Starting phenix.real_space_refine
on Wed Jul 30 06:11:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bm0_7114/07_2025/6bm0_7114.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bm0_7114/07_2025/6bm0_7114.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bm0_7114/07_2025/6bm0_7114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bm0_7114/07_2025/6bm0_7114.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bm0_7114/07_2025/6bm0_7114.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bm0_7114/07_2025/6bm0_7114.cif"
  }
  resolution = 3.8
  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=   0.010
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    7841      2.51       5
     N    2127      2.21       5
     O    2202      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 12244
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1175, 9318
          Classifications: {'peptide': 1175}
          Link IDs: {'PTRANS': 66, 'TRANS': 1108}
          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: 7.22, per 1000 atoms: 0.59
  Number of scatterers: 12244
  At special positions: 0
  Unit cell: (88.81, 135.89, 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    2202      8.00
     N    2127      7.00
     C    7841      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: 2.51
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2880

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 36 sheets defined
      5.8% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 487 through 491
      removed outlier: 3.616A  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 1153 through 1156
    Processing helix  chain 'A' and resid 1352 through 1369
      removed outlier: 3.777A  pdb=" N   ARG A1358 " --> pdb=" O   LYS A1354 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A1359 " --> pdb=" O   THR A1355 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A1362 " --> pdb=" O   ARG A1358 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   THR A1368 " --> pdb=" O   ASN A1364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1372 through 1376
      removed outlier: 3.552A  pdb=" N   LEU A1376 " --> pdb=" O   HIS A1373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1382
    Processing helix  chain 'A' and resid 1403 through 1407
    Processing helix  chain 'A' and resid 1414 through 1423
      removed outlier: 3.897A  pdb=" N   LEU A1418 " --> pdb=" O   GLU A1414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1425 through 1440
      removed outlier: 4.010A  pdb=" N   ILE A1429 " --> pdb=" O   THR A1425 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU A1435 " --> pdb=" O   ASP A1431 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   THR A1436 " --> pdb=" O   ASP A1432 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A1440 " --> pdb=" O   THR A1436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 71
      removed outlier: 4.033A  pdb=" N   ILE B  71 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1349 through 1350
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9
      removed outlier: 6.209A  pdb=" N   ILE A1345 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 20
      removed outlier: 4.077A  pdb=" N   GLN A  37 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ARG A  42 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   LEU A  68 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASN A  44 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   LEU A  66 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 82
      removed outlier: 3.759A  pdb=" N   LYS A 102 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A 103 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   LEU A 120 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A 105 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 143
    Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 208
      removed outlier: 3.855A  pdb=" N   ASP A 205 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 270
      removed outlier: 4.296A  pdb=" N   GLN A 267 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   SER A 285 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   GLY A 297 " --> pdb=" O   ARG A 313 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 330
      removed outlier: 4.122A  pdb=" N   LYS A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   THR A 348 " --> pdb=" O   PHE A 360 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   PHE A 360 " --> pdb=" O   THR A 348 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ILE A 350 " --> pdb=" O   ARG A 358 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 326 through 330
      removed outlier: 4.122A  pdb=" N   LYS A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ILE A 344 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 375 through 377
      removed outlier: 3.555A  pdb=" N   LEU A 392 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 478 through 481
    Processing sheet with id=AB3, first strand: chain 'A' and resid 522 through 526
      removed outlier: 5.282A  pdb=" N   VAL A 523 " --> pdb=" O   VAL A1000 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL A1000 " --> pdb=" O   VAL A 523 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR A 525 " --> pdb=" O   ILE A 998 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TYR A 989 " --> pdb=" O   ARG A 997 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   SER A 974 " --> pdb=" O   PHE A 990 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 532 through 539
      removed outlier: 3.914A  pdb=" N   ASP A 534 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 608 through 612
      removed outlier: 3.682A  pdb=" N   PHE A 608 " --> pdb=" O   VAL A 621 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 646 through 650
      removed outlier: 3.616A  pdb=" N   GLN A 648 " --> pdb=" O   MET A 659 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 670 through 671
    Processing sheet with id=AB8, first strand: chain 'A' and resid 695 through 702
