Starting phenix.real_space_refine
on Wed Sep 17 23:10:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bm0_7114/09_2025/6bm0_7114.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bm0_7114/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bm0_7114/09_2025/6bm0_7114.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bm0_7114/09_2025/6bm0_7114.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bm0_7114/09_2025/6bm0_7114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bm0_7114/09_2025/6bm0_7114.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 3.29, per 1000 atoms: 0.27
  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: 1.09
  Conformation dependent library (CDL) restraints added in 560.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.66
  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: 2.97

  Time building geometry restraints manager: 1.49 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.240
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.360
-------------------------------------------------------------------------------
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 : 18.90
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.010   0.001   ARG A 932 
 TYR   0.029   0.003   TYR A   2 
 PHE   0.032   0.004   PHE A  72 
 TRP   0.048   0.004   TRP A1312 
 HIS   0.013   0.002   HIS B 171 

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

*********************** 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  : 0.497 
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: 0.8707 (t)
REVERT: A 1220 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6463 (t0)
REVERT: A 1259 ASP cc_start: 0.7142 (t0) cc_final: 0.6697 (t0)
REVERT: A 1277 ASN cc_start: 0.8202 (m-40) cc_final: 0.7997 (m-40)
REVERT: A 1386 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7434 (p)
REVERT: B  353 ASP cc_start: 0.6342 (p0) cc_final: 0.5770 (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: 0.1358
  time to fit residues: 87.0634
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  : 0.482 
-------------------------------------------------------------------------------
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 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0770
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.0144

-------------------------------------------------------------------------------
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
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: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.116876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.098291 restraints weight = 21632.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.101205 restraints weight = 12071.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.103179 restraints weight = 8075.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.104500 restraints weight = 6099.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.105380 restraints weight = 5015.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  12544  Z= 0.161
  Angle     :  0.764  11.118  17022  Z= 0.392
  Chirality :  0.049   0.252   1901
  Planarity :  0.006   0.103   2169
  Dihedral  :  7.041  58.185   1685
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  6.16 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.10 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.12 (0.19), residues: 1510
  helix: -2.94 (0.41), residues: 84
  sheet: -1.41 (0.20), residues: 607
  loop : -2.54 (0.18), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 112 
 TYR   0.026   0.002   TYR A  19 
 PHE   0.022   0.002   PHE B 217 
 TRP   0.015   0.002   TRP A1337 
 HIS   0.014   0.001   HIS B 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12544)
  covalent geometry    : angle       0.76440 (17022)
  hydrogen bonds       : bond        0.04576 (  315)
  hydrogen bonds       : angle       7.39040 (  834)

*********************** 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
  309 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 262
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 GLU cc_start: 0.7963 (pt0) cc_final: 0.7692 (pt0)
REVERT: A  189 TYR cc_start: 0.8699 (p90) cc_final: 0.8254 (p90)
REVERT: A  302 SER cc_start: 0.8087 (p) cc_final: 0.7743 (m)
REVERT: A  498 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8618 (pp)
REVERT: A  996 LEU cc_start: 0.9156 (tp) cc_final: 0.8902 (tt)
REVERT: A  999 SER cc_start: 0.9161 (m) cc_final: 0.8922 (t)
REVERT: A 1142 MET cc_start: 0.7255 (mtm) cc_final: 0.6693 (mtm)
REVERT: A 1235 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7359 (ptm160)
REVERT: A 1259 ASP cc_start: 0.7751 (t0) cc_final: 0.7418 (t0)
REVERT: B  192 MET cc_start: 0.8629 (mmt) cc_final: 0.8070 (mmp)
REVERT: B  320 LEU cc_start: 0.7595 (mt) cc_final: 0.7354 (mt)
  outliers start: 47
  outliers final: 28
  residues processed: 295
  average time/residue: 0.1013
  time to fit residues: 44.5886
Evaluate side-chains
  214 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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  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  619 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue 1093 GLU
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  135 VAL
Chi-restraints excluded: chain B residue  139 SER
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  203 GLU
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 136 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0170
   chunk 152 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0670
   chunk 93 optimal weight:    8.9990
   overall best weight:    1.7560

