Starting phenix.real_space_refine
on Thu Jun 12 01:19:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ip3_60756/06_2025/9ip3_60756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ip3_60756/06_2025/9ip3_60756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ip3_60756/06_2025/9ip3_60756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ip3_60756/06_2025/9ip3_60756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ip3_60756/06_2025/9ip3_60756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ip3_60756/06_2025/9ip3_60756.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.078
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      79      5.16       5
     C    8613      2.51       5
     N    2289      2.21       5
     O    2482      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13464
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1365, 10948
          Classifications: {'peptide': 1365}
          Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1292}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1684
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 218, 1677
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 201}
      Conformer: "B"
        Number of residues, atoms: 218, 1677
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 201}
          bond proxies already assigned to first conformer: 1704
    Chain: "C"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 417
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 231
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "E"
      Number of atoms: 183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 183
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9137  SG  CYS A1150      80.692  80.049  25.267  1.00 50.25           S
  ATOM   9159  SG  CYS A1153      81.704  83.492  26.350  1.00 79.12           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATHR B 335 " occ=0.42
      ... (12 atoms not shown)
      pdb=" CG2BTHR B 335 " occ=0.58
  Time building chain proxies: 8.87, per 1000 atoms: 0.66
  Number of scatterers: 13464
  At special positions: 0
  Unit cell: (99.51, 123.69, 122.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      79     16.00
     O    2482      8.00
     N    2289      7.00
     C    8613      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1105 " - pdb=" SG  CYS A1352 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.50
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1501 "
        pdb="ZN    ZN A1501 " - pdb=" ND1 HIS A1345 "
        pdb="ZN    ZN A1501 " - pdb=" NE2 HIS A1347 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A1150 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A1153 "
      Number of angles added : 2


  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3228

  Finding SS restraints...
    Secondary structure from input PDB file:
      90 helices and 9 sheets defined
      59.9% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 30
      removed outlier: 3.546A  pdb=" N   ARG A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 44
      removed outlier: 4.035A  pdb=" N   ASN A  43 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
      removed outlier: 3.983A  pdb=" N   ARG A  52 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 55
      No H-bonds generated for 'chain 'A' and resid 53 through 55'
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 3.779A  pdb=" N   THR A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 84
      removed outlier: 3.622A  pdb=" N   ILE A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
      Proline residue:  A  78  - end of helix
    Processing helix  chain 'A' and resid 95 through 122
      removed outlier: 4.118A  pdb=" N   PHE A  99 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LEU A 100 " --> pdb=" O   CYS A  96 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ASP A 101 " --> pdb=" O   GLN A  97 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   GLU A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 105 " --> pdb=" O   ASP A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 143
    Processing helix  chain 'A' and resid 145 through 165
    Processing helix  chain 'A' and resid 168 through 172
      removed outlier: 3.636A  pdb=" N   SER A 171 " --> pdb=" O   ASN A 168 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   THR A 172 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 168 through 172'
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 206 through 213
      removed outlier: 3.523A  pdb=" N   MET A 210 " --> pdb=" O   PRO A 206 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ASP A 211 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   TRP A 212 " --> pdb=" O   ALA A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 234 through 261
    Processing helix  chain 'A' and resid 269 through 288
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 297 through 308
    Processing helix  chain 'A' and resid 313 through 336
      removed outlier: 3.688A  pdb=" N   GLY A 317 " --> pdb=" O   THR A 313 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ARG A 318 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   PHE A 319 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 349
      removed outlier: 3.872A  pdb=" N   ARG A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 358
    Processing helix  chain 'A' and resid 361 through 369
    Processing helix  chain 'A' and resid 370 through 376
      removed outlier: 5.882A  pdb=" N   LYS A 373 " --> pdb=" O   SER A 370 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   TRP A 375 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 394
      removed outlier: 3.911A  pdb=" N   LYS A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   VAL A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   HIS A 392 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 424
    Processing helix  chain 'A' and resid 438 through 446
      removed outlier: 3.790A  pdb=" N   TYR A 442 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 458
      removed outlier: 3.630A  pdb=" N   LEU A 457 " --> pdb=" O   MET A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.679A  pdb=" N   ILE A 482 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 498
