Starting phenix.real_space_refine
on Sun Jun 22 15:10:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fpj_29366/06_2025/8fpj_29366_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fpj_29366/06_2025/8fpj_29366.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fpj_29366/06_2025/8fpj_29366.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fpj_29366/06_2025/8fpj_29366.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fpj_29366/06_2025/8fpj_29366_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fpj_29366/06_2025/8fpj_29366_trim.cif"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.052
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: 6
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    8157      2.51       5
     N    2206      2.21       5
     O    2383      1.98       5
     F       1      1.80       5
     H   13143      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.10s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 25960
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 21983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1345, 21983
          Classifications: {'peptide': 1345}
          Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1293}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1491
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 1, 'TRANS': 93}
    Chain: "C"
      Number of atoms: 975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 975
          Classifications: {'peptide': 63}
          Link IDs: {'PTRANS': 1, 'TRANS': 61}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 736
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "E"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 740
          Classifications: {'peptide': 46}
          Link IDs: {'TRANS': 45}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y6L': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 13.81, per 1000 atoms: 0.53
  Number of scatterers: 25960
  At special positions: 0
  Unit cell: (115.92, 102.48, 109.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      70     16.00
     F       1      9.00
     O    2383      8.00
     N    2206      7.00
     C    8157      6.00
     H   13143      1.00
    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: 7.06
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3038

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 9 sheets defined
      61.3% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 36
      removed outlier: 3.528A  pdb=" N   THR A  27 " --> pdb=" O   SER A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 52
      removed outlier: 3.638A  pdb=" N   LYS A  47 " --> pdb=" O   ASP A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 67
      removed outlier: 3.577A  pdb=" N   LYS A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.687A  pdb=" N   ASP A  72 " --> pdb=" O   LYS A  69 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR A  73 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 69 through 73'
    Processing helix  chain 'A' and resid 77 through 80
    Processing helix  chain 'A' and resid 81 through 88
    Processing helix  chain 'A' and resid 93 through 120
      removed outlier: 3.584A  pdb=" N   LEU A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TRP A 118 " --> pdb=" O   MET A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 135 through 139
      removed outlier: 3.658A  pdb=" N   PHE A 138 " --> pdb=" O   ASP A 135 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ILE A 139 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 135 through 139'
    Processing helix  chain 'A' and resid 143 through 167
      removed outlier: 3.516A  pdb=" N   PHE A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE A 166 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 231
    Processing helix  chain 'A' and resid 243 through 261
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 271 through 285
    Processing helix  chain 'A' and resid 286 through 316
      removed outlier: 3.515A  pdb=" N   SER A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   LYS A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   ASN A 310 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 324
      removed outlier: 4.196A  pdb=" N   ASN A 323 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 347
      removed outlier: 3.672A  pdb=" N   VAL A 332 " --> pdb=" O   MET A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 357
    Processing helix  chain 'A' and resid 358 through 362
      removed outlier: 3.956A  pdb=" N   PHE A 361 " --> pdb=" O   TYR A 358 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG A 362 " --> pdb=" O   TYR A 359 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 358 through 362'
    Processing helix  chain 'A' and resid 370 through 380
      removed outlier: 3.640A  pdb=" N   ALA A 374 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   MET A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASP A 376 " --> pdb=" O   ARG A 372 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU A 380 " --> pdb=" O   ASP A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 413
    Processing helix  chain 'A' and resid 425 through 435
    Processing helix  chain 'A' and resid 444 through 452
      removed outlier: 3.704A  pdb=" N   PHE A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 472
    Processing helix  chain 'A' and resid 481 through 488
      removed outlier: 3.723A  pdb=" N   ILE A 484 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   TRP A 485 " --> pdb=" O   ARG A 482 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   SER A 486 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR A 488 " --> pdb=" O   TRP A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 493
    Processing helix  chain 'A' and resid 494 through 508
      removed outlier: 3.566A  pdb=" N   PHE A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASN A 507 " --> pdb=" O   GLU A 503 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 514
      removed outlier: 3.616A  pdb=" N   LYS A 513 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   THR A 514 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 510 through 514'
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 530 through 539
      removed outlier: 3.798A  pdb=" N   SER A 534 " --> pdb=" O   LYS A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 586
      removed outlier: 3.629A  pdb=" N   ILE A 574 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 595
      removed outlier: 3.520A  pdb=" N   LEU A 594 " --> pdb=" O   PHE A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 643
      removed outlier: 3.731A  pdb=" N   ALA A 642 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 660