      removed outlier: 7.020A  pdb=" N   VAL A 788 " --> pdb=" O   ILE A 696 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LEU A 698 " --> pdb=" O   LEU A 786 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU A 786 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU A 700 " --> pdb=" O   TRP A 784 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   TRP A 784 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   MET A 794 " --> pdb=" O   LEU A 807 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   LEU A 807 " --> pdb=" O   MET A 794 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE A 796 " --> pdb=" O   VAL A 805 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 854
      removed outlier: 6.502A  pdb=" N   HIS A 866 " --> pdb=" O   LYS A 847 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   VAL A 849 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU A 864 " --> pdb=" O   VAL A 849 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   LEU A 851 " --> pdb=" O   TYR A 862 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   TYR A 862 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ALA A 853 " --> pdb=" O   ARG A 860 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ARG A 860 " --> pdb=" O   ALA A 853 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL A 865 " --> pdb=" O   LEU A 872 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU A 872 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 877 through 878
    Processing sheet with id=AC2, first strand: chain 'A' and resid 931 through 937
      removed outlier: 5.469A  pdb=" N   TYR A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1022 through 1028
      removed outlier: 3.669A  pdb=" N   TYR A1024 " --> pdb=" O   ALA A1037 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A1033 " --> pdb=" O   HIS A1028 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1041 through 1043
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1046 through 1050
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1098 through 1106
      removed outlier: 6.733A  pdb=" N   GLY A1124 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   MET A1103 " --> pdb=" O   ALA A1122 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ALA A1122 " --> pdb=" O   MET A1103 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   THR A1105 " --> pdb=" O   TYR A1120 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   TYR A1120 " --> pdb=" O   THR A1105 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   GLY A1137 " --> pdb=" O   GLU A1167 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   GLU A1167 " --> pdb=" O   GLY A1137 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ILE A1139 " --> pdb=" O   GLU A1165 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLU A1165 " --> pdb=" O   ILE A1139 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ILE A1141 " --> pdb=" O   LEU A1163 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1176 through 1178
      removed outlier: 6.956A  pdb=" N   LEU A1192 " --> pdb=" O   MET A1203 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   MET A1203 " --> pdb=" O   LEU A1192 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 1212 through 1217
      removed outlier: 3.662A  pdb=" N   GLN A1214 " --> pdb=" O   ALA A1225 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 1233 through 1237
      removed outlier: 7.228A  pdb=" N   LEU A1233 " --> pdb=" O   VAL A1246 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   THR A1242 " --> pdb=" O   GLN A1237 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'A' and resid 1257 through 1258
      removed outlier: 3.700A  pdb=" N   SER A1257 " --> pdb=" O   SER A1272 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 1257 through 1258
      removed outlier: 3.700A  pdb=" N   SER A1257 " --> pdb=" O   SER A1272 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   LEU A1278 " --> pdb=" O   ASP A1301 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ASP A1301 " --> pdb=" O   LEU A1278 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL A1280 " --> pdb=" O   ARG A1299 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 109 through 113
      removed outlier: 6.655A  pdb=" N   PHE B 401 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS B 400 " --> pdb=" O   SER B 392 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   ILE B 389 " --> pdb=" O   TRP B 383 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   TRP B 383 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   CYS B 391 " --> pdb=" O   LEU B 381 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   LEU B 381 " --> pdb=" O   CYS B 391 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLY B 393 " --> pdb=" O   TRP B 379 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 122 through 127
      removed outlier: 3.573A  pdb=" N   VAL B 124 " --> pdb=" O   GLY B 137 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 167 through 169
      removed outlier: 6.999A  pdb=" N   VAL B 185 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   MET B 197 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   TYR B 187 " --> pdb=" O   VAL B 195 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 205 through 210
      removed outlier: 7.064A  pdb=" N   CYS B 220 " --> pdb=" O   ARG B 206 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ALA B 208 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   PHE B 210 " --> pdb=" O   LYS B 216 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   LYS B 216 " --> pdb=" O   PHE B 210 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B 226 " --> pdb=" O   LEU B 240 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG B 238 " --> pdb=" O   ILE B 228 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ASP B 230 " --> pdb=" O   GLU B 236 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLU B 236 " --> pdb=" O   ASP B 230 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'B' and resid 250 through 252
      removed outlier: 3.510A  pdb=" N   ALA B 282 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'B' and resid 291 through 296
    Processing sheet with id=AD9, first strand: chain 'B' and resid 338 through 339
      removed outlier: 3.849A  pdb=" N   GLY B 368 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    834 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: 5.58

  Time building geometry restraints manager: 3.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3837
        1.33 -     1.45: 1951