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

Flipped N/Q/H residues before XYZ refinement:
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 GLN
B 325 GLN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.108914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.089410 restraints weight = 22037.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.092310 restraints weight = 12478.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.094268 restraints weight = 8472.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.095599 restraints weight = 6498.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.096425 restraints weight = 5394.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  12544  Z= 0.177
  Angle     :  0.708   9.851  17022  Z= 0.363
  Chirality :  0.047   0.204   1901
  Planarity :  0.006   0.107   2169
  Dihedral  :  6.420  57.664   1679
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.75 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 14.82 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.65 (0.20), residues: 1510
  helix: -1.92 (0.50), residues: 82
  sheet: -1.11 (0.20), residues: 601
  loop : -2.28 (0.19), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 358 
 TYR   0.021   0.002   TYR A 213 
 PHE   0.026   0.002   PHE A 221 
 TRP   0.041   0.002   TRP A1097 
 HIS   0.014   0.001   HIS A1442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12544)
  covalent geometry    : angle       0.70767 (17022)
  hydrogen bonds       : bond        0.03981 (  315)
  hydrogen bonds       : angle       6.70452 (  834)

*********************** 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
  252 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 204
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8615 (pp)
REVERT: A  794 MET cc_start: 0.8401 (ttp) cc_final: 0.8065 (ttt)
REVERT: A 1150 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5565 (tm-30)
REVERT: A 1220 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.7340 (t0)
REVERT: A 1228 MET cc_start: 0.8817 (mmm) cc_final: 0.8612 (mmt)
REVERT: A 1244 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8576 (t)
REVERT: A 1259 ASP cc_start: 0.7796 (t0) cc_final: 0.7425 (t0)
REVERT: B  165 ARG cc_start: 0.8939 (tpp-160) cc_final: 0.8457 (mmm160)
REVERT: B  192 MET cc_start: 0.8746 (mmt) cc_final: 0.8181 (mmp)
REVERT: B  210 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6890 (p90)
REVERT: B  256 LYS cc_start: 0.8641 (mttt) cc_final: 0.8375 (mtpt)
REVERT: B  297 ASN cc_start: 0.8205 (m-40) cc_final: 0.7655 (t0)
  outliers start: 48
  outliers final: 32
  residues processed: 232
  average time/residue: 0.0900
  time to fit residues: 32.7310
Evaluate side-chains
  210 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 173
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  388 LEU
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  819 VAL
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1150 GLU
Chi-restraints excluded: chain A residue 1220 ASN
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 1257 SER
Chi-restraints excluded: chain A residue 1297 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 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  311 LEU
Chi-restraints excluded: chain B residue  346 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 51 optimal weight:    0.0270
   chunk 139 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 130 optimal weight:    9.9990
   chunk 119 optimal weight:    0.0170
   chunk 118 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 142 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 611 ASN
A1237 GLN
B  69 ASN
B 325 GLN
B 397 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.112454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.093823 restraints weight = 21747.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.096740 restraints weight = 12191.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.098729 restraints weight = 8163.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.100086 restraints weight = 6159.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.100856 restraints weight = 5053.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  12544  Z= 0.119
  Angle     :  0.658  10.620  17022  Z= 0.331
  Chirality :  0.046   0.196   1901
  Planarity :  0.005   0.107   2169
  Dihedral  :  5.991  55.894   1677
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.62 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.34 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.31 (0.20), residues: 1510
  helix: -1.42 (0.53), residues: 82
  sheet: -0.82 (0.21), residues: 597
  loop : -2.13 (0.20), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 308 
 TYR   0.023   0.001   TYR A  19 
 PHE   0.026   0.001   PHE A 221 
 TRP   0.044   0.002   TRP A1097 
 HIS   0.006   0.001   HIS B 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12544)
  covalent geometry    : angle       0.65754 (17022)
  hydrogen bonds       : bond        0.03468 (  315)
  hydrogen bonds       : angle       6.34601 (  834)