      removed outlier: 5.762A  pdb=" N   ASP A 495 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL A 497 " --> pdb=" O   TRP A 494 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE A 498 " --> pdb=" O   ASP A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 504
    Processing helix  chain 'A' and resid 515 through 523
    Processing helix  chain 'A' and resid 527 through 537
    Processing helix  chain 'A' and resid 538 through 546
      Proline residue:  A 543  - end of helix
    Processing helix  chain 'A' and resid 567 through 584
    Processing helix  chain 'A' and resid 585 through 589
    Processing helix  chain 'A' and resid 601 through 609
    Processing helix  chain 'A' and resid 635 through 640
      removed outlier: 3.857A  pdb=" N   ALA A 639 " --> pdb=" O   LYS A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 656
      Proline residue:  A 647  - end of helix
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 670 through 672
      No H-bonds generated for 'chain 'A' and resid 670 through 672'
    Processing helix  chain 'A' and resid 712 through 732
    Processing helix  chain 'A' and resid 757 through 784
    Processing helix  chain 'A' and resid 815 through 820
    Processing helix  chain 'A' and resid 832 through 850
    Processing helix  chain 'A' and resid 854 through 875
    Processing helix  chain 'A' and resid 884 through 891
      removed outlier: 3.632A  pdb=" N   THR A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 890 " --> pdb=" O   GLY A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 903
    Processing helix  chain 'A' and resid 916 through 921
    Processing helix  chain 'A' and resid 927 through 943
    Processing helix  chain 'A' and resid 945 through 947
      No H-bonds generated for 'chain 'A' and resid 945 through 947'
    Processing helix  chain 'A' and resid 948 through 954
    Processing helix  chain 'A' and resid 961 through 968
    Processing helix  chain 'A' and resid 980 through 996
    Processing helix  chain 'A' and resid 998 through 1003
    Processing helix  chain 'A' and resid 1008 through 1021
    Processing helix  chain 'A' and resid 1027 through 1036
    Processing helix  chain 'A' and resid 1038 through 1048
    Processing helix  chain 'A' and resid 1052 through 1059
    Processing helix  chain 'A' and resid 1069 through 1087
    Processing helix  chain 'A' and resid 1093 through 1100
    Processing helix  chain 'A' and resid 1105 through 1118
    Processing helix  chain 'A' and resid 1118 through 1123
    Processing helix  chain 'A' and resid 1134 through 1138
    Processing helix  chain 'A' and resid 1150 through 1156
      removed outlier: 3.558A  pdb=" N   ALA A1156 " --> pdb=" O   GLN A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1184
      No H-bonds generated for 'chain 'A' and resid 1182 through 1184'
    Processing helix  chain 'A' and resid 1213 through 1230
    Processing helix  chain 'A' and resid 1235 through 1246
      Proline residue:  A1242  - end of helix
    Processing helix  chain 'A' and resid 1251 through 1259
    Processing helix  chain 'A' and resid 1266 through 1274
      removed outlier: 3.918A  pdb=" N   GLN A1274 " --> pdb=" O   ARG A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1296 through 1303
      removed outlier: 3.553A  pdb=" N   GLY A1300 " --> pdb=" O   ASN A1297 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   GLU A1301 " --> pdb=" O   THR A1298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1315 through 1331
    Processing helix  chain 'A' and resid 1335 through 1339
    Processing helix  chain 'A' and resid 1350 through 1353
      removed outlier: 3.508A  pdb=" N   THR A1353 " --> pdb=" O   LYS A1350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1350 through 1353'
    Processing helix  chain 'A' and resid 1370 through 1376
      removed outlier: 3.535A  pdb=" N   ARG A1373 " --> pdb=" O   ASP A1370 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   GLU A1376 " --> pdb=" O   ARG A1373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 149
    Processing helix  chain 'B' and resid 155 through 166
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 193 through 206
      removed outlier: 3.698A  pdb=" N   THR B 206 " --> pdb=" O   ASN B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 209
      No H-bonds generated for 'chain 'B' and resid 207 through 209'
    Processing helix  chain 'B' and resid 220 through 232
      removed outlier: 3.840A  pdb=" N   HIS B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 254
      removed outlier: 3.504A  pdb=" N   GLN B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS B 248 " --> pdb=" O   GLN B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 269
    Processing helix  chain 'B' and resid 272 through 284
      removed outlier: 3.735A  pdb=" N   VAL B 284 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 288
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'C' and resid 125 through 144
      removed outlier: 3.678A  pdb=" N   ASP C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU C 144 " --> pdb=" O   ALA C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 167
    Processing helix  chain 'D' and resid 121 through 146
      removed outlier: 3.520A  pdb=" N   LEU D 144 " --> pdb=" O   ALA D 140 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 124 through 133
    Processing helix  chain 'E' and resid 134 through 146
      removed outlier: 3.617A  pdb=" N   LEU E 145 " --> pdb=" O   LYS E 141 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 194
    Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399
    Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 550
    Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740
      removed outlier: 3.513A  pdb=" N   VAL A 630 " --> pdb=" O   PHE A 793 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   PHE A 793 " --> pdb=" O   VAL A 630 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 799
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1144
      removed outlier: 3.717A  pdb=" N   ARG A1343 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1175 through 1176
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1208 through 1209
      removed outlier: 3.778A  pdb=" N   LYS A1208 " --> pdb=" O   ASN A1391 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 313

    667 hydrogen bonds defined for protein.