        1.45 -     1.57: 6636
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 12544
  Sorted by residual:
  bond pdb=" CA  ASN B 101 "
       pdb=" C   ASN B 101 "
    ideal  model  delta    sigma   weight residual
    1.532  1.507  0.025 6.50e-03 2.37e+04 1.48e+01
  bond pdb=" CA  VAL B 106 "
       pdb=" C   VAL B 106 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.026 8.60e-03 1.35e+04 9.36e+00
  bond pdb=" CA  PRO B  95 "
       pdb=" C   PRO B  95 "
    ideal  model  delta    sigma   weight residual
    1.521  1.554 -0.033 1.25e-02 6.40e+03 7.13e+00
  bond pdb=" CA  ASN A 202 "
       pdb=" C   ASN A 202 "
    ideal  model  delta    sigma   weight residual
    1.522  1.491  0.030 1.20e-02 6.94e+03 6.38e+00
  bond pdb=" C   ASN B 101 "
       pdb=" O   ASN B 101 "
    ideal  model  delta    sigma   weight residual
    1.233  1.222  0.011 4.80e-03 4.34e+04 5.43e+00
  ... (remaining 12539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 16374
        2.47 -     4.93: 532
        4.93 -     7.40: 84
        7.40 -     9.86: 26
        9.86 -    12.33: 6
  Bond angle restraints: 17022
  Sorted by residual:
  angle pdb=" C   ASN B 101 "
        pdb=" N   PRO B 102 "
        pdb=" CA  PRO B 102 "
      ideal   model   delta    sigma   weight residual
     119.56  130.38  -10.82 1.02e+00 9.61e-01 1.13e+02
  angle pdb=" C   VAL B 106 "
        pdb=" CA  VAL B 106 "
        pdb=" CB  VAL B 106 "
      ideal   model   delta    sigma   weight residual
     113.22  102.63   10.59 1.12e+00 7.97e-01 8.94e+01
  angle pdb=" C   ASP A 653 "
        pdb=" N   PRO A 654 "
        pdb=" CA  PRO A 654 "
      ideal   model   delta    sigma   weight residual
     119.84  130.10  -10.26 1.25e+00 6.40e-01 6.74e+01
  angle pdb=" N   LEU A 624 "
        pdb=" CA  LEU A 624 "
        pdb=" C   LEU A 624 "
      ideal   model   delta    sigma   weight residual
     111.36  119.87   -8.51 1.09e+00 8.42e-01 6.09e+01
  angle pdb=" N   ALA A 232 "
        pdb=" CA  ALA A 232 "
        pdb=" C   ALA A 232 "
      ideal   model   delta    sigma   weight residual
     114.62  106.38    8.24 1.14e+00 7.69e-01 5.23e+01
  ... (remaining 17017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.37: 6929
       14.37 -    28.73: 408
       28.73 -    43.10: 93
       43.10 -    57.46: 27
       57.46 -    71.83: 8
  Dihedral angle restraints: 7465
    sinusoidal: 3009
      harmonic: 4456
  Sorted by residual:
  dihedral pdb=" C   HIS A1385 "
           pdb=" N   HIS A1385 "
           pdb=" CA  HIS A1385 "
           pdb=" CB  HIS A1385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.45   14.85     0      2.50e+00 1.60e-01 3.53e+01
  dihedral pdb=" CA  SER A1272 "
           pdb=" C   SER A1272 "
           pdb=" N   ASP A1273 "
           pdb=" CA  ASP A1273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.36  -29.64     0      5.00e+00 4.00e-02 3.51e+01
  dihedral pdb=" N   HIS A1385 "
           pdb=" C   HIS A1385 "
           pdb=" CA  HIS A1385 "
           pdb=" CB  HIS A1385 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.52  -14.72     0      2.50e+00 1.60e-01 3.47e+01
  ... (remaining 7462 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.136: 1826
       0.136 -    0.272: 67
       0.272 -    0.407: 4
       0.407 -    0.543: 3
       0.543 -    0.679: 1
  Chirality restraints: 1901
  Sorted by residual:
  chirality pdb=" CA  HIS A1385 "
            pdb=" N   HIS A1385 "
            pdb=" C   HIS A1385 "
            pdb=" CB  HIS A1385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.15e+01
  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    1.98    0.54 2.00e-01 2.50e+01 7.16e+00
  chirality pdb=" CA  ASN A1220 "
            pdb=" N   ASN A1220 "
            pdb=" C   ASN A1220 "
            pdb=" CB  ASN A1220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.49e+00
  ... (remaining 1898 not shown)

  Planarity restraints: 2169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 653 "    0.064 5.00e-02 4.00e+02   9.50e-02 1.44e+01
        pdb=" N   PRO A 654 "   -0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO A 654 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 654 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1382 "   -0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   ARG A1382 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ARG A1382 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   MET A1383 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1312 "   -0.032 2.00e-02 2.50e+03   1.90e-02 9.06e+00
        pdb=" CG  TRP A1312 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1312 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1312 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1312 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1312 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1312 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1312 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1312 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1312 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 2166 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 105
        2.56 -     3.15: 8948
        3.15 -     3.73: 17870
        3.73 -     4.32: 26018
        4.32 -     4.90: 44191
  Nonbonded interactions: 97132
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 396 "
            pdb=" N   HIS B 397 "
     model   vdw
     1.978 3.120
  nonbonded pdb=" N   GLU B 333 "
            pdb=" OE1 GLU B 333 "
     model   vdw
     2.077 3.120
  nonbonded pdb=" O   MET B 103 "
            pdb=" O   ASN B 104 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" O   PHE A 811 "
            pdb=" O   PRO A 812 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   SER A 302 "
            pdb=" OG  SER A 302 "
     model   vdw
     2.174 3.040
  ... (remaining 97127 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.600
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
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      :  0.007   0.069  12544  Z= 0.331
  Angle     :  1.092  12.329  17022  Z= 0.643
  Chirality :  0.067   0.679   1901
  Planarity :  0.008   0.095   2169
  Dihedral  : 10.665  71.831   4585
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 19.11
  Ramachandran Plot:
    Outliers :  0.93 %
