG   0.006   0.001   ARG A1274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  326)
  hydrogen bonds       : angle       6.68569 (  888)
  covalent geometry    : bond        0.00431 (12563)
  covalent geometry    : angle       0.68459 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.9102 (ptp) cc_final: 0.8861 (ptt)
REVERT: A  320 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8187 (pt)
REVERT: A  857 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7800 (mmm-85)
REVERT: A 1032 LYS cc_start: 0.9152 (mttt) cc_final: 0.8874 (mtmm)
REVERT: A 1208 THR cc_start: 0.8578 (t) cc_final: 0.8129 (p)
REVERT: A 1291 PHE cc_start: 0.7139 (m-10) cc_final: 0.6934 (m-10)
REVERT: A 1393 ASN cc_start: 0.6711 (t0) cc_final: 0.6459 (t0)
REVERT: A 1431 ASP cc_start: 0.9014 (t0) cc_final: 0.8758 (t0)
REVERT: B   75 ASP cc_start: 0.7595 (m-30) cc_final: 0.7216 (m-30)
REVERT: B  142 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B  207 GLU cc_start: 0.7736 (tp30) cc_final: 0.7519 (tp30)
REVERT: B  229 TRP cc_start: 0.8659 (m100) cc_final: 0.8355 (m100)
  outliers start: 33
  outliers final: 16
  residues processed: 210
  average time/residue: 0.2736
  time to fit residues: 84.0003
Evaluate side-chains
  179 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1176 CYS
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 72 optimal weight:    0.1980
   chunk 46 optimal weight:    9.9990
   chunk 83 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 14 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 151 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 636 HIS
B 310 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 = 0.129562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.109797 restraints weight = 17465.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.14
r_work: 0.3148 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  12563  Z= 0.128
  Angle     :  0.597   7.704  17047  Z= 0.310
  Chirality :  0.046   0.209   1904
  Planarity :  0.005   0.102   2172
  Dihedral  :  5.797  44.145   1674
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.61 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 10.33 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.20), residues: 1512
  helix: -2.09 (0.51), residues: 79
  sheet: -1.17 (0.20), residues: 619
  loop : -2.27 (0.20), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1337 
 HIS   0.004   0.001   HIS A1372 
 PHE   0.014   0.002   PHE B 217 
 TYR   0.016   0.001   TYR A   2 
 ARG   0.004   0.000   ARG A 313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03599 (  326)
  hydrogen bonds       : angle       5.97788 (  888)
  covalent geometry    : bond        0.00306 (12563)
  covalent geometry    : angle       0.59748 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 191
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 TRP cc_start: 0.8606 (t60) cc_final: 0.8195 (t60)
REVERT: A  340 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8199 (pttt)
REVERT: A  671 LYS cc_start: 0.6428 (ptmm) cc_final: 0.6168 (ptmm)
REVERT: A  857 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7889 (mmm-85)
REVERT: A 1032 LYS cc_start: 0.9189 (mttt) cc_final: 0.8955 (mttp)
REVERT: A 1208 THR cc_start: 0.8403 (t) cc_final: 0.7939 (m)
REVERT: A 1233 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8930 (tp)
REVERT: A 1273 ASP cc_start: 0.8663 (p0) cc_final: 0.8438 (p0)
REVERT: A 1393 ASN cc_start: 0.7039 (t0) cc_final: 0.6559 (t0)
REVERT: A 1414 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7936 (mt-10)
REVERT: B   75 ASP cc_start: 0.7515 (m-30) cc_final: 0.7160 (m-30)
REVERT: B  142 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8104 (mt-10)
  outliers start: 35
  outliers final: 18
  residues processed: 209
  average time/residue: 0.2433
  time to fit residues: 76.2830
Evaluate side-chains
  191 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 1.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 121 optimal weight:    0.0770
   chunk 138 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0870
   chunk 23 optimal weight:    0.4980
   chunk 89 optimal weight:    4.9990
   chunk 114 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.131051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111350 restraints weight = 17273.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.13
r_work: 0.3170 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  12563  Z= 0.106
  Angle     :  0.564   6.988  17047  Z= 0.292
  Chirality :  0.045   0.260   1904
  Planarity :  0.005   0.104   2172
  Dihedral  :  5.398  48.995   1673
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.95 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.52 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.20), residues: 1512