    1903 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: 4.64

  Time building geometry restraints manager: 4.12 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 4213
        1.34 -     1.47: 3496
        1.47 -     1.60: 5956
        1.60 -     1.72: 1
        1.72 -     1.85: 116
  Bond restraints: 13782
  Sorted by residual:
  bond pdb=" CG  TYR A1381 "
       pdb=" CD2 TYR A1381 "
    ideal  model  delta    sigma   weight residual
    1.389  1.497 -0.108 2.10e-02 2.27e+03 2.66e+01
  bond pdb=" CA  PRO C 169 "
       pdb=" C   PRO C 169 "
    ideal  model  delta    sigma   weight residual
    1.517  1.470  0.047 9.30e-03 1.16e+04 2.51e+01
  bond pdb=" CB  TRP A1085 "
       pdb=" CG  TRP A1085 "
    ideal  model  delta    sigma   weight residual
    1.498  1.366  0.132 3.10e-02 1.04e+03 1.80e+01
  bond pdb=" CB  TYR A 188 "
       pdb=" CG  TYR A 188 "
    ideal  model  delta    sigma   weight residual
    1.512  1.429  0.083 2.20e-02 2.07e+03 1.42e+01
  bond pdb=" CA  PRO A 694 "
       pdb=" C   PRO A 694 "
    ideal  model  delta    sigma   weight residual
    1.514  1.535 -0.021 5.50e-03 3.31e+04 1.42e+01
  ... (remaining 13777 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 18180
        3.20 -     6.41: 470
        6.41 -     9.61: 50
        9.61 -    12.82: 10
       12.82 -    16.02: 1
  Bond angle restraints: 18711
  Sorted by residual:
  angle pdb=" N   TYR A1381 "
        pdb=" CA  TYR A1381 "
        pdb=" C   TYR A1381 "
      ideal   model   delta    sigma   weight residual
     109.31  100.82    8.49 1.42e+00 4.96e-01 3.57e+01
  angle pdb=" C   ILE A1380 "
        pdb=" N   TYR A1381 "
        pdb=" CA  TYR A1381 "
      ideal   model   delta    sigma   weight residual
     122.15  113.31    8.84 1.74e+00 3.30e-01 2.58e+01
  angle pdb=" N   ILE A 829 "
        pdb=" CA  ILE A 829 "
        pdb=" C   ILE A 829 "
      ideal   model   delta    sigma   weight residual
     109.30  103.49    5.81 1.25e+00 6.40e-01 2.16e+01
  angle pdb=" CA  LEU A 972 "
        pdb=" CB  LEU A 972 "
        pdb=" CG  LEU A 972 "
      ideal   model   delta    sigma   weight residual
     116.30  100.28   16.02 3.50e+00 8.16e-02 2.10e+01
  angle pdb=" NE  ARG A 318 "
        pdb=" CZ  ARG A 318 "
        pdb=" NH2 ARG A 318 "
      ideal   model   delta    sigma   weight residual
     119.20  123.29   -4.09 9.00e-01 1.23e+00 2.06e+01
  ... (remaining 18706 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 7815
       17.73 -    35.46: 423
       35.46 -    53.19: 65
       53.19 -    70.92: 12
       70.92 -    88.65: 7
  Dihedral angle restraints: 8322
    sinusoidal: 3341
      harmonic: 4981
  Sorted by residual:
  dihedral pdb=" CB  CYS A1105 "
           pdb=" SG  CYS A1105 "
           pdb=" SG  CYS A1352 "
           pdb=" CB  CYS A1352 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.47  -49.47     1      1.00e+01 1.00e-02 3.36e+01
  dihedral pdb=" CA  TYR A1381 "
           pdb=" C   TYR A1381 "
           pdb=" N   ASP A1382 "
           pdb=" CA  ASP A1382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.41   24.59     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  ASN A 663 "
           pdb=" C   ASN A 663 "
           pdb=" N   TRP A 664 "
           pdb=" CA  TRP A 664 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.81  -24.19     0      5.00e+00 4.00e-02 2.34e+01
  ... (remaining 8319 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 2006
       0.125 -    0.249: 94
       0.249 -    0.374: 7
       0.374 -    0.499: 1
       0.499 -    0.624: 1
  Chirality restraints: 2109
  Sorted by residual:
  chirality pdb=" CG  LEU A 396 "
            pdb=" CB  LEU A 396 "
            pdb=" CD1 LEU A 396 "
            pdb=" CD2 LEU A 396 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.21    0.62 2.00e-01 2.50e+01 9.72e+00
  chirality pdb=" CB  ILE A 799 "
            pdb=" CA  ILE A 799 "
            pdb=" CG1 ILE A 799 "
            pdb=" CG2 ILE A 799 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CB  ILE A  73 "
            pdb=" CA  ILE A  73 "
            pdb=" CG1 ILE A  73 "
            pdb=" CG2 ILE A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.00   -0.36 2.00e-01 2.50e+01 3.24e+00
  ... (remaining 2106 not shown)

  Planarity restraints: 2391
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 867 "    0.048 2.00e-02 2.50e+03   4.98e-02 4.34e+01
        pdb=" CG  PHE A 867 "   -0.115 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 867 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 867 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 867 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 867 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 867 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 319 "    0.013 2.00e-02 2.50e+03   4.68e-02 3.84e+01