    Allowed  :  8.94 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  2.68 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.21 %
  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: -3.90 (0.18), residues: 1510
  helix: -4.68 (0.16), residues: 89
  sheet: -1.98 (0.19), residues: 589
  loop : -2.85 (0.18), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.004   TRP A1312 
 HIS   0.013   0.002   HIS B 171 
 PHE   0.032   0.004   PHE A  72 
 TYR   0.029   0.003   TYR A   2 
 ARG   0.010   0.001   ARG A 932 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26820 (  315)
  hydrogen bonds       : angle      10.61278 (  834)
  covalent geometry    : bond        0.00688 (12544)
  covalent geometry    : angle       1.09191 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  476 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 438
  time to evaluate  : 1.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 TYR cc_start: 0.8463 (p90) cc_final: 0.8002 (p90)
REVERT: A  202 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7368 (m-40)
REVERT: A  523 VAL cc_start: 0.8636 (t) cc_final: 0.7099 (t)
REVERT: A  996 LEU cc_start: 0.8234 (tp) cc_final: 0.7931 (tt)
REVERT: A 1183 VAL cc_start: 0.8936 (t) cc_final: 0.8706 (t)
REVERT: A 1220 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6459 (t0)
REVERT: A 1259 ASP cc_start: 0.7142 (t0) cc_final: 0.6695 (t0)
REVERT: A 1277 ASN cc_start: 0.8202 (m-40) cc_final: 0.7996 (m-40)
REVERT: A 1386 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7431 (p)
REVERT: B  353 ASP cc_start: 0.6342 (p0) cc_final: 0.5771 (p0)
REVERT: B  403 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8384 (t)
  outliers start: 38
  outliers final: 7
  residues processed: 467
  average time/residue: 0.2866
  time to fit residues: 183.4191
Evaluate side-chains
  242 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 231
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue 1220 ASN
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1386 VAL
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  403 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 129 optimal weight:    8.9990
   chunk 115 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 119 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 138 optimal weight:    5.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 202 ASN
A 225 GLN
A 620 GLN
A 634 GLN
A 648 GLN
A 866 HIS
A 879 HIS
A1095 GLN
A1442 HIS
B  69 ASN
B  83 GLN
B 101 ASN
B 116 ASN
** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 289 ASN
B 325 GLN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 ASN
B 416 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.114317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.095486 restraints weight = 21576.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.098382 restraints weight = 12207.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.100330 restraints weight = 8235.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  12544  Z= 0.191
  Angle     :  0.779  11.182  17022  Z= 0.400
  Chirality :  0.049   0.273   1901
  Planarity :  0.006   0.106   2169
  Dihedral  :  7.099  58.993   1685
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.49 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 12.81 %
    Favored  : 83.17 %
  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: -3.16 (0.19), residues: 1510
  helix: -2.99 (0.40), residues: 84
  sheet: -1.43 (0.20), residues: 608
  loop : -2.56 (0.18), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1312 
 HIS   0.014   0.002   HIS B 397 
 PHE   0.023   0.002   PHE B 210 
 TYR   0.025   0.002   TYR A  19 
 ARG   0.008   0.001   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05085 (  315)
  hydrogen bonds       : angle       7.44370 (  834)
  covalent geometry    : bond        0.00436 (12544)
  covalent geometry    : angle       0.77915 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 249
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 TYR cc_start: 0.8567 (t80) cc_final: 0.8362 (t80)
REVERT: A  107 GLU cc_start: 0.7978 (pt0) cc_final: 0.7720 (pt0)
REVERT: A  189 TYR cc_start: 0.8721 (p90) cc_final: 0.8266 (p90)
REVERT: A  302 SER cc_start: 0.8162 (p) cc_final: 0.7418 (m)
REVERT: A  498 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8742 (pp)
REVERT: A  996 LEU cc_start: 0.9204 (tp) cc_final: 0.8947 (tt)
REVERT: A  999 SER cc_start: 0.9169 (m) cc_final: 0.8964 (t)
REVERT: A 1097 TRP cc_start: 0.8374 (m100) cc_final: 0.7689 (m100)
REVERT: A 1220 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7493 (t0)
REVERT: A 1259 ASP cc_start: 0.7797 (t0) cc_final: 0.7437 (t0)
REVERT: B  192 MET cc_start: 0.8677 (mmt) cc_final: 0.8145 (mmp)
REVERT: B  304 LEU cc_start: 0.9058 (tp) cc_final: 0.8853 (tp)
REVERT: B  320 LEU cc_start: 0.7663 (mt) cc_final: 0.7414 (mt)
REVERT: B  353 ASP cc_start: 0.8201 (p0) cc_final: 0.7563 (p0)
  outliers start: 54
  outliers final: 34
  residues processed: 287
  average time/residue: 0.2253
  time to fit residues: 96.8818
Evaluate side-chains
  213 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 177
  time to evaluate  : 1.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 THR
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  489 GLU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1220 ASN
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1351 MET
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  346 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 130 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 131 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   chunk 94 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1023 HIS
A1095 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1442 HIS
B  73 GLN
B  83 GLN
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.097093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.077838 restraints weight = 22726.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.080469 restraints weight = 13011.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.082248 restraints weight = 8946.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  12544  Z= 0.307
  Angle     :  0.810  11.272  17022  Z= 0.413
  Chirality :  0.050   0.191   1901
  Planarity :  0.006   0.115   2169