  helix: -1.28 (0.58), residues: 79
  sheet: -0.94 (0.20), residues: 623
  loop : -2.08 (0.20), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1337 
 HIS   0.005   0.001   HIS A1385 
 PHE   0.011   0.001   PHE A 987 
 TYR   0.011   0.001   TYR A   2 
 ARG   0.007   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03073 (  326)
  hydrogen bonds       : angle       5.63008 (  888)
  covalent geometry    : bond        0.00251 (12563)
  covalent geometry    : angle       0.56412 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 195
  time to evaluate  : 2.132 
Fit side-chains
REVERT: A  256 TRP cc_start: 0.8481 (t60) cc_final: 0.8030 (t60)
REVERT: A  364 LYS cc_start: 0.8229 (tttp) cc_final: 0.8026 (tttp)
REVERT: A  392 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8830 (pp)
REVERT: A  857 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7849 (mmm-85)
REVERT: A 1208 THR cc_start: 0.8385 (t) cc_final: 0.7987 (m)
REVERT: A 1221 PHE cc_start: 0.8278 (m-80) cc_final: 0.7998 (m-80)
REVERT: A 1273 ASP cc_start: 0.8701 (p0) cc_final: 0.8467 (p0)
REVERT: A 1336 THR cc_start: 0.7676 (p) cc_final: 0.7466 (p)
REVERT: A 1393 ASN cc_start: 0.7109 (t0) cc_final: 0.6704 (t0)
REVERT: A 1414 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7943 (mt-10)
REVERT: B   75 ASP cc_start: 0.7398 (m-30) cc_final: 0.7070 (m-30)
REVERT: B  142 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8050 (mt-10)
REVERT: B  372 MET cc_start: 0.7318 (tmm) cc_final: 0.7067 (tmm)
  outliers start: 34
  outliers final: 19
  residues processed: 216
  average time/residue: 0.2507
  time to fit residues: 81.6140
Evaluate side-chains
  190 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  973 ASP
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 129 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 86 optimal weight:   10.0000
   chunk 111 optimal weight:    7.9990
   chunk 74 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 139 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 858 GLN
A1099 HIS
B  60 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.118162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.098030 restraints weight = 17879.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.16
r_work: 0.2980 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.091  12563  Z= 0.394
  Angle     :  0.835   9.779  17047  Z= 0.424
  Chirality :  0.054   0.280   1904
  Planarity :  0.007   0.111   2172
  Dihedral  :  6.231  34.938   1671
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.13 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 12.19 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.20), residues: 1512
  helix: -1.42 (0.57), residues: 79
  sheet: -1.12 (0.20), residues: 638
  loop : -2.02 (0.21), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A1312 
 HIS   0.012   0.002   HIS A   9 
 PHE   0.034   0.003   PHE A 892 
 TYR   0.031   0.003   TYR A 345 
 ARG   0.008   0.001   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04241 (  326)
  hydrogen bonds       : angle       6.05632 (  888)
  covalent geometry    : bond        0.00947 (12563)
  covalent geometry    : angle       0.83478 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 152
  time to evaluate  : 1.583 
Fit side-chains
REVERT: A  320 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8510 (pp)
REVERT: A  364 LYS cc_start: 0.8675 (tttp) cc_final: 0.8406 (ttmp)
REVERT: A  392 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9035 (pp)
REVERT: A  635 LEU cc_start: 0.8534 (tp) cc_final: 0.8085 (tt)
REVERT: A  667 MET cc_start: 0.8134 (ttp) cc_final: 0.7927 (ttp)
REVERT: A  857 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.8091 (mmm-85)
REVERT: A 1208 THR cc_start: 0.8391 (t) cc_final: 0.8161 (m)
REVERT: A 1230 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7812 (m)
REVERT: A 1393 ASN cc_start: 0.6826 (t0) cc_final: 0.6440 (t0)
REVERT: B  142 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8105 (mt-10)
REVERT: B  210 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.5967 (p90)
REVERT: B  371 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7764 (mm-30)
  outliers start: 51
  outliers final: 34
  residues processed: 197
  average time/residue: 0.3046
  time to fit residues: 90.1586
Evaluate side-chains
  178 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLN
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1230 SER
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1247 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  154 GLU
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  410 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 140 optimal weight:    6.9990
   chunk 130 optimal weight:    1.9990