      removed outlier: 4.443A  pdb=" N   ILE A 650 " --> pdb=" O   GLU A 646 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   CYS A 651 " --> pdb=" O   THR A 647 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   VAL A 654 " --> pdb=" O   ILE A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 672
    Processing helix  chain 'A' and resid 673 through 675
      No H-bonds generated for 'chain 'A' and resid 673 through 675'
    Processing helix  chain 'A' and resid 693 through 697
    Processing helix  chain 'A' and resid 715 through 734
      removed outlier: 3.699A  pdb=" N   LEU A 727 " --> pdb=" O   ALA A 723 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP A 728 " --> pdb=" O   ILE A 724 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A 729 " --> pdb=" O   SER A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 785
      removed outlier: 3.761A  pdb=" N   ILE A 785 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 806
    Processing helix  chain 'A' and resid 834 through 847
    Processing helix  chain 'A' and resid 847 through 852
    Processing helix  chain 'A' and resid 856 through 874
    Processing helix  chain 'A' and resid 883 through 901
    Processing helix  chain 'A' and resid 905 through 913
      removed outlier: 4.040A  pdb=" N   VAL A 909 " --> pdb=" O   GLU A 905 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ASP A 910 " --> pdb=" O   ASN A 906 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU A 911 " --> pdb=" O   GLU A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 915
      No H-bonds generated for 'chain 'A' and resid 914 through 915'
    Processing helix  chain 'A' and resid 916 through 920
    Processing helix  chain 'A' and resid 926 through 931
    Processing helix  chain 'A' and resid 937 through 953
    Processing helix  chain 'A' and resid 957 through 970
      removed outlier: 3.545A  pdb=" N   LYS A 961 " --> pdb=" O   LYS A 957 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 962 " --> pdb=" O   ASN A 958 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   PHE A 965 " --> pdb=" O   LYS A 961 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS A 966 " --> pdb=" O   VAL A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 985
    Processing helix  chain 'A' and resid 997 through 1012
      removed outlier: 3.632A  pdb=" N   ILE A1001 " --> pdb=" O   VAL A 997 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   THR A1004 " --> pdb=" O   ASP A1000 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   ALA A1005 " --> pdb=" O   ILE A1001 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU A1012 " --> pdb=" O   SER A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1033
      removed outlier: 4.629A  pdb=" N   SER A1026 " --> pdb=" O   ALA A1022 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   ARG A1027 " --> pdb=" O   ILE A1023 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY A1033 " --> pdb=" O   GLU A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1053
    Processing helix  chain 'A' and resid 1055 through 1068
      removed outlier: 3.849A  pdb=" N   GLY A1068 " --> pdb=" O   ASN A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1097
    Processing helix  chain 'A' and resid 1099 through 1105
    Processing helix  chain 'A' and resid 1123 through 1135
    Processing helix  chain 'A' and resid 1207 through 1224
    Processing helix  chain 'A' and resid 1229 through 1242
    Processing helix  chain 'A' and resid 1245 through 1250
    Processing helix  chain 'A' and resid 1251 through 1253
      No H-bonds generated for 'chain 'A' and resid 1251 through 1253'
    Processing helix  chain 'A' and resid 1260 through 1265
    Processing helix  chain 'A' and resid 1279 through 1284
    Processing helix  chain 'A' and resid 1290 through 1301
    Processing helix  chain 'A' and resid 1309 through 1328
      removed outlier: 3.505A  pdb=" N   GLU A1325 " --> pdb=" O   MET A1321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1344
    Processing helix  chain 'A' and resid 1358 through 1368
      removed outlier: 4.417A  pdb=" N   ASP A1362 " --> pdb=" O   TYR A1358 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LYS A1363 " --> pdb=" O   LYS A1359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1369 through 1372
    Processing helix  chain 'B' and resid 173 through 193
    Processing helix  chain 'B' and resid 214 through 226
    Processing helix  chain 'B' and resid 228 through 239
      removed outlier: 3.610A  pdb=" N   GLU B 232 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 263
      removed outlier: 4.114A  pdb=" N   LEU B 258 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 198
      removed outlier: 3.681A  pdb=" N   ALA C 198 " --> pdb=" O   ASN C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 205
      removed outlier: 3.594A  pdb=" N   ASP C 205 " --> pdb=" O   THR C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 213
    Processing helix  chain 'C' and resid 217 through 233
    Processing helix  chain 'D' and resid 173 through 193
      removed outlier: 3.758A  pdb=" N   THR D 192 " --> pdb=" O   GLY D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 204
      No H-bonds generated for 'chain 'D' and resid 202 through 204'
    Processing helix  chain 'D' and resid 205 through 218
      removed outlier: 4.195A  pdb=" N   ASP D 209 " --> pdb=" O   ASP D 205 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ALA D 210 " --> pdb=" O   GLY D 206 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ARG D 215 " --> pdb=" O   MET D 211 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLU D 216 " --> pdb=" O   ILE D 212 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU D 218 " --> pdb=" O   ILE D 214 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 174 through 191
      removed outlier: 3.720A  pdb=" N   SER E 184 " --> pdb=" O   GLU E 180 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   MET E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 205 through 226
      removed outlier: 3.637A  pdb=" N   GLU E 217 " --> pdb=" O   GLY E 213 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE E 219 " --> pdb=" O   ARG E 215 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA E 220 " --> pdb=" O   GLU E 216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75
      removed outlier: 6.043A  pdb=" N   LYS A  74 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   PHE A 200 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 389
    Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 551
    Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 743
    Processing sheet with id=AA6, first strand: chain 'A' and resid 807 through 809
      removed outlier: 4.305A  pdb=" N   ILE A 807 " --> pdb=" O   HIS A 814 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1153 through 1157
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1196 through 1197
    Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 200

    656 hydrogen bonds defined for protein.