  Dihedral  :  6.836  58.920   1681
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.88 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 14.37 %
    Favored  : 80.71 %
  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: 1510
  helix: -1.97 (0.50), residues: 82
  sheet: -1.28 (0.20), residues: 607
  loop : -2.18 (0.20), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1337 
 HIS   0.039   0.002   HIS A1442 
 PHE   0.025   0.002   PHE A 221 
 TYR   0.019   0.002   TYR A 213 
 ARG   0.009   0.001   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (  315)
  hydrogen bonds       : angle       6.62255 (  834)
  covalent geometry    : bond        0.00709 (12544)
  covalent geometry    : angle       0.80974 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 194
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8782 (pp)
REVERT: A  857 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7974 (mtt90)
REVERT: A 1093 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7215 (mt-10)
REVERT: A 1226 ASP cc_start: 0.8522 (t0) cc_final: 0.8222 (t0)
REVERT: A 1228 MET cc_start: 0.8967 (mmm) cc_final: 0.8476 (mmm)
REVERT: A 1244 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8696 (t)
REVERT: B  192 MET cc_start: 0.8846 (mmt) cc_final: 0.8322 (mmp)
REVERT: B  207 GLU cc_start: 0.7591 (tp30) cc_final: 0.7258 (tp30)
REVERT: B  292 MET cc_start: 0.8094 (mtp) cc_final: 0.7825 (mtp)
  outliers start: 66
  outliers final: 44
  residues processed: 241
  average time/residue: 0.2256
  time to fit residues: 86.8843
Evaluate side-chains
  200 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 153
  time to evaluate  : 1.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  184 SER
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1013 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain A residue 1244 SER
Chi-restraints excluded: chain A residue 1247 SER
Chi-restraints excluded: chain A residue 1257 SER
Chi-restraints excluded: chain A residue 1261 MET
Chi-restraints excluded: chain A residue 1297 LEU
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   chunk 4 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 116 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 140 optimal weight:    9.9990
   chunk 115 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    1.1580

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

Flipped N/Q/H residues before XYZ refinement:
A 783 HIS
** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
B 397 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.098763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.080084 restraints weight = 22240.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.082786 restraints weight = 12468.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.084607 restraints weight = 8452.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  12544  Z= 0.145
  Angle     :  0.682  10.015  17022  Z= 0.346
  Chirality :  0.047   0.187   1901
  Planarity :  0.005   0.113   2169
  Dihedral  :  6.258  58.771   1677
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.15 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.42 %
    Favored  : 79.00 %
  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: 1510
  helix: -1.41 (0.53), residues: 81
  sheet: -1.01 (0.20), residues: 591
  loop : -2.09 (0.20), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A1097 
 HIS   0.007   0.001   HIS B 397 
 PHE   0.022   0.002   PHE B 217 
 TYR   0.018   0.001   TYR A  19 
 ARG   0.008   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03634 (  315)
  hydrogen bonds       : angle       6.36513 (  834)
  covalent geometry    : bond        0.00340 (12544)
  covalent geometry    : angle       0.68175 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 188
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  996 LEU cc_start: 0.9420 (tp) cc_final: 0.9139 (tt)
REVERT: A 1140 LEU cc_start: 0.9443 (tt) cc_final: 0.9223 (tt)
REVERT: A 1430 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8860 (mm)
REVERT: A 1442 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.8145 (t-90)
REVERT: B  192 MET cc_start: 0.8838 (mmt) cc_final: 0.8481 (mmp)
REVERT: B  210 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7045 (p90)
REVERT: B  251 ASP cc_start: 0.8713 (t0) cc_final: 0.8359 (t0)
REVERT: B  292 MET cc_start: 0.7989 (mtp) cc_final: 0.7766 (mtp)
REVERT: B  301 ASN cc_start: 0.9022 (m-40) cc_final: 0.8803 (m-40)
  outliers start: 48
  outliers final: 33
  residues processed: 224
  average time/residue: 0.2182
  time to fit residues: 77.8006
Evaluate side-chains
  191 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain A residue 1314 THR
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 124 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 112 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 115 optimal weight:    0.2980
   chunk 141 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 509 ASN
A 648 GLN
A 783 HIS
** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.099468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.080934 restraints weight = 22152.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.083588 restraints weight = 12457.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.085441 restraints weight = 8479.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.5209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12544  Z= 0.188
  Angle     :  0.679  10.070  17022  Z= 0.346
  Chirality :  0.047   0.221   1901
  Planarity :  0.005   0.118   2169
  Dihedral  :  6.077  58.505   1676
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.88 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 17.87 %
    Favored  : 78.18 %
  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: -2.21 (0.21), residues: 1510
  helix: -1.12 (0.53), residues: 81
  sheet: -0.89 (0.21), residues: 598
  loop : -1.98 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A1097 
 HIS   0.007   0.001   HIS A1385 
 PHE   0.021   0.002   PHE A 221 
 TYR   0.024   0.002   TYR A 213 
 ARG   0.008   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  315)
  hydrogen bonds       : angle       6.17717 (  834)
  covalent geometry    : bond        0.00443 (12544)
  covalent geometry    : angle       0.67877 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 178