*********************** 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
  254 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 202
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 TYR cc_start: 0.8678 (p90) cc_final: 0.8280 (p90)
REVERT: A  498 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8514 (pp)
REVERT: A  953 LEU cc_start: 0.8980 (tp) cc_final: 0.8771 (tt)
REVERT: A  996 LEU cc_start: 0.9347 (tp) cc_final: 0.8995 (tt)
REVERT: A 1099 HIS cc_start: 0.7268 (m170) cc_final: 0.7066 (m170)
REVERT: A 1220 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.7380 (t0)
REVERT: A 1259 ASP cc_start: 0.7910 (t0) cc_final: 0.7516 (t0)
REVERT: A 1342 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7769 (t0)
REVERT: B  192 MET cc_start: 0.8694 (mmt) cc_final: 0.8165 (mmp)
REVERT: B  197 MET cc_start: 0.7310 (ttm) cc_final: 0.7003 (ttt)
REVERT: B  256 LYS cc_start: 0.8607 (mttt) cc_final: 0.8396 (mtpt)
REVERT: B  353 ASP cc_start: 0.8396 (p0) cc_final: 0.7892 (p0)
  outliers start: 52
  outliers final: 34
  residues processed: 234
  average time/residue: 0.0860
  time to fit residues: 32.4557
Evaluate side-chains
  208 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 171
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  227 TRP
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  388 LEU
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  626 ILE
Chi-restraints excluded: chain A residue  658 ILE
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 1000 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1220 ASN
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 1336 THR
Chi-restraints excluded: chain A residue 1342 ASP
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 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  247 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 150 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 122 optimal weight:    3.9990
   chunk 143 optimal weight:    0.5980
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  69 ASN
B 325 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.085654 restraints weight = 22141.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.088373 restraints weight = 12710.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.090120 restraints weight = 8724.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.091468 restraints weight = 6785.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.092322 restraints weight = 5654.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  12544  Z= 0.197
  Angle     :  0.679   9.492  17022  Z= 0.347
  Chirality :  0.048   0.356   1901
  Planarity :  0.005   0.119   2169
  Dihedral  :  5.932  54.937   1674
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.68 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 16.38 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.21), residues: 1510
  helix: -1.16 (0.55), residues: 82
  sheet: -0.83 (0.20), residues: 600
  loop : -1.95 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 358 
 TYR   0.025   0.002   TYR A 213 
 PHE   0.030   0.002   PHE A 221 
 TRP   0.039   0.002   TRP A1097 
 HIS   0.008   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (12544)
  covalent geometry    : angle       0.67948 (17022)
  hydrogen bonds       : bond        0.03527 (  315)
  hydrogen bonds       : angle       6.07223 (  834)

*********************** 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
  251 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 187
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 SER cc_start: 0.9132 (p) cc_final: 0.8727 (m)
REVERT: A  498 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8708 (pp)
REVERT: A  996 LEU cc_start: 0.9388 (tp) cc_final: 0.9158 (tt)
REVERT: A 1093 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7025 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8630 (m-90) cc_final: 0.8227 (m-90)
REVERT: A 1220 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.7416 (t0)
REVERT: A 1244 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8678 (t)
REVERT: A 1259 ASP cc_start: 0.8170 (t0) cc_final: 0.7709 (t0)
REVERT: B  192 MET cc_start: 0.8697 (mmt) cc_final: 0.8127 (mmp)
REVERT: B  229 TRP cc_start: 0.7723 (m100) cc_final: 0.7447 (m100)
REVERT: B  292 MET cc_start: 0.7709 (mtp) cc_final: 0.7404 (mtt)
REVERT: B  297 ASN cc_start: 0.8341 (m-40) cc_final: 0.7748 (t0)
  outliers start: 64
  outliers final: 40
  residues processed: 229
  average time/residue: 0.0830
  time to fit residues: 30.9714
Evaluate side-chains
  204 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 160
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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  227 TRP
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  374 MET
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  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  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 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1216 ILE
Chi-restraints excluded: chain A residue 1220 ASN
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 1261 MET
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 B residue  122 VAL
Chi-restraints excluded: chain B residue  124 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  247 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 139 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0670
   chunk 64 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 43 optimal weight:   10.0000
   chunk 110 optimal weight:    6.9990
   chunk 136 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.8722