    1854 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: 10.28

  Time building geometry restraints manager: 8.49 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 13122
        1.03 -     1.23: 31
        1.23 -     1.42: 5213
        1.42 -     1.62: 7684
        1.62 -     1.81: 119
  Bond restraints: 26169
  Sorted by residual:
  bond pdb=" O   Y6L A9901 "
       pdb=" C19 Y6L A9901 "
    ideal  model  delta    sigma   weight residual
    1.412  1.452 -0.040 2.00e-02 2.50e+03 4.07e+00
  bond pdb=" C20 Y6L A9901 "
       pdb=" C21 Y6L A9901 "
    ideal  model  delta    sigma   weight residual
    1.514  1.485  0.029 2.00e-02 2.50e+03 2.04e+00
  bond pdb=" C   ALA A 954 "
       pdb=" N   ASN A 955 "
    ideal  model  delta    sigma   weight residual
    1.332  1.313  0.019 1.40e-02 5.10e+03 1.87e+00
  bond pdb=" C14 Y6L A9901 "
       pdb=" N3  Y6L A9901 "
    ideal  model  delta    sigma   weight residual
    1.369  1.345  0.024 2.00e-02 2.50e+03 1.48e+00
  bond pdb=" CB  ASN A1312 "
       pdb=" CG  ASN A1312 "
    ideal  model  delta    sigma   weight residual
    1.516  1.487  0.029 2.50e-02 1.60e+03 1.34e+00
  ... (remaining 26164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 44985
        1.20 -     2.39: 2326
        2.39 -     3.59: 130
        3.59 -     4.79: 28
        4.79 -     5.99: 3
  Bond angle restraints: 47472
  Sorted by residual:
  angle pdb=" N   VAL A 423 "
        pdb=" CA  VAL A 423 "
        pdb=" C   VAL A 423 "
      ideal   model   delta    sigma   weight residual
     112.29  108.65    3.64 9.40e-01 1.13e+00 1.50e+01
  angle pdb=" N   ILE A 818 "
        pdb=" CA  ILE A 818 "
        pdb=" C   ILE A 818 "
      ideal   model   delta    sigma   weight residual
     106.21  109.96   -3.75 1.07e+00 8.73e-01 1.23e+01
  angle pdb=" N   HIS A  90 "
        pdb=" CA  HIS A  90 "
        pdb=" C   HIS A  90 "
      ideal   model   delta    sigma   weight residual
     109.65  105.17    4.48 1.56e+00 4.11e-01 8.25e+00
  angle pdb=" C   VAL A1155 "
        pdb=" N   ILE A1156 "
        pdb=" CA  ILE A1156 "
      ideal   model   delta    sigma   weight residual
     123.46  120.40    3.06 1.37e+00 5.33e-01 4.97e+00
  angle pdb=" N   LYS A  19 "
        pdb=" CA  LYS A  19 "
        pdb=" CB  LYS A  19 "
      ideal   model   delta    sigma   weight residual
     112.78  109.51    3.27 1.53e+00 4.27e-01 4.57e+00
  ... (remaining 47467 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 11028
       17.52 -    35.04: 837
       35.04 -    52.55: 191
       52.55 -    70.07: 66
       70.07 -    87.59: 15
  Dihedral angle restraints: 12137
    sinusoidal: 6825
      harmonic: 5312
  Sorted by residual:
  dihedral pdb=" CA  ARG A 362 "
           pdb=" C   ARG A 362 "
           pdb=" N   ILE A 363 "
           pdb=" CA  ILE A 363 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.19  -23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  CYS A 261 "
           pdb=" C   CYS A 261 "
           pdb=" N   CYS A 262 "
           pdb=" CA  CYS A 262 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.08  -22.92     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ASN A 204 "
           pdb=" C   ASN A 204 "
           pdb=" N   GLN A 205 "
           pdb=" CA  GLN A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.88  -22.12     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 12134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1235
       0.028 -    0.057: 537
       0.057 -    0.085: 147
       0.085 -    0.113: 69
       0.113 -    0.142: 33
  Chirality restraints: 2021
  Sorted by residual:
  chirality pdb=" CA  VAL A1267 "
            pdb=" N   VAL A1267 "
            pdb=" C   VAL A1267 "
            pdb=" CB  VAL A1267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  ILE A1039 "
            pdb=" N   ILE A1039 "
            pdb=" C   ILE A1039 "
            pdb=" CB  ILE A1039 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  ILE A 915 "
            pdb=" N   ILE A 915 "
            pdb=" C   ILE A 915 "
            pdb=" CB  ILE A 915 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.71e-01
  ... (remaining 2018 not shown)

  Planarity restraints: 3753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C14 Y6L A9901 "    0.034 2.00e-02 2.50e+03   7.06e-02 6.22e+01
        pdb=" C15 Y6L A9901 "   -0.067 2.00e-02 2.50e+03
        pdb=" N2  Y6L A9901 "   -0.088 2.00e-02 2.50e+03
        pdb=" N3  Y6L A9901 "    0.106 2.00e-02 2.50e+03
        pdb=" O2  Y6L A9901 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 Y6L A9901 "   -0.037 2.00e-02 2.50e+03   3.91e-02 1.91e+01
        pdb=" C13 Y6L A9901 "    0.018 2.00e-02 2.50e+03
        pdb=" N2  Y6L A9901 "    0.060 2.00e-02 2.50e+03
        pdb=" N3  Y6L A9901 "   -0.048 2.00e-02 2.50e+03
        pdb=" O3  Y6L A9901 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 415 "    0.011 2.00e-02 2.50e+03   1.10e-02 4.82e+00