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 LYS cc_start: 0.8958 (tptm) cc_final: 0.8733 (tppt)
REVERT: A  990 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8259 (m-10)
REVERT: A 1093 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7098 (mt-10)
REVERT: A 1140 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9218 (tt)
REVERT: A 1259 ASP cc_start: 0.8145 (t0) cc_final: 0.7887 (t70)
REVERT: B  207 GLU cc_start: 0.7511 (tp30) cc_final: 0.7200 (tp30)
REVERT: B  210 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7096 (p90)
REVERT: B  251 ASP cc_start: 0.8737 (t0) cc_final: 0.8400 (t0)
REVERT: B  292 MET cc_start: 0.8106 (mtp) cc_final: 0.7654 (tpp)
REVERT: B  301 ASN cc_start: 0.9055 (m-40) cc_final: 0.8834 (m-40)
  outliers start: 53
  outliers final: 39
  residues processed: 214
  average time/residue: 0.2426
  time to fit residues: 81.9591
Evaluate side-chains
  204 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 161
  time to evaluate  : 1.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  990 PHE
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 LEU
Chi-restraints excluded: chain A residue 1261 MET
Chi-restraints excluded: chain A residue 1314 THR
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1385 HIS
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 147 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 132 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 79 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 151 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 1 optimal weight:    0.1980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.099348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.080736 restraints weight = 22590.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.083409 restraints weight = 12729.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.085232 restraints weight = 8598.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.5470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12544  Z= 0.168
  Angle     :  0.676  11.193  17022  Z= 0.339
  Chirality :  0.046   0.199   1901
  Planarity :  0.005   0.118   2169
  Dihedral  :  5.968  58.039   1676
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.68 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 18.54 %
    Favored  : 76.40 %
  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: -2.09 (0.21), residues: 1510
  helix: -0.73 (0.56), residues: 82
  sheet: -0.84 (0.21), residues: 598
  loop : -1.90 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A1097 
 HIS   0.008   0.001   HIS A1385 
 PHE   0.026   0.002   PHE B 217 
 TYR   0.031   0.001   TYR A  19 
 ARG   0.012   0.000   ARG A 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03393 (  315)
  hydrogen bonds       : angle       6.02923 (  834)
  covalent geometry    : bond        0.00397 (12544)
  covalent geometry    : angle       0.67593 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 183
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 TYR cc_start: 0.8586 (p90) cc_final: 0.8215 (p90)
REVERT: A  628 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8579 (tt)
REVERT: A  990 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8255 (m-10)
REVERT: A 1093 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6984 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8645 (m-90) cc_final: 0.8283 (m-90)
REVERT: A 1105 THR cc_start: 0.9329 (m) cc_final: 0.8902 (t)
REVERT: A 1140 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9209 (tt)
REVERT: A 1259 ASP cc_start: 0.8140 (t70) cc_final: 0.7813 (t70)
REVERT: B  207 GLU cc_start: 0.7510 (tp30) cc_final: 0.7203 (tp30)
REVERT: B  210 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6245 (p90)
REVERT: B  285 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.6628 (p90)
REVERT: B  292 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7656 (tpp)
REVERT: B  301 ASN cc_start: 0.9070 (m-40) cc_final: 0.8748 (m-40)
  outliers start: 68
  outliers final: 43
  residues processed: 230
  average time/residue: 0.2042
  time to fit residues: 73.3062
Evaluate side-chains
  217 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 167
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  990 PHE
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1261 MET
Chi-restraints excluded: chain A residue 1314 THR
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  285 HIS
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 138 optimal weight:    9.9990
   chunk 109 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 16 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9990
   chunk 129 optimal weight:    2.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.101403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.082833 restraints weight = 22162.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.085551 restraints weight = 12542.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.087386 restraints weight = 8516.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.5605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  12544  Z= 0.142
  Angle     :  0.669  10.699  17022  Z= 0.333
  Chirality :  0.047   0.310   1901
  Planarity :  0.005   0.121   2169
  Dihedral  :  5.495  57.445   1668
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.02 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 19.43 %
    Favored  : 76.69 %
  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: -1.99 (0.21), residues: 1510
  helix: -0.44 (0.58), residues: 81
  sheet: -0.76 (0.21), residues: 595
  loop : -1.86 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A1097 
 HIS   0.006   0.001   HIS A1385 
 PHE   0.024   0.001   PHE B 217 
 TYR   0.032   0.001   TYR A  19 
 ARG   0.012   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03230 (  315)
  hydrogen bonds       : angle       5.94036 (  834)
  covalent geometry    : bond        0.00336 (12544)
  covalent geometry    : angle       0.66916 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 179
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ASN cc_start: 0.8492 (p0) cc_final: 0.8250 (p0)
REVERT: A  189 TYR cc_start: 0.8561 (p90) cc_final: 0.8235 (p90)
REVERT: A 1093 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7000 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8641 (m-90) cc_final: 0.8312 (m-90)