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1023 HIS
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.104657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.085723 restraints weight = 21970.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.088472 restraints weight = 12449.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.090203 restraints weight = 8504.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.091575 restraints weight = 6622.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.092447 restraints weight = 5497.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.5147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12544  Z= 0.175
  Angle     :  0.665   9.773  17022  Z= 0.335
  Chirality :  0.047   0.282   1901
  Planarity :  0.005   0.117   2169
  Dihedral  :  5.866  57.316   1674
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.55 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.39 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.21), residues: 1510
  helix: -0.81 (0.56), residues: 82
  sheet: -0.75 (0.21), residues: 588
  loop : -1.89 (0.21), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 358 
 TYR   0.027   0.001   TYR A  19 
 PHE   0.029   0.002   PHE A 221 
 TRP   0.029   0.002   TRP A1097 
 HIS   0.008   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12544)
  covalent geometry    : angle       0.66494 (17022)
  hydrogen bonds       : bond        0.03368 (  315)
  hydrogen bonds       : angle       5.95746 (  834)

*********************** 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
  233 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 179
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A   24 ASN cc_start: 0.8403 (p0) cc_final: 0.8136 (p0)
REVERT: A  386 SER cc_start: 0.9065 (p) cc_final: 0.8696 (m)
REVERT: A  653 ASP cc_start: 0.6702 (m-30) cc_final: 0.5366 (m-30)
REVERT: A 1093 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7023 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8635 (m-90) cc_final: 0.8248 (m-90)
REVERT: A 1105 THR cc_start: 0.9281 (m) cc_final: 0.8838 (t)
REVERT: A 1108 LEU cc_start: 0.8552 (mt) cc_final: 0.8066 (mt)
REVERT: A 1220 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.7428 (t0)
REVERT: A 1244 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8698 (t)
REVERT: A 1259 ASP cc_start: 0.8092 (t0) cc_final: 0.7591 (t0)
REVERT: B  229 TRP cc_start: 0.7898 (m100) cc_final: 0.7334 (m100)
REVERT: B  236 GLU cc_start: 0.8104 (tt0) cc_final: 0.7715 (tt0)
REVERT: B  292 MET cc_start: 0.7721 (mtp) cc_final: 0.7461 (mtt)
  outliers start: 54
  outliers final: 37
  residues processed: 216
  average time/residue: 0.0895
  time to fit residues: 30.5450
Evaluate side-chains
  203 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 163
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
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  374 MET
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  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  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 1093 GLU
Chi-restraints excluded: chain A residue 1125 THR
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1220 ASN
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 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 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  247 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  346 LEU
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 3 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 151 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 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 = 0.3218 r_free = 0.3218 target = 0.103923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.085032 restraints weight = 22014.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.087774 restraints weight = 12517.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.089624 restraints weight = 8573.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.090899 restraints weight = 6612.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.091671 restraints weight = 5500.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.5413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12544  Z= 0.163
  Angle     :  0.667  10.599  17022  Z= 0.334
  Chirality :  0.047   0.260   1901
  Planarity :  0.005   0.116   2169
  Dihedral  :  5.599  53.363   1672
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.81 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.91 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.21), residues: 1510
  helix: -0.46 (0.58), residues: 81
  sheet: -0.71 (0.21), residues: 590
  loop : -1.79 (0.21), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 358 
 TYR   0.024   0.001   TYR A  19 
 PHE   0.032   0.002   PHE A 221 
 TRP   0.028   0.001   TRP A1312 
 HIS   0.008   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (12544)
  covalent geometry    : angle       0.66658 (17022)
  hydrogen bonds       : bond        0.03272 (  315)
  hydrogen bonds       : angle       5.87705 (  834)