   chunk 134 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.124228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.104081 restraints weight = 17754.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.17
r_work: 0.3074 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  12563  Z= 0.141
  Angle     :  0.609   8.615  17047  Z= 0.313
  Chirality :  0.046   0.245   1904
  Planarity :  0.005   0.115   2172
  Dihedral  :  5.669  41.051   1671
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.69 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.23 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.21), residues: 1512
  helix: -0.87 (0.60), residues: 79
  sheet: -0.92 (0.20), residues: 633
  loop : -1.94 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1337 
 HIS   0.007   0.001   HIS A1372 
 PHE   0.013   0.002   PHE A 975 
 TYR   0.015   0.001   TYR A 989 
 ARG   0.004   0.000   ARG A 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03225 (  326)
  hydrogen bonds       : angle       5.72224 (  888)
  covalent geometry    : bond        0.00341 (12563)
  covalent geometry    : angle       0.60868 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 160
  time to evaluate  : 1.822 
Fit side-chains
REVERT: A  256 TRP cc_start: 0.8439 (t60) cc_final: 0.8129 (t60)
REVERT: A  364 LYS cc_start: 0.8579 (tttp) cc_final: 0.8305 (ttmp)
REVERT: A  857 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.8032 (mmm-85)
REVERT: A 1008 ASP cc_start: 0.8526 (t0) cc_final: 0.8259 (t0)
REVERT: A 1092 ILE cc_start: 0.9217 (mm) cc_final: 0.9007 (mm)
REVERT: A 1230 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7739 (m)
REVERT: A 1291 PHE cc_start: 0.7294 (m-10) cc_final: 0.7093 (m-10)
REVERT: A 1393 ASN cc_start: 0.6655 (t0) cc_final: 0.5712 (p0)
REVERT: A 1414 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: B   75 ASP cc_start: 0.7514 (m-30) cc_final: 0.7128 (m-30)
REVERT: B  142 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: B  371 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7346 (mm-30)
  outliers start: 30
  outliers final: 24
  residues processed: 181
  average time/residue: 0.3042
  time to fit residues: 82.8827
Evaluate side-chains
  177 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 1.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1230 SER
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9980
   chunk 127 optimal weight:   10.0000
   chunk 130 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 142 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.122213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.102161 restraints weight = 17671.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.16
r_work: 0.3041 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  12563  Z= 0.206
  Angle     :  0.646   8.673  17047  Z= 0.330
  Chirality :  0.047   0.309   1904
  Planarity :  0.005   0.116   2172
  Dihedral  :  5.707  52.268   1671
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.74 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.38 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.21), residues: 1512
  helix: -0.72 (0.61), residues: 79
  sheet: -0.85 (0.20), residues: 631
  loop : -1.90 (0.21), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1312 
 HIS   0.007   0.001   HIS A1372 
 PHE   0.016   0.002   PHE A 892 
 TYR   0.022   0.002   TYR A 989 
 ARG   0.004   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03349 (  326)
  hydrogen bonds       : angle       5.69060 (  888)
  covalent geometry    : bond        0.00501 (12563)
  covalent geometry    : angle       0.64561 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
REVERT: A  162 LEU cc_start: 0.9039 (mp) cc_final: 0.8335 (tp)
REVERT: A  592 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7547 (mt)
REVERT: A  857 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.8070 (mmm-85)
REVERT: A 1008 ASP cc_start: 0.8552 (t0) cc_final: 0.8289 (t0)
REVERT: A 1092 ILE cc_start: 0.9235 (mm) cc_final: 0.9014 (mm)
REVERT: A 1230 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7773 (m)
REVERT: A 1273 ASP cc_start: 0.8726 (p0) cc_final: 0.8496 (p0)
REVERT: A 1393 ASN cc_start: 0.6749 (t0) cc_final: 0.5748 (p0)
REVERT: A 1414 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8230 (mt-10)
REVERT: A 1434 LEU cc_start: 0.9335 (mt) cc_final: 0.9084 (mp)
REVERT: B   75 ASP cc_start: 0.7633 (m-30) cc_final: 0.7236 (m-30)
REVERT: B  142 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8045 (mt-10)
  outliers start: 38
  outliers final: 31
  residues processed: 176
  average time/residue: 0.2260
  time to fit residues: 60.6650
Evaluate side-chains
  178 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1128 MET
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1230 SER