        pdb=" CG  PHE A 319 "   -0.088 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 319 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 319 "    0.074 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 319 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 319 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 319 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1381 "    0.035 2.00e-02 2.50e+03   4.07e-02 3.32e+01
        pdb=" CG  TYR A1381 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1381 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1381 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1381 "    0.034 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1381 "    0.056 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1381 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A1381 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 2388 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2319
        2.75 -     3.29: 14159
        3.29 -     3.83: 22787
        3.83 -     4.36: 28246
        4.36 -     4.90: 47193
  Nonbonded interactions: 114704
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1021 "
            pdb=" NH2 ARG A1125 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OE2 GLU A 643 "
            pdb=" OG1 THR C 153 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" NH1 ARG B 300 "
            pdb=" OE1 GLN B 308 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG1 THR B 159 "
            pdb=" OG  SER B 174 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   GLU A1148 "
            pdb=" NH2 ARG A1343 "
     model   vdw
     2.240 3.120
  ... (remaining 114699 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=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     37.120
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
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      :  0.012   0.147  13787  Z= 0.632
  Angle     :  1.220  16.024  18715  Z= 0.661
  Chirality :  0.065   0.624   2109
  Planarity :  0.006   0.050   2391
  Dihedral  : 11.484  88.645   5091
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.19), residues: 1680
  helix: -0.65 (0.16), residues: 879
  sheet: -1.46 (0.44), residues: 107
  loop : -0.54 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.004   TRP A 664 
 HIS   0.018   0.004   HIS C 166 
 PHE   0.115   0.005   PHE A 867 
 TYR   0.082   0.005   TYR A1381 
 ARG   0.017   0.002   ARG A1081 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16790 (  667)
  hydrogen bonds       : angle       7.10059 ( 1903)
  metal coordination   : bond        0.09014 (    4)
  metal coordination   : angle       8.71570 (    2)
  SS BOND              : bond        0.01522 (    1)
  SS BOND              : angle       0.76624 (    2)
  covalent geometry    : bond        0.01238 (13782)
  covalent geometry    : angle       1.21701 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 1.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 LYS cc_start: 0.8593 (tttp) cc_final: 0.8080 (mtmm)
REVERT: A  332 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7909 (mt-10)
REVERT: A  470 PHE cc_start: 0.8771 (m-80) cc_final: 0.8475 (m-80)
REVERT: A  514 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7365 (pttt)
REVERT: A  518 GLU cc_start: 0.8715 (tt0) cc_final: 0.8084 (mt-10)
REVERT: A  533 SER cc_start: 0.8972 (m) cc_final: 0.8637 (p)
REVERT: A  713 GLN cc_start: 0.8019 (tp40) cc_final: 0.7537 (tt0)
REVERT: A  740 MET cc_start: 0.7955 (tpp) cc_final: 0.7648 (mtt)
REVERT: A 1217 ARG cc_start: 0.7455 (ttm110) cc_final: 0.6888 (ttp80)
REVERT: B  188 ARG cc_start: 0.6426 (mmp80) cc_final: 0.5687 (tpt90)
REVERT: B  244 GLN cc_start: 0.8837 (pt0) cc_final: 0.8524 (pt0)
REVERT: C  124 MET cc_start: 0.4362 (mmp) cc_final: 0.4106 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 328
  average time/residue: 0.3247
  time to fit residues: 145.4658
Evaluate side-chains
  210 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 141 optimal weight:    0.7980
   chunk 126 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0370
   chunk 130 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 151 optimal weight:    0.9980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A  97 GLN
** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 HIS
A 663 ASN
A 876 HIS
A 924 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.167546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.134295 restraints weight = 30717.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 3.27
r_work: 0.3333 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3335
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13787  Z= 0.140
  Angle     :  0.608   9.107  18715  Z= 0.306
  Chirality :  0.041   0.165   2109