*********************** 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
  229 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 180
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A   24 ASN cc_start: 0.8382 (p0) cc_final: 0.8100 (p0)
REVERT: A  386 SER cc_start: 0.9108 (p) cc_final: 0.8670 (m)
REVERT: A  535 MET cc_start: 0.9071 (ptm) cc_final: 0.8807 (ptm)
REVERT: A  628 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8509 (tt)
REVERT: A 1093 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7051 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8651 (m-90) cc_final: 0.8235 (m-90)
REVERT: A 1105 THR cc_start: 0.9292 (m) cc_final: 0.8881 (t)
REVERT: A 1220 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.7492 (t0)
REVERT: A 1259 ASP cc_start: 0.8155 (t0) cc_final: 0.7527 (t0)
REVERT: B  210 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.5827 (p90)
REVERT: B  285 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6554 (p90)
REVERT: B  292 MET cc_start: 0.7807 (mtp) cc_final: 0.7555 (mtt)
REVERT: B  366 GLU cc_start: 0.7900 (pm20) cc_final: 0.7542 (pm20)
  outliers start: 49
  outliers final: 31
  residues processed: 212
  average time/residue: 0.0949
  time to fit residues: 31.2376
Evaluate side-chains
  207 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 171
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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  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  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  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  899 ILE
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 1220 ASN
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 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  335 THR
Chi-restraints excluded: chain B residue  346 LEU
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 151 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0570
   chunk 112 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.3904

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1277 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 = 0.3233 r_free = 0.3233 target = 0.105084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.086586 restraints weight = 21915.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.089347 restraints weight = 12362.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.091221 restraints weight = 8363.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.092436 restraints weight = 6407.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.093316 restraints weight = 5340.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.5593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  12544  Z= 0.149
  Angle     :  0.670   9.929  17022  Z= 0.335
  Chirality :  0.047   0.258   1901
  Planarity :  0.005   0.114   2169
  Dihedral  :  5.411  52.824   1670
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.09 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.58 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.21), residues: 1510
  helix: -0.30 (0.59), residues: 81
  sheet: -0.67 (0.21), residues: 590
  loop : -1.78 (0.21), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 194 
 TYR   0.028   0.001   TYR A  19 
 PHE   0.026   0.002   PHE A 221 
 TRP   0.028   0.002   TRP B 229 
 HIS   0.006   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (12544)
  covalent geometry    : angle       0.67028 (17022)
  hydrogen bonds       : bond        0.03231 (  315)
  hydrogen bonds       : angle       5.87555 (  834)