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  255 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 122 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0370
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 127 optimal weight:   10.0000
   overall best weight:    2.2066

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 297 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.122898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.102750 restraints weight = 17791.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.18
r_work: 0.3057 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  12563  Z= 0.181
  Angle     :  0.627   8.462  17047  Z= 0.321
  Chirality :  0.047   0.292   1904
  Planarity :  0.005   0.119   2172
  Dihedral  :  5.612  48.670   1671
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.61 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.38 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.21), residues: 1512
  helix: -0.60 (0.62), residues: 79
  sheet: -0.77 (0.20), residues: 630
  loop : -1.85 (0.21), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1312 
 HIS   0.006   0.001   HIS A1372 
 PHE   0.015   0.002   PHE B 198 
 TYR   0.023   0.001   TYR A 989 
 ARG   0.004   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (  326)
  hydrogen bonds       : angle       5.63246 (  888)
  covalent geometry    : bond        0.00442 (12563)
  covalent geometry    : angle       0.62653 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 151
  time to evaluate  : 1.401 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.9076 (mp) cc_final: 0.8425 (tp)
REVERT: A  252 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8078 (p-80)
REVERT: A  592 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7538 (mt)
REVERT: A  857 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8072 (mmm-85)
REVERT: A 1008 ASP cc_start: 0.8563 (t0) cc_final: 0.8289 (t0)
REVERT: A 1092 ILE cc_start: 0.9280 (mm) cc_final: 0.9059 (mm)
REVERT: A 1230 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7714 (m)
REVERT: A 1273 ASP cc_start: 0.8764 (p0) cc_final: 0.8503 (p0)
REVERT: A 1393 ASN cc_start: 0.6713 (t0) cc_final: 0.5740 (p0)
REVERT: A 1414 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8209 (mt-10)
REVERT: A 1434 LEU cc_start: 0.9312 (mt) cc_final: 0.9048 (mp)
REVERT: B   75 ASP cc_start: 0.7864 (m-30) cc_final: 0.7405 (m-30)
REVERT: B  142 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8037 (mt-10)
REVERT: B  229 TRP cc_start: 0.8694 (m100) cc_final: 0.8396 (m100)
  outliers start: 42
  outliers final: 34
  residues processed: 182
  average time/residue: 0.2217
  time to fit residues: 61.6548
Evaluate side-chains
  182 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1128 MET
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1230 SER
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1316 CYS
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  297 ASN
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 125 optimal weight:    0.9990
   chunk 134 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 112 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 151 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 297 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.126326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.106298 restraints weight = 17464.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.17
r_work: 0.3110 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  12563  Z= 0.116
  Angle     :  0.574   7.455  17047  Z= 0.295
  Chirality :  0.046   0.327   1904
  Planarity :  0.005   0.118   2172
  Dihedral  :  5.178  28.955   1671
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.55 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.39 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.21), residues: 1512
  helix: -0.33 (0.63), residues: 79
  sheet: -0.52 (0.21), residues: 618
  loop : -1.80 (0.21), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1337 
 HIS   0.005   0.001   HIS A1385 
 PHE   0.013   0.001   PHE A 975 
 TYR   0.022   0.001   TYR A 989 
 ARG   0.002   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (  326)
  hydrogen bonds       : angle       5.46227 (  888)
  covalent geometry    : bond        0.00281 (12563)
  covalent geometry    : angle       0.57387 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 1.573 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.9078 (mp) cc_final: 0.8444 (tp)
REVERT: A  252 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8050 (p-80)
REVERT: A  857 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.8020 (mmm-85)
REVERT: A 1230 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7567 (m)
REVERT: A 1273 ASP cc_start: 0.8640 (p0) cc_final: 0.8408 (p0)
REVERT: A 1393 ASN cc_start: 0.6701 (t0) cc_final: 0.5766 (p0)