        pdb=" CG  TRP A 415 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 415 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 415 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 415 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 415 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 415 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 415 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 415 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 415 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 415 "    0.008 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 415 "    0.003 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 415 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 415 "   -0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 415 "    0.002 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 415 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 3750 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 927
        2.18 -     2.78: 52078
        2.78 -     3.39: 71087
        3.39 -     3.99: 92647
        3.99 -     4.60: 146719
  Nonbonded interactions: 363458
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 653 "
            pdb="HH22 ARG C 215 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" OE2 GLU A1060 "
            pdb="HD21 ASN A1064 "
     model   vdw
     1.611 2.450
  nonbonded pdb="HD22 ASN A  88 "
            pdb=" O   LEU A 176 "
     model   vdw
     1.616 2.450
  nonbonded pdb="HH22 ARG A 341 "
            pdb=" O   GLU B 265 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" H   LYS A1117 "
            pdb=" O   ARG A1121 "
     model   vdw
     1.636 2.450
  ... (remaining 363453 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=0.00 max=1.00 mean=0.49
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.880
  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:             0.470
  Extract box with map and model:          1.120
  Check model and map are aligned:         0.110
  Set scattering table:                    0.260
  Process input model:                     57.950
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   75.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13026  Z= 0.153
  Angle     :  0.573   5.987  17566  Z= 0.322
  Chirality :  0.039   0.142   2021
  Planarity :  0.004   0.071   2220
  Dihedral  : 13.899  87.590   5007
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.21), residues: 1578
  helix:  0.89 (0.18), residues: 835
  sheet: -0.15 (0.63), residues: 72
  loop : -1.53 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 415 
 HIS   0.012   0.002   HIS A 286 
 PHE   0.013   0.001   PHE A1310 
 TYR   0.014   0.001   TYR A 706 
 ARG   0.004   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17082 (  656)
  hydrogen bonds       : angle       6.03423 ( 1854)
  covalent geometry    : bond        0.00340 (13026)
  covalent geometry    : angle       0.57349 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 2.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8425 (ttp) cc_final: 0.8153 (ttm)
REVERT: A  910 ASP cc_start: 0.7515 (m-30) cc_final: 0.7302 (m-30)
REVERT: A 1096 GLU cc_start: 0.7376 (tt0) cc_final: 0.7059 (tp30)
REVERT: A 1307 ASN cc_start: 0.7372 (m110) cc_final: 0.7164 (m-40)
REVERT: A 1340 GLN cc_start: 0.7205 (mt0) cc_final: 0.6709 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 3.0236
  time to fit residues: 667.2499
Evaluate side-chains
  155 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 2.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 142 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1295 GLN
B 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.158009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124106 restraints weight = 39103.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.91
r_work: 0.3332 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13026  Z= 0.148
  Angle     :  0.551   6.023  17566  Z= 0.299
  Chirality :  0.039   0.144   2021
  Planarity :  0.004   0.048   2220
  Dihedral  :  4.950  25.351   1751
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.08 %
    Favored  : 90.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.21), residues: 1578
  helix:  1.09 (0.18), residues: 860
  sheet: -0.12 (0.61), residues: 72
  loop : -1.46 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 142 
 HIS   0.011   0.001   HIS A 286 
 PHE   0.013   0.001   PHE A1310 
 TYR   0.015   0.001   TYR A 706 
 ARG   0.005   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05868 (  656)
  hydrogen bonds       : angle       4.52204 ( 1854)
  covalent geometry    : bond        0.00337 (13026)
  covalent geometry    : angle       0.55053 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 2.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8651 (ttp) cc_final: 0.8371 (ttm)
REVERT: A  440 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7022 (tm-30)
REVERT: A  503 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7329 (tt0)
REVERT: A  790 LYS cc_start: 0.8244 (mttp) cc_final: 0.7459 (mtpp)
REVERT: A 1096 GLU cc_start: 0.8141 (tt0) cc_final: 0.7742 (tp30)
REVERT: A 1247 LYS cc_start: 0.7956 (pttt) cc_final: 0.7387 (pptt)
REVERT: A 1340 GLN cc_start: 0.7545 (mt0) cc_final: 0.6788 (mm110)
REVERT: A 1345 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6873 (m-30)
REVERT: B  250 LYS cc_start: 0.8223 (tttm) cc_final: 0.7484 (tptt)
  outliers start: 16
  outliers final: 4
  residues processed: 169
  average time/residue: 2.8617
  time to fit residues: 529.4494
Evaluate side-chains
  155 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 148
  time to evaluate  : 2.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1345 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 138 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 115 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 141 optimal weight:    1.9990