*********************** 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
  227 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 183
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ASN cc_start: 0.8338 (p0) cc_final: 0.8031 (p0)
REVERT: A  100 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8082 (t0)
REVERT: A  189 TYR cc_start: 0.8559 (p90) cc_final: 0.8227 (p90)
REVERT: A  386 SER cc_start: 0.9097 (p) cc_final: 0.8659 (m)
REVERT: A  628 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8517 (tt)
REVERT: A 1093 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7058 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8622 (m-90) cc_final: 0.8254 (m-90)
REVERT: A 1105 THR cc_start: 0.9302 (m) cc_final: 0.8886 (t)
REVERT: A 1220 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.7490 (t0)
REVERT: A 1259 ASP cc_start: 0.8116 (t0) cc_final: 0.7506 (t0)
REVERT: B  210 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.5979 (p90)
REVERT: B  229 TRP cc_start: 0.7893 (m100) cc_final: 0.7354 (m100)
REVERT: B  292 MET cc_start: 0.7878 (mtp) cc_final: 0.7613 (mtt)
  outliers start: 44
  outliers final: 35
  residues processed: 211
  average time/residue: 0.0893
  time to fit residues: 29.4700
Evaluate side-chains
  207 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 167
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  251 VAL
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  487 SER
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  865 VAL
Chi-restraints excluded: chain A residue  897 HIS
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  946 CYS
Chi-restraints excluded: chain A residue 1000 VAL
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1067 ILE
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 1231 ILE
Chi-restraints excluded: chain A residue 1255 VAL
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  135 VAL
Chi-restraints excluded: chain B residue  156 ILE
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  346 LEU
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 84 optimal weight:    9.9990
   chunk 62 optimal weight:    0.0170
   chunk 1 optimal weight:    0.1980
   chunk 28 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 137 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 122 optimal weight:    1.9990
   chunk 143 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 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 = 0.3249 r_free = 0.3249 target = 0.106140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.087576 restraints weight = 21791.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.090374 restraints weight = 12210.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.092278 restraints weight = 8243.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.093527 restraints weight = 6283.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.094412 restraints weight = 5217.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.5725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  12544  Z= 0.118
  Angle     :  0.655  11.101  17022  Z= 0.325
  Chirality :  0.046   0.251   1901
  Planarity :  0.005   0.116   2169
  Dihedral  :  5.184  51.047   1668
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.09 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.48 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.21), residues: 1510
  helix: -0.17 (0.60), residues: 81
  sheet: -0.59 (0.21), residues: 588
  loop : -1.76 (0.21), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 194 
 TYR   0.030   0.001   TYR A  19 
 PHE   0.026   0.001   PHE A 221 
 TRP   0.026   0.001   TRP A1312 
 HIS   0.006   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12544)
  covalent geometry    : angle       0.65493 (17022)
  hydrogen bonds       : bond        0.03058 (  315)
  hydrogen bonds       : angle       5.84000 (  834)

*********************** 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
  235 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A   24 ASN cc_start: 0.8221 (p0) cc_final: 0.7952 (p0)
REVERT: A  189 TYR cc_start: 0.8533 (p90) cc_final: 0.8232 (p90)
REVERT: A  202 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7057 (t0)
REVERT: A  386 SER cc_start: 0.9071 (p) cc_final: 0.8552 (m)
REVERT: A  535 MET cc_start: 0.9118 (ptm) cc_final: 0.8854 (ptm)
REVERT: A  628 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8525 (tt)
REVERT: A 1093 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7002 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8582 (m-90) cc_final: 0.8315 (m-90)
REVERT: A 1220 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.7495 (t0)
REVERT: A 1231 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8035 (mm)
REVERT: A 1259 ASP cc_start: 0.7898 (t0) cc_final: 0.7477 (t0)
REVERT: B  210 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6028 (p90)
REVERT: B  285 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.6470 (p90)
REVERT: B  292 MET cc_start: 0.7774 (mtp) cc_final: 0.7543 (mtt)
REVERT: B  366 GLU cc_start: 0.7643 (pm20) cc_final: 0.7317 (pm20)
  outliers start: 41
  outliers final: 28
  residues processed: 222
  average time/residue: 0.0885
  time to fit residues: 30.6671
Evaluate side-chains
  213 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 178
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ASP
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  252 HIS
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  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 1050 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1220 ASN
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1255 VAL
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 B residue  122 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  156 ILE
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  396 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 152 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 126 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 110 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 116 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0030
   overall best weight:    1.7794