  Planarity :  0.004   0.044   2391
  Dihedral  :  4.544  21.658   1836
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  7.83 %
    Favored  : 90.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.33 (0.21), residues: 1680
  helix:  0.70 (0.18), residues: 896
  sheet: -1.07 (0.45), residues: 105
  loop : -0.03 (0.25), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1019 
 HIS   0.005   0.001   HIS A 864 
 PHE   0.030   0.002   PHE A 867 
 TYR   0.017   0.001   TYR A 106 
 ARG   0.004   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04456 (  667)
  hydrogen bonds       : angle       4.95037 ( 1903)
  metal coordination   : bond        0.01223 (    4)
  metal coordination   : angle       3.88864 (    2)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       1.92977 (    2)
  covalent geometry    : bond        0.00322 (13782)
  covalent geometry    : angle       0.60655 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 233
  time to evaluate  : 1.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8568 (ttpp)
REVERT: A  214 GLN cc_start: 0.8065 (tt0) cc_final: 0.7369 (mm-40)
REVERT: A  271 LYS cc_start: 0.8533 (tttp) cc_final: 0.8035 (mtmm)
REVERT: A  444 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7991 (mtmt)
REVERT: A  453 MET cc_start: 0.7806 (tpt) cc_final: 0.7522 (tpt)
REVERT: A  514 LYS cc_start: 0.7556 (ptpt) cc_final: 0.7118 (pttt)
REVERT: A  518 GLU cc_start: 0.8084 (tt0) cc_final: 0.7577 (mt-10)
REVERT: A  532 LEU cc_start: 0.8448 (mt) cc_final: 0.8231 (tp)
REVERT: A  635 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7846 (mmtm)
REVERT: A  742 ASP cc_start: 0.6956 (m-30) cc_final: 0.6652 (m-30)
REVERT: A  999 LYS cc_start: 0.7966 (tppt) cc_final: 0.7592 (mttm)
REVERT: A 1015 MET cc_start: 0.8146 (mmm) cc_final: 0.7840 (mmp)
REVERT: A 1217 ARG cc_start: 0.7048 (ttm110) cc_final: 0.6595 (ttp80)
REVERT: B  188 ARG cc_start: 0.6204 (mmp80) cc_final: 0.5357 (tpt90)
REVERT: B  202 ASN cc_start: 0.8865 (m110) cc_final: 0.8389 (m110)
REVERT: C  177 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8291 (mm-30)
  outliers start: 18
  outliers final: 10
  residues processed: 245
  average time/residue: 0.4550
  time to fit residues: 159.5802
Evaluate side-chains
  205 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 194
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1220 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 139 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 164 optimal weight:    5.9990
   chunk 160 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  97 GLN
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 HIS
A 608 GLN
A 663 ASN
A 666 HIS
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1318 ASN
B 244 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.168997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.133790 restraints weight = 36664.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 4.77
r_work: 0.3264 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13787  Z= 0.144
  Angle     :  0.569   7.511  18715  Z= 0.285
  Chirality :  0.041   0.163   2109
  Planarity :  0.004   0.046   2391
  Dihedral  :  4.405  23.226   1836
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 10.31 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.68 (0.21), residues: 1680
  helix:  1.01 (0.18), residues: 893
  sheet: -0.94 (0.46), residues: 105
  loop :  0.10 (0.25), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 324 
 HIS   0.004   0.001   HIS A 607 
 PHE   0.022   0.001   PHE A 867 
 TYR   0.012   0.001   TYR A 106 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  667)
  hydrogen bonds       : angle       4.66199 ( 1903)
  metal coordination   : bond        0.00891 (    4)
  metal coordination   : angle       2.95545 (    2)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       1.72432 (    2)
  covalent geometry    : bond        0.00347 (13782)
  covalent geometry    : angle       0.56803 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 216
  time to evaluate  : 2.121 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLN cc_start: 0.8136 (tt0) cc_final: 0.7381 (mm-40)
REVERT: A  253 ILE cc_start: 0.8682 (mt) cc_final: 0.8474 (mt)
REVERT: A  271 LYS cc_start: 0.8547 (tttp) cc_final: 0.7984 (mtmm)
REVERT: A  444 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7959 (mtmt)
REVERT: A  514 LYS cc_start: 0.7627 (ptpt) cc_final: 0.7056 (pttt)
REVERT: A  518 GLU cc_start: 0.8120 (tt0) cc_final: 0.7522 (mt-10)
REVERT: A  635 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7863 (mmtm)
REVERT: A  736 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7273 (mmt180)
REVERT: A  967 LEU cc_start: 0.8294 (mt) cc_final: 0.8070 (mt)
REVERT: A  999 LYS cc_start: 0.8071 (tppt) cc_final: 0.7706 (mttm)