   chunk 126 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 743 ASN
A1028 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1295 GLN
A1353 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.154754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.120515 restraints weight = 38861.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.92
r_work: 0.3275 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13026  Z= 0.182
  Angle     :  0.579   6.018  17566  Z= 0.313
  Chirality :  0.040   0.150   2021
  Planarity :  0.004   0.049   2220
  Dihedral  :  5.019  25.152   1751
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.55 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.21), residues: 1578
  helix:  1.12 (0.18), residues: 861
  sheet: -0.23 (0.59), residues: 72
  loop : -1.51 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 415 
 HIS   0.010   0.001   HIS A 286 
 PHE   0.015   0.002   PHE A1310 
 TYR   0.017   0.002   TYR A 706 
 ARG   0.005   0.001   ARG A1178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06269 (  656)
  hydrogen bonds       : angle       4.38807 ( 1854)
  covalent geometry    : bond        0.00440 (13026)
  covalent geometry    : angle       0.57866 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 2.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8706 (ttp) cc_final: 0.8429 (ttm)
REVERT: A  282 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7784 (ttm170)
REVERT: A  440 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7048 (tm-30)
REVERT: A  503 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7322 (tt0)
REVERT: A  691 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7678 (pp20)
REVERT: A  790 LYS cc_start: 0.8268 (mttp) cc_final: 0.7474 (mtpp)
REVERT: A 1096 GLU cc_start: 0.8194 (tt0) cc_final: 0.7788 (tp30)
REVERT: A 1247 LYS cc_start: 0.8072 (pttt) cc_final: 0.7472 (pptt)
REVERT: A 1333 LYS cc_start: 0.8146 (tptt) cc_final: 0.7873 (tptt)
REVERT: A 1340 GLN cc_start: 0.7740 (mt0) cc_final: 0.7033 (mm110)
REVERT: A 1345 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7025 (m-30)
  outliers start: 21
  outliers final: 8
  residues processed: 167
  average time/residue: 3.0813
  time to fit residues: 564.7446
Evaluate side-chains
  161 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 2.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1345 ASP
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  194 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 115 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1353 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.156481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.124698 restraints weight = 41372.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.87
r_work: 0.3352 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13026  Z= 0.137
  Angle     :  0.531   5.900  17566  Z= 0.285
  Chirality :  0.038   0.142   2021
  Planarity :  0.004   0.047   2220
  Dihedral  :  4.848  23.704   1751
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.08 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.21), residues: 1578
  helix:  1.22 (0.18), residues: 867
  sheet: -0.22 (0.58), residues: 72
  loop : -1.50 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 142 
 HIS   0.009   0.001   HIS A 286 
 PHE   0.013   0.001   PHE A1310 
 TYR   0.013   0.001   TYR A 706 
 ARG   0.005   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05354 (  656)
  hydrogen bonds       : angle       4.22678 ( 1854)
  covalent geometry    : bond        0.00322 (13026)
  covalent geometry    : angle       0.53055 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 2.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8685 (ttp) cc_final: 0.8440 (ttm)
REVERT: A  282 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7771 (ttm170)
REVERT: A  373 ASP cc_start: 0.8186 (t0) cc_final: 0.7811 (t0)
REVERT: A  375 MET cc_start: 0.8484 (mtp) cc_final: 0.8141 (mtp)
REVERT: A  440 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7129 (tm-30)
REVERT: A  503 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7271 (tt0)
REVERT: A  790 LYS cc_start: 0.8338 (mttp) cc_final: 0.7584 (mtpp)
REVERT: A 1096 GLU cc_start: 0.8137 (tt0) cc_final: 0.7725 (tp30)
REVERT: A 1247 LYS cc_start: 0.8171 (pttt) cc_final: 0.7617 (pptt)
REVERT: A 1340 GLN cc_start: 0.7787 (mt0) cc_final: 0.7193 (mm110)
REVERT: C  211 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7435 (mtt)
  outliers start: 27
  outliers final: 8
  residues processed: 171
  average time/residue: 2.9324
  time to fit residues: 548.8696
Evaluate side-chains
  160 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 1.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain C residue  211 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0980
   chunk 62 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 154 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 139 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 525 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.155153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.123018 restraints weight = 41048.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.90
r_work: 0.3332 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13026  Z= 0.155
  Angle     :  0.547   5.848  17566  Z= 0.294
  Chirality :  0.039   0.146   2021
  Planarity :  0.004   0.049   2220
  Dihedral  :  4.863  24.045   1751