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

Flipped N/Q/H residues before XYZ refinement:
** B 101 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 = 0.3221 r_free = 0.3221 target = 0.104240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.085570 restraints weight = 21949.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.088298 restraints weight = 12461.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.090179 restraints weight = 8520.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.091364 restraints weight = 6526.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.092240 restraints weight = 5460.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.5872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  12544  Z= 0.166
  Angle     :  0.682  10.299  17022  Z= 0.340
  Chirality :  0.047   0.265   1901
  Planarity :  0.005   0.116   2169
  Dihedral  :  5.240  50.192   1668
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.68 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 21.30 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.21), residues: 1510
  helix: -0.06 (0.60), residues: 81
  sheet: -0.67 (0.21), residues: 597
  loop : -1.73 (0.21), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 358 
 TYR   0.036   0.002   TYR A  19 
 PHE   0.026   0.002   PHE A 221 
 TRP   0.035   0.002   TRP B 229 
 HIS   0.007   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (12544)
  covalent geometry    : angle       0.68229 (17022)
  hydrogen bonds       : bond        0.03182 (  315)
  hydrogen bonds       : angle       5.82831 (  834)

********************** 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
  213 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   24 ASN cc_start: 0.8351 (p0) cc_final: 0.8049 (p0)
REVERT: A  100 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8057 (t0)
REVERT: A  189 TYR cc_start: 0.8518 (p90) cc_final: 0.8167 (p90)
REVERT: A  203 ILE cc_start: 0.8684 (mm) cc_final: 0.8458 (mm)
REVERT: A  386 SER cc_start: 0.9163 (p) cc_final: 0.8644 (m)
REVERT: A  628 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8556 (tt)
REVERT: A  996 LEU cc_start: 0.9177 (tp) cc_final: 0.8857 (tt)
REVERT: A 1093 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7040 (mt-10)
REVERT: A 1097 TRP cc_start: 0.8600 (m-90) cc_final: 0.8214 (m-90)
REVERT: A 1220 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.7508 (t0)
REVERT: A 1259 ASP cc_start: 0.8122 (t0) cc_final: 0.7543 (t0)
REVERT: B  210 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6091 (p90)
REVERT: B  285 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.6481 (p90)
REVERT: B  292 MET cc_start: 0.7924 (mtp) cc_final: 0.7661 (mtt)
REVERT: B  366 GLU cc_start: 0.7674 (pm20) cc_final: 0.7333 (pm20)
  outliers start: 37
  outliers final: 27
  residues processed: 202
  average time/residue: 0.0843
  time to fit residues: 27.3130
Evaluate side-chains
  203 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  251 VAL
Chi-restraints excluded: chain A residue  252 HIS
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  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 1050 MET
Chi-restraints excluded: chain A residue 1067 ILE
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1220 ASN
Chi-restraints excluded: chain A residue 1255 VAL
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 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  285 HIS
Chi-restraints excluded: chain B residue  346 LEU
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 48 optimal weight:    2.9990
   chunk 129 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 86 optimal weight:    2.9990
   chunk 125 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 82 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.099713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.080902 restraints weight = 22179.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.083588 restraints weight = 12638.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.085392 restraints weight = 8633.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.086611 restraints weight = 6667.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.087372 restraints weight = 5577.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.6043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  12544  Z= 0.191
  Angle     :  0.701  10.145  17022  Z= 0.351
  Chirality :  0.048   0.252   1901
  Planarity :  0.005   0.119   2169
  Dihedral  :  5.386  49.280   1668
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.75 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.77 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.22), residues: 1510
  helix: -0.07 (0.61), residues: 81
  sheet: -0.61 (0.21), residues: 591
  loop : -1.72 (0.21), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 194 
 TYR   0.032   0.002   TYR A  19 
 PHE   0.028   0.002   PHE A 221 
 TRP   0.036   0.002   TRP A1312 
 HIS   0.007   0.001   HIS A1385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (12544)
  covalent geometry    : angle       0.70133 (17022)
  hydrogen bonds       : bond        0.03254 (  315)
  hydrogen bonds       : angle       5.87389 (  834)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1907.78 seconds
wall clock time: 33 minutes 55.37 seconds (2035.37 seconds total)