REVERT: A 1015 MET cc_start: 0.8334 (mmm) cc_final: 0.8003 (mmp)
REVERT: A 1217 ARG cc_start: 0.7140 (ttm110) cc_final: 0.6675 (ttp80)
REVERT: A 1280 PHE cc_start: 0.7255 (m-10) cc_final: 0.6866 (m-10)
REVERT: A 1375 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7712 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6210 (mmp80) cc_final: 0.5341 (tpt90)
REVERT: B  202 ASN cc_start: 0.8927 (m110) cc_final: 0.8386 (m110)
REVERT: C  177 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8396 (mm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 236
  average time/residue: 0.3730
  time to fit residues: 126.5272
Evaluate side-chains
  207 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 192
  time to evaluate  : 1.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  628 SER
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1326 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 159 optimal weight:    2.9990
   chunk 143 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 166 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 536 GLN
A 608 GLN
A 663 ASN
E 132 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.168470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.132715 restraints weight = 32294.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 3.75
r_work: 0.3313 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13787  Z= 0.144
  Angle     :  0.558   7.604  18715  Z= 0.279
  Chirality :  0.041   0.158   2109
  Planarity :  0.004   0.045   2391
  Dihedral  :  4.320  23.860   1836
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.31 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.84 (0.21), residues: 1680
  helix:  1.11 (0.18), residues: 896
  sheet: -0.88 (0.46), residues: 105
  loop :  0.22 (0.25), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 324 
 HIS   0.005   0.001   HIS A 864 
 PHE   0.017   0.001   PHE A 411 
 TYR   0.011   0.001   TYR A 153 
 ARG   0.007   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03707 (  667)
  hydrogen bonds       : angle       4.58060 ( 1903)
  metal coordination   : bond        0.01024 (    4)
  metal coordination   : angle       2.95967 (    2)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       1.66012 (    2)
  covalent geometry    : bond        0.00348 (13782)
  covalent geometry    : angle       0.55651 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 207
  time to evaluate  : 1.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8592 (ttmm)
REVERT: A  178 ASP cc_start: 0.7905 (m-30) cc_final: 0.7083 (m-30)
REVERT: A  214 GLN cc_start: 0.8089 (tt0) cc_final: 0.7382 (mm-40)
REVERT: A  253 ILE cc_start: 0.8651 (mt) cc_final: 0.8416 (mt)
REVERT: A  444 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7976 (mtmt)
REVERT: A  514 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7071 (pttt)
REVERT: A  518 GLU cc_start: 0.7953 (tt0) cc_final: 0.7481 (mt-10)
REVERT: A  736 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7305 (mmt180)
REVERT: A  999 LYS cc_start: 0.8011 (tppt) cc_final: 0.7664 (mttm)
REVERT: A 1217 ARG cc_start: 0.7152 (ttm110) cc_final: 0.6714 (ttp80)
REVERT: A 1280 PHE cc_start: 0.7289 (m-10) cc_final: 0.6928 (m-10)
REVERT: A 1334 THR cc_start: 0.9096 (t) cc_final: 0.8793 (p)
REVERT: A 1375 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7652 (ttm-80)
REVERT: A 1383 SER cc_start: 0.7922 (m) cc_final: 0.7428 (p)
REVERT: A 1384 ASN cc_start: 0.8313 (m-40) cc_final: 0.8095 (m-40)
REVERT: B  182 ARG cc_start: 0.7722 (tpp80) cc_final: 0.6998 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6215 (mmp80) cc_final: 0.5337 (tpt90)
REVERT: B  202 ASN cc_start: 0.8890 (m110) cc_final: 0.8256 (m110)
REVERT: C  177 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8386 (mm-30)
  outliers start: 28
  outliers final: 18
  residues processed: 226
  average time/residue: 0.3270
  time to fit residues: 105.9283
Evaluate side-chains
  215 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  628 SER
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1311 ASP
Chi-restraints excluded: chain A residue 1326 LEU
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain B residue  176 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 144 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 133 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 60 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 377 HIS
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 ASN
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 ASN
E 132 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.166234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.132297 restraints weight = 28500.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.83
r_work: 0.3378 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13787  Z= 0.153