REVERT: A 1414 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8207 (mt-10)
REVERT: A 1434 LEU cc_start: 0.9300 (mt) cc_final: 0.9037 (mp)
REVERT: B   75 ASP cc_start: 0.7652 (m-30) cc_final: 0.7291 (m-30)
REVERT: B  142 GLU cc_start: 0.8210 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: B  198 PHE cc_start: 0.7838 (p90) cc_final: 0.7410 (p90)
  outliers start: 28
  outliers final: 23
  residues processed: 184
  average time/residue: 0.2286
  time to fit residues: 63.9566
Evaluate side-chains
  175 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1230 SER
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1316 CYS
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 151 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 147 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 133 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 113 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.122767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.102537 restraints weight = 17669.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.17
r_work: 0.3053 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  12563  Z= 0.206
  Angle     :  0.646   8.765  17047  Z= 0.330
  Chirality :  0.048   0.337   1904
  Planarity :  0.005   0.121   2172
  Dihedral  :  5.353  24.541   1669
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.21 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.61 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.21), residues: 1512
  helix: -0.35 (0.62), residues: 79
  sheet: -0.55 (0.21), residues: 624
  loop : -1.79 (0.21), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1312 
 HIS   0.007   0.001   HIS A1372 
 PHE   0.016   0.002   PHE A 892 
 TYR   0.027   0.002   TYR A 989 
 ARG   0.005   0.000   ARG A1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (  326)
  hydrogen bonds       : angle       5.55649 (  888)
  covalent geometry    : bond        0.00502 (12563)
  covalent geometry    : angle       0.64628 (17047)

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 1.638 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.9037 (mp) cc_final: 0.8355 (tp)
REVERT: A  592 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7513 (mt)
REVERT: A  857 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8104 (mmm-85)
REVERT: A 1230 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7745 (m)
REVERT: A 1273 ASP cc_start: 0.8768 (p0) cc_final: 0.8512 (p0)
REVERT: A 1393 ASN cc_start: 0.6498 (t0) cc_final: 0.5683 (p0)
REVERT: A 1414 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8221 (mt-10)
REVERT: A 1434 LEU cc_start: 0.9316 (mt) cc_final: 0.9050 (mp)
REVERT: B   75 ASP cc_start: 0.7738 (m-30) cc_final: 0.7297 (m-30)
REVERT: B  142 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8018 (mt-10)
REVERT: B  229 TRP cc_start: 0.8696 (m100) cc_final: 0.8457 (m100)
  outliers start: 30
  outliers final: 27
  residues processed: 167
  average time/residue: 0.2898
  time to fit residues: 74.0462
Evaluate side-chains
  173 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  693 SER
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1230 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1312 TRP
Chi-restraints excluded: chain A residue 1316 CYS
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  255 THR
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  372 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 151 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0980
   chunk 138 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.125988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.105807 restraints weight = 17479.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.17
r_work: 0.3102 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  12563  Z= 0.125
  Angle     :  0.581   8.157  17047  Z= 0.298
  Chirality :  0.046   0.329   1904
  Planarity :  0.005   0.121   2172
  Dihedral  :  5.098  22.966   1669
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.75 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.91 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.21), residues: 1512
  helix: -0.18 (0.63), residues: 79
  sheet: -0.38 (0.21), residues: 619
  loop : -1.77 (0.21), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1337 
 HIS   0.006   0.001   HIS A1385 
 PHE   0.012   0.001   PHE A 975 
 TYR   0.024   0.001   TYR A 989 
 ARG   0.004   0.000   ARG B 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02903 (  326)
  hydrogen bonds       : angle       5.43446 (  888)
  covalent geometry    : bond        0.00300 (12563)
  covalent geometry    : angle       0.58106 (17047)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6543.43 seconds
wall clock time: 118 minutes 20.74 seconds (7100.74 seconds total)