REVERT: A 1105 THR cc_start: 0.9263 (m) cc_final: 0.8851 (t)
REVERT: A 1140 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9207 (tt)
REVERT: A 1259 ASP cc_start: 0.8186 (t70) cc_final: 0.7801 (t70)
REVERT: B  210 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6153 (p90)
REVERT: B  285 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.6543 (p90)
REVERT: B  292 MET cc_start: 0.8083 (mtp) cc_final: 0.7581 (tpp)
REVERT: B  301 ASN cc_start: 0.9067 (m-40) cc_final: 0.8861 (m-40)
  outliers start: 52
  outliers final: 36
  residues processed: 213
  average time/residue: 0.1926
  time to fit residues: 64.6451
Evaluate side-chains
  208 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1261 MET
Chi-restraints excluded: chain A residue 1314 THR
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  285 HIS
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 103 optimal weight:    0.0010
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 146 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0020
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.101612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.083269 restraints weight = 22363.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.086014 restraints weight = 12442.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.087833 restraints weight = 8358.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  12544  Z= 0.124
  Angle     :  0.652  10.540  17022  Z= 0.325
  Chirality :  0.046   0.286   1901
  Planarity :  0.005   0.124   2169
  Dihedral  :  5.362  57.435   1668
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.89 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.06 %
    Favored  : 76.92 %
  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: -1.90 (0.21), residues: 1510
  helix: -0.26 (0.59), residues: 81
  sheet: -0.65 (0.21), residues: 585
  loop : -1.84 (0.21), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1312 
 HIS   0.006   0.001   HIS A1385 
 PHE   0.023   0.001   PHE B 217 
 TYR   0.030   0.001   TYR A  19 
 ARG   0.009   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (  315)
  hydrogen bonds       : angle       5.84186 (  834)
  covalent geometry    : bond        0.00294 (12544)
  covalent geometry    : angle       0.65171 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 177
  time to evaluate  : 1.603 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ASN cc_start: 0.8346 (p0) cc_final: 0.8096 (p0)
REVERT: A  189 TYR cc_start: 0.8467 (p90) cc_final: 0.8176 (p90)
REVERT: A  202 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7132 (t0)
REVERT: A  273 LYS cc_start: 0.8943 (tptm) cc_final: 0.8702 (tppt)
REVERT: A  628 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8606 (tt)
REVERT: A  993 GLN cc_start: 0.8468 (mp10) cc_final: 0.8183 (mp10)
REVERT: A 1093 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7010 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8626 (m-90) cc_final: 0.8288 (m-90)
REVERT: A 1105 THR cc_start: 0.9234 (m) cc_final: 0.8826 (t)
REVERT: A 1140 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9166 (tt)
REVERT: A 1231 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8278 (mm)
REVERT: A 1259 ASP cc_start: 0.8135 (t70) cc_final: 0.7676 (t70)
REVERT: A 1361 MET cc_start: 0.7433 (mpp) cc_final: 0.7175 (mpp)
REVERT: B  103 MET cc_start: 0.8881 (mmp) cc_final: 0.8541 (mmp)
REVERT: B  210 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.5861 (p90)
REVERT: B  285 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.6565 (p90)
REVERT: B  292 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7553 (tpp)
REVERT: B  301 ASN cc_start: 0.9047 (m-40) cc_final: 0.8841 (m-40)
  outliers start: 54
  outliers final: 35
  residues processed: 210
  average time/residue: 0.2855
  time to fit residues: 92.9789
Evaluate side-chains
  210 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 167
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1261 MET
Chi-restraints excluded: chain A residue 1314 THR
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1351 MET
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  285 HIS
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 112 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 18 optimal weight:    0.2980
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.099376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.081021 restraints weight = 22276.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.083676 restraints weight = 12566.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.085515 restraints weight = 8546.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.5902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  12544  Z= 0.215
  Angle     :  0.693  11.209  17022  Z= 0.345
  Chirality :  0.048   0.286   1901
  Planarity :  0.005   0.127   2169
  Dihedral  :  5.519  57.363   1668
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.08 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.21 %
    Favored  : 76.40 %
  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: -1.92 (0.21), residues: 1510
  helix: -0.23 (0.59), residues: 81
  sheet: -0.78 (0.21), residues: 584
  loop : -1.76 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A1312 
 HIS   0.007   0.001   HIS A1385 
 PHE   0.021   0.002   PHE B 217 
 TYR   0.035   0.002   TYR A  19 
 ARG   0.011   0.001   ARG A 520 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  315)
  hydrogen bonds       : angle       5.87034 (  834)
  covalent geometry    : bond        0.00510 (12544)
  covalent geometry    : angle       0.69267 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 168
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASN cc_start: 0.8427 (p0) cc_final: 0.8158 (p0)
REVERT: A  189 TYR cc_start: 0.8561 (p90) cc_final: 0.8231 (p90)
REVERT: A  467 ASP cc_start: 0.7027 (m-30) cc_final: 0.6786 (m-30)
REVERT: A  628 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8614 (tt)
REVERT: A 1093 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7069 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8663 (m-90) cc_final: 0.8242 (m-90)
REVERT: A 1105 THR cc_start: 0.9279 (m) cc_final: 0.8887 (t)