  Angle     :  0.557   7.576  18715  Z= 0.278
  Chirality :  0.041   0.153   2109
  Planarity :  0.004   0.045   2391
  Dihedral  :  4.296  24.245   1836
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.65 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.87 (0.21), residues: 1680
  helix:  1.13 (0.18), residues: 897
  sheet: -0.84 (0.47), residues: 105
  loop :  0.24 (0.25), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1019 
 HIS   0.005   0.001   HIS A 864 
 PHE   0.017   0.001   PHE A 411 
 TYR   0.011   0.001   TYR A 153 
 ARG   0.006   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (  667)
  hydrogen bonds       : angle       4.54807 ( 1903)
  metal coordination   : bond        0.00947 (    4)
  metal coordination   : angle       3.13642 (    2)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       1.61999 (    2)
  covalent geometry    : bond        0.00373 (13782)
  covalent geometry    : angle       0.55608 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 1.661 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 LYS cc_start: 0.8217 (mmmt) cc_final: 0.8014 (mmmt)
REVERT: A  119 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8680 (ttmm)
REVERT: A  178 ASP cc_start: 0.7819 (m-30) cc_final: 0.6977 (m-30)
REVERT: A  214 GLN cc_start: 0.8038 (tt0) cc_final: 0.7428 (mm-40)
REVERT: A  444 LYS cc_start: 0.8223 (mtpp) cc_final: 0.8015 (mtmt)
REVERT: A  514 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7112 (pttt)
REVERT: A  518 GLU cc_start: 0.7875 (tt0) cc_final: 0.7567 (mt-10)
REVERT: A  598 GLU cc_start: 0.6800 (mp0) cc_final: 0.6545 (mm-30)
REVERT: A  736 ARG cc_start: 0.8076 (mmt90) cc_final: 0.7395 (mmt90)
REVERT: A  999 LYS cc_start: 0.8027 (tppt) cc_final: 0.7685 (mttm)
REVERT: A 1217 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6754 (ttp80)
REVERT: A 1271 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5120 (t80)
REVERT: A 1280 PHE cc_start: 0.7449 (m-10) cc_final: 0.7155 (m-10)
REVERT: A 1334 THR cc_start: 0.9086 (t) cc_final: 0.8735 (p)
REVERT: A 1375 ARG cc_start: 0.8403 (ttm110) cc_final: 0.7568 (ttt-90)
REVERT: A 1383 SER cc_start: 0.7912 (m) cc_final: 0.7365 (p)
REVERT: A 1384 ASN cc_start: 0.8285 (m-40) cc_final: 0.7989 (m-40)
REVERT: B  182 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7060 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6226 (mmp80) cc_final: 0.5391 (tpt90)
REVERT: B  202 ASN cc_start: 0.8788 (m110) cc_final: 0.8157 (m110)
REVERT: C  177 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8345 (mm-30)
REVERT: E  132 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7839 (m-40)
  outliers start: 25
  outliers final: 17
  residues processed: 220
  average time/residue: 0.4360
  time to fit residues: 139.3914
Evaluate side-chains
  214 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 194
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1311 ASP
Chi-restraints excluded: chain A residue 1326 LEU
Chi-restraints excluded: chain A residue 1362 THR
Chi-restraints excluded: chain E residue  132 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 134 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 153 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0270
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6842

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

Flipped N/Q/H residues before XYZ refinement:
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 501 ASN
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1266 ASN
D 132 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.166817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133404 restraints weight = 28812.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 3.19
r_work: 0.3377 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3360
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13787  Z= 0.118
  Angle     :  0.539   7.497  18715  Z= 0.268
  Chirality :  0.039   0.153   2109
  Planarity :  0.004   0.044   2391
  Dihedral  :  4.212  24.368   1836
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.78 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.21), residues: 1680
  helix:  1.24 (0.18), residues: 898
  sheet: -0.78 (0.48), residues: 105
  loop :  0.29 (0.25), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1019 
 HIS   0.004   0.001   HIS A 864 
 PHE   0.019   0.001   PHE A1011 
 TYR   0.012   0.001   TYR A 153 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  667)
  hydrogen bonds       : angle       4.48239 ( 1903)
  metal coordination   : bond        0.01113 (    4)
  metal coordination   : angle       3.05605 (    2)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       1.53111 (    2)
  covalent geometry    : bond        0.00279 (13782)