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.06 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.21), residues: 1578
  helix:  1.20 (0.18), residues: 867
  sheet: -0.22 (0.58), residues: 72
  loop : -1.50 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 142 
 HIS   0.007   0.001   HIS A 286 
 PHE   0.014   0.001   PHE A1310 
 TYR   0.015   0.002   TYR A 706 
 ARG   0.005   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05621 (  656)
  hydrogen bonds       : angle       4.20153 ( 1854)
  covalent geometry    : bond        0.00372 (13026)
  covalent geometry    : angle       0.54714 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 2.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8701 (ttp) cc_final: 0.8442 (ttm)
REVERT: A  282 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7806 (ttm170)
REVERT: A  341 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7714 (mtp180)
REVERT: A  375 MET cc_start: 0.8544 (mtp) cc_final: 0.8343 (mtp)
REVERT: A  440 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7025 (tm-30)
REVERT: A  503 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7264 (tt0)
REVERT: A  790 LYS cc_start: 0.8339 (mttp) cc_final: 0.7577 (mtpp)
REVERT: A  791 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6891 (mm-30)
REVERT: A 1096 GLU cc_start: 0.8146 (tt0) cc_final: 0.7762 (tp30)
REVERT: A 1247 LYS cc_start: 0.8211 (pttt) cc_final: 0.7646 (pptt)
REVERT: A 1340 GLN cc_start: 0.7877 (mt0) cc_final: 0.7312 (mm110)
REVERT: A 1345 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7050 (m-30)
  outliers start: 28
  outliers final: 13
  residues processed: 174
  average time/residue: 2.8248
  time to fit residues: 537.0207
Evaluate side-chains
  164 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  791 GLU
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1345 ASP
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  185 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 154 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 147 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 142 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 525 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.153534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.121665 restraints weight = 41147.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.85
r_work: 0.3313 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13026  Z= 0.178
  Angle     :  0.573   5.682  17566  Z= 0.308
  Chirality :  0.040   0.149   2021
  Planarity :  0.004   0.055   2220
  Dihedral  :  4.968  24.967   1751
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.17 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.21), residues: 1578
  helix:  1.16 (0.18), residues: 864
  sheet: -0.22 (0.59), residues: 72
  loop : -1.53 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 142 
 HIS   0.011   0.002   HIS A 945 
 PHE   0.014   0.002   PHE A1310 
 TYR   0.016   0.002   TYR A 706 
 ARG   0.007   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06016 (  656)
  hydrogen bonds       : angle       4.18918 ( 1854)
  covalent geometry    : bond        0.00432 (13026)
  covalent geometry    : angle       0.57298 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 1.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8706 (ttp) cc_final: 0.8450 (ttm)
REVERT: A  282 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7835 (ttm170)
REVERT: A  341 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7702 (mtp180)
REVERT: A  440 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7037 (tm-30)
REVERT: A  503 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7302 (tt0)
REVERT: A  790 LYS cc_start: 0.8420 (mttp) cc_final: 0.7671 (mtpp)
REVERT: A  791 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6752 (mm-30)
REVERT: A 1096 GLU cc_start: 0.8134 (tt0) cc_final: 0.7754 (tp30)
REVERT: A 1247 LYS cc_start: 0.8250 (pttt) cc_final: 0.7672 (pptt)
REVERT: A 1340 GLN cc_start: 0.7869 (mt0) cc_final: 0.7443 (mm110)
  outliers start: 30
  outliers final: 12
  residues processed: 172
  average time/residue: 2.7785
  time to fit residues: 523.4289
Evaluate side-chains
  164 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 2.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  791 GLU
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  194 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0770
   chunk 83 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3944

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.154677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.122910 restraints weight = 41131.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.85
r_work: 0.3329 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13026  Z= 0.143
  Angle     :  0.545   5.800  17566  Z= 0.292
  Chirality :  0.039   0.143   2021
  Planarity :  0.004   0.057   2220
  Dihedral  :  4.887  24.252   1751
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.87 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.21), residues: 1578
  helix:  1.22 (0.18), residues: 867
  sheet: -0.19 (0.59), residues: 72
  loop : -1.48 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 142 
 HIS   0.006   0.001   HIS A 286 
 PHE   0.015   0.001   PHE A1310 
 TYR   0.013   0.001   TYR A 706 
 ARG   0.007   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05463 (  656)
  hydrogen bonds       : angle       4.11817 ( 1854)