REVERT: A 1140 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9221 (tt)
REVERT: A 1259 ASP cc_start: 0.8439 (t70) cc_final: 0.8067 (t70)
REVERT: A 1361 MET cc_start: 0.7564 (mpp) cc_final: 0.7212 (mpp)
REVERT: B  103 MET cc_start: 0.9009 (mmp) cc_final: 0.8650 (mmp)
REVERT: B  210 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6109 (p90)
REVERT: B  285 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.6521 (p90)
REVERT: B  301 ASN cc_start: 0.8988 (m-40) cc_final: 0.8774 (m-40)
  outliers start: 59
  outliers final: 47
  residues processed: 210
  average time/residue: 0.2086
  time to fit residues: 68.7738
Evaluate side-chains
  215 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 163
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  707 MET
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1216 ILE
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1261 MET
Chi-restraints excluded: chain A residue 1314 THR
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain A residue 1442 HIS
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  285 HIS
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0770
   chunk 132 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.100694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.082455 restraints weight = 22154.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.085176 restraints weight = 12414.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.087005 restraints weight = 8393.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.5966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082  12544  Z= 0.127
  Angle     :  0.667  10.486  17022  Z= 0.332
  Chirality :  0.047   0.273   1901
  Planarity :  0.005   0.128   2169
  Dihedral  :  5.399  56.461   1668
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.62 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.81 %
    Favored  : 76.55 %
  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: -1.88 (0.21), residues: 1510
  helix: -0.10 (0.59), residues: 81
  sheet: -0.69 (0.21), residues: 573
  loop : -1.80 (0.21), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A1312 
 HIS   0.006   0.001   HIS A1385 
 PHE   0.021   0.001   PHE B 217 
 TYR   0.038   0.002   TYR A  19 
 ARG   0.011   0.000   ARG A 520 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03158 (  315)
  hydrogen bonds       : angle       5.83040 (  834)
  covalent geometry    : bond        0.00302 (12544)
  covalent geometry    : angle       0.66660 (17022)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 181
  time to evaluate  : 1.477 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ASN cc_start: 0.8300 (p0) cc_final: 0.8028 (p0)
REVERT: A  189 TYR cc_start: 0.8470 (p90) cc_final: 0.8180 (p90)
REVERT: A  273 LYS cc_start: 0.8964 (tptm) cc_final: 0.8740 (tppt)
REVERT: A  614 ASP cc_start: 0.8193 (p0) cc_final: 0.7946 (p0)
REVERT: A  628 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8605 (tt)
REVERT: A 1093 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7041 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8640 (m-90) cc_final: 0.8325 (m-90)
REVERT: A 1105 THR cc_start: 0.9220 (m) cc_final: 0.8848 (t)
REVERT: A 1140 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9193 (tt)
REVERT: A 1259 ASP cc_start: 0.8286 (t70) cc_final: 0.7839 (t70)
REVERT: A 1341 LEU cc_start: 0.9358 (tp) cc_final: 0.9155 (tt)
REVERT: A 1361 MET cc_start: 0.7457 (mpp) cc_final: 0.7089 (mpp)
REVERT: B  103 MET cc_start: 0.8880 (mmp) cc_final: 0.8578 (mmp)
REVERT: B  210 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6024 (p90)
REVERT: B  285 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.6563 (p90)
REVERT: B  301 ASN cc_start: 0.9026 (m-40) cc_final: 0.8570 (m-40)
  outliers start: 49
  outliers final: 35
  residues processed: 212
  average time/residue: 0.2065
  time to fit residues: 68.4856
Evaluate side-chains
  212 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  628 LEU
Chi-restraints excluded: chain A residue  635 LEU
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1216 ILE
Chi-restraints excluded: chain A residue 1221 PHE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1261 MET
Chi-restraints excluded: chain A residue 1336 THR
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  210 PHE
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  285 HIS
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 109 optimal weight:    0.9990
   chunk 134 optimal weight:    0.8980
   chunk 112 optimal weight:    9.9990
   chunk 98 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0060
   chunk 14 optimal weight:    7.9990
   chunk 151 optimal weight:    6.9990
   overall best weight:    1.3800

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

Flipped N/Q/H residues before XYZ refinement:
** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 HIS
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.101813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.083573 restraints weight = 22240.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.086275 restraints weight = 12593.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.088114 restraints weight = 8558.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.6039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12544  Z= 0.147
  Angle     :  0.720  36.856  17022  Z= 0.338
  Chirality :  0.047   0.318   1901
  Planarity :  0.006   0.218   2169
  Dihedral  :  5.376  55.794   1668
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.75 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.66 %
    Favored  : 76.62 %
  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: -1.82 (0.21), residues: 1510
  helix: -0.07 (0.59), residues: 81
  sheet: -0.66 (0.21), residues: 582
  loop : -1.75 (0.21), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1312 
 HIS   0.007   0.001   HIS A1385 
 PHE   0.019   0.002   PHE B 217 
 TYR   0.037   0.002   TYR A  19 
 ARG   0.010   0.000   ARG A 520 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03165 (  315)
  hydrogen bonds       : angle       5.77758 (  834)
  covalent geometry    : bond        0.00350 (12544)
  covalent geometry    : angle       0.72019 (17022)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4071.87 seconds
wall clock time: 74 minutes 57.81 seconds (4497.81 seconds total)