  covalent geometry    : bond        0.00337 (13026)
  covalent geometry    : angle       0.54533 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 2.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8685 (ttp) cc_final: 0.8453 (ttm)
REVERT: A  282 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7802 (ttm170)
REVERT: A  341 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7674 (mtp180)
REVERT: A  440 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7091 (tm-30)
REVERT: A  503 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7289 (tt0)
REVERT: A  677 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8686 (mmm)
REVERT: A  790 LYS cc_start: 0.8359 (mttp) cc_final: 0.7601 (mtpp)
REVERT: A  791 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6783 (mm-30)
REVERT: A 1096 GLU cc_start: 0.8159 (tt0) cc_final: 0.7766 (tp30)
REVERT: A 1247 LYS cc_start: 0.8223 (pttt) cc_final: 0.7640 (pptt)
REVERT: A 1340 GLN cc_start: 0.7809 (mt0) cc_final: 0.7395 (mm-40)
  outliers start: 22
  outliers final: 12
  residues processed: 168
  average time/residue: 2.8992
  time to fit residues: 533.1821
Evaluate side-chains
  167 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 2.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  791 GLU
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  185 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 152 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 140 optimal weight:    2.9990
   chunk 132 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 525 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.153123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.120931 restraints weight = 41043.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.89
r_work: 0.3304 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13026  Z= 0.174
  Angle     :  0.573   5.829  17566  Z= 0.308
  Chirality :  0.040   0.148   2021
  Planarity :  0.004   0.062   2220
  Dihedral  :  4.973  24.810   1751
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.29 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.21), residues: 1578
  helix:  1.17 (0.18), residues: 864
  sheet: -0.33 (0.59), residues: 73
  loop : -1.52 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 142 
 HIS   0.007   0.001   HIS A 683 
 PHE   0.015   0.002   PHE A1310 
 TYR   0.015   0.002   TYR A 706 
 ARG   0.009   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05940 (  656)
  hydrogen bonds       : angle       4.13433 ( 1854)
  covalent geometry    : bond        0.00423 (13026)
  covalent geometry    : angle       0.57308 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 2.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8682 (ttp) cc_final: 0.8439 (ttm)
REVERT: A  282 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7765 (ttm170)
REVERT: A  341 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7634 (mtp180)
REVERT: A  440 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7082 (tm-30)
REVERT: A  503 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7274 (tt0)
REVERT: A  677 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8665 (mmm)
REVERT: A  790 LYS cc_start: 0.8379 (mttp) cc_final: 0.7607 (mtpp)
REVERT: A  791 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6775 (mm-30)
REVERT: A  905 GLU cc_start: 0.7453 (tp30) cc_final: 0.7127 (tp30)
REVERT: A 1096 GLU cc_start: 0.8125 (tt0) cc_final: 0.7711 (tp30)
REVERT: A 1247 LYS cc_start: 0.8208 (pttt) cc_final: 0.7851 (tttm)
REVERT: A 1340 GLN cc_start: 0.7766 (mt0) cc_final: 0.7329 (mm110)
REVERT: A 1345 ASP cc_start: 0.7519 (m-30) cc_final: 0.6944 (m-30)
  outliers start: 24
  outliers final: 14
  residues processed: 174
  average time/residue: 2.8249
  time to fit residues: 539.1796
Evaluate side-chains
  172 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 2.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  791 GLU
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  194 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 139 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.152933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120884 restraints weight = 41144.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.88
r_work: 0.3300 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13026  Z= 0.177
  Angle     :  0.577   5.825  17566  Z= 0.310
  Chirality :  0.040   0.146   2021
  Planarity :  0.004   0.069   2220
  Dihedral  :  5.015  25.216   1751
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.43 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.21), residues: 1578
  helix:  1.14 (0.18), residues: 864
  sheet: -0.35 (0.58), residues: 73
  loop : -1.54 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 142 
 HIS   0.007   0.001   HIS A 683 
 PHE   0.015   0.002   PHE A1310 
 TYR   0.016   0.002   TYR A 706 
 ARG   0.009   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05969 (  656)
  hydrogen bonds       : angle       4.14277 ( 1854)
  covalent geometry    : bond        0.00429 (13026)
  covalent geometry    : angle       0.57671 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 2.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 MET cc_start: 0.8702 (ttp) cc_final: 0.8474 (ttm)
REVERT: A  282 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7806 (ttm170)
REVERT: A  341 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7674 (mtp180)
REVERT: A  380 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8276 (tt)
REVERT: A  440 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7081 (tm-30)
REVERT: A  503 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7300 (tt0)
REVERT: A  677 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8632 (mmm)
REVERT: A  790 LYS cc_start: 0.8409 (mttp) cc_final: 0.7666 (mtpp)
REVERT: A  791 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6815 (mm-30)
REVERT: A 1096 GLU cc_start: 0.8148 (tt0) cc_final: 0.7723 (tp30)
REVERT: A 1247 LYS cc_start: 0.8243 (pttt) cc_final: 0.7900 (tttm)
REVERT: A 1330 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7914 (ttp-110)
REVERT: A 1340 GLN cc_start: 0.7753 (mt0) cc_final: 0.7443 (mm110)
REVERT: A 1345 ASP cc_start: 0.7592 (m-30) cc_final: 0.7034 (m-30)
REVERT: C  233 MET cc_start: 0.3549 (ppp) cc_final: 0.2468 (pmt)
  outliers start: 22
  outliers final: 15
  residues processed: 172
  average time/residue: 2.8596
  time to fit residues: 538.8082
Evaluate side-chains
  176 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 2.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  282 ARG
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  791 GLU
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  194 ASN
Chi-restraints excluded: chain C residue  183 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9980
   chunk 156 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 116 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.156407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124631 restraints weight = 41002.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.87
r_work: 0.3352 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13026  Z= 0.114
  Angle     :  0.515   5.607  17566  Z= 0.275
  Chirality :  0.038   0.138   2021
  Planarity :  0.004   0.067   2220
  Dihedral  :  4.769  23.775   1751
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.19 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.22), residues: 1578
  helix:  1.35 (0.18), residues: 866
  sheet: -0.26 (0.59), residues: 73
  loop : -1.44 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 142 
 HIS   0.006   0.001   HIS A 286 
 PHE   0.014   0.001   PHE A1310 
 TYR   0.012   0.001   TYR A 645 
 ARG   0.009   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04830 (  656)
  hydrogen bonds       : angle       4.01964 ( 1854)
  covalent geometry    : bond        0.00258 (13026)
  covalent geometry    : angle       0.51462 (17566)

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

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

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3156 Ramachandran restraints generated.
    1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 2.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  341 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7628 (mtp180)
REVERT: A  380 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8223 (tt)
REVERT: A  440 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7071 (tm-30)
REVERT: A  677 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8570 (mmm)
REVERT: A  790 LYS cc_start: 0.8419 (mttp) cc_final: 0.7671 (mtpp)
REVERT: A  806 VAL cc_start: 0.7983 (p) cc_final: 0.7731 (t)
REVERT: A 1096 GLU cc_start: 0.8157 (tt0) cc_final: 0.7724 (tp30)
REVERT: A 1247 LYS cc_start: 0.8201 (pttt) cc_final: 0.7859 (tttm)
REVERT: A 1340 GLN cc_start: 0.7716 (mt0) cc_final: 0.7440 (mm110)
REVERT: A 1345 ASP cc_start: 0.7570 (m-30) cc_final: 0.7138 (t0)
REVERT: B  250 LYS cc_start: 0.8252 (tttm) cc_final: 0.7583 (tptt)
REVERT: C  233 MET cc_start: 0.3692 (ppp) cc_final: 0.2603 (pmt)
  outliers start: 17
  outliers final: 11
  residues processed: 171
  average time/residue: 2.8626
  time to fit residues: 539.4457
Evaluate side-chains
  167 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 2.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  440 GLN
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  962 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1362 ASP
Chi-restraints excluded: chain B residue  185 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 138 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 411 ASN
A 743 ASN
** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.157562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125346 restraints weight = 40946.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.91
r_work: 0.3354 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13026  Z= 0.116
  Angle     :  0.511   5.591  17566  Z= 0.273
  Chirality :  0.038   0.142   2021
  Planarity :  0.004   0.068   2220
  Dihedral  :  4.675  23.629   1751
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.54 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.22), residues: 1578
  helix:  1.48 (0.18), residues: 866
  sheet: -0.27 (0.59), residues: 73
  loop : -1.39 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 142 
 HIS   0.007   0.001   HIS A 286 
 PHE   0.015   0.001   PHE A1310 
 TYR   0.012   0.001   TYR A 706 
 ARG   0.009   0.000   ARG A 852 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04686 (  656)
  hydrogen bonds       : angle       3.96807 ( 1854)
  covalent geometry    : bond        0.00266 (13026)
  covalent geometry    : angle       0.51061 (17566)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16456.74 seconds
wall clock time: 279 minutes 42.36 seconds (16782.36 seconds total)