  covalent geometry    : angle       0.53826 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8064 (tpm170) cc_final: 0.7824 (tpm170)
REVERT: A   48 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7992 (mmmt)
REVERT: A  119 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8705 (ttmm)
REVERT: A  178 ASP cc_start: 0.7854 (m-30) cc_final: 0.7010 (m-30)
REVERT: A  214 GLN cc_start: 0.8066 (tt0) cc_final: 0.7454 (mm-40)
REVERT: A  444 LYS cc_start: 0.8266 (mtpp) cc_final: 0.8050 (mtmt)
REVERT: A  514 LYS cc_start: 0.7521 (ptpt) cc_final: 0.7032 (pttt)
REVERT: A  518 GLU cc_start: 0.7851 (tt0) cc_final: 0.7521 (mt-10)
REVERT: A  598 GLU cc_start: 0.6769 (mp0) cc_final: 0.6567 (mm-30)
REVERT: A  736 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7405 (mmt180)
REVERT: A  999 LYS cc_start: 0.8021 (tppt) cc_final: 0.7681 (mttm)
REVERT: A 1011 PHE cc_start: 0.8532 (t80) cc_final: 0.8303 (t80)
REVERT: A 1015 MET cc_start: 0.8168 (mmm) cc_final: 0.7904 (mpp)
REVERT: A 1027 MET cc_start: 0.8634 (ttm) cc_final: 0.8434 (ttm)
REVERT: A 1217 ARG cc_start: 0.7132 (ttm110) cc_final: 0.6744 (ttp80)
REVERT: A 1271 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5187 (t80)
REVERT: A 1334 THR cc_start: 0.9095 (t) cc_final: 0.8750 (p)
REVERT: A 1375 ARG cc_start: 0.8429 (ttm110) cc_final: 0.7620 (ttt-90)
REVERT: A 1383 SER cc_start: 0.7843 (m) cc_final: 0.6948 (p)
REVERT: A 1384 ASN cc_start: 0.8300 (m-40) cc_final: 0.7793 (m-40)
REVERT: B  182 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7064 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6244 (mmp80) cc_final: 0.5403 (tpt90)
REVERT: B  202 ASN cc_start: 0.8710 (m110) cc_final: 0.8105 (m110)
REVERT: C  177 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8323 (mm-30)
  outliers start: 25
  outliers final: 15
  residues processed: 218
  average time/residue: 0.2951
  time to fit residues: 91.1075
Evaluate side-chains
  202 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1311 ASP
Chi-restraints excluded: chain A residue 1326 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 65 optimal weight:    0.4980
   chunk 128 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 52 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 122 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 141 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 ASN
A 671 GLN
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 ASN
E 132 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.167379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.133381 restraints weight = 34592.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.64
r_work: 0.3362 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13787  Z= 0.115
  Angle     :  0.532   7.206  18715  Z= 0.264
  Chirality :  0.039   0.152   2109
  Planarity :  0.004   0.044   2391
  Dihedral  :  4.144  24.592   1836
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.25 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.21), residues: 1680
  helix:  1.35 (0.18), residues: 898
  sheet: -0.72 (0.49), residues: 105
  loop :  0.32 (0.26), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1019 
 HIS   0.004   0.001   HIS A 864 
 PHE   0.020   0.001   PHE A 983 
 TYR   0.012   0.001   TYR A 153 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03334 (  667)
  hydrogen bonds       : angle       4.41763 ( 1903)
  metal coordination   : bond        0.01179 (    4)
  metal coordination   : angle       2.98617 (    2)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       1.34097 (    2)
  covalent geometry    : bond        0.00271 (13782)
  covalent geometry    : angle       0.53058 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 201
  time to evaluate  : 1.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8019 (tpm170) cc_final: 0.7813 (tpm170)
REVERT: A   48 LYS cc_start: 0.8272 (mmmt) cc_final: 0.8031 (mmmt)
REVERT: A  119 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8690 (ttmm)
REVERT: A  178 ASP cc_start: 0.7910 (m-30) cc_final: 0.7065 (m-30)
REVERT: A  183 LEU cc_start: 0.8152 (tt) cc_final: 0.7847 (tp)
REVERT: A  214 GLN cc_start: 0.8072 (tt0) cc_final: 0.7479 (mm110)
REVERT: A  514 LYS cc_start: 0.7499 (ptpt) cc_final: 0.6997 (pttt)
REVERT: A  518 GLU cc_start: 0.7882 (tt0) cc_final: 0.7539 (mt-10)
REVERT: A  736 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7412 (mmt180)
REVERT: A  999 LYS cc_start: 0.8049 (tppt) cc_final: 0.7702 (mttm)
REVERT: A 1217 ARG cc_start: 0.7133 (ttm110) cc_final: 0.6805 (ttp80)
REVERT: A 1271 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5290 (t80)
REVERT: A 1334 THR cc_start: 0.9109 (t) cc_final: 0.8756 (p)
REVERT: A 1375 ARG cc_start: 0.8465 (ttm110) cc_final: 0.7676 (ttt-90)
REVERT: A 1383 SER cc_start: 0.7818 (m) cc_final: 0.7183 (p)
REVERT: A 1384 ASN cc_start: 0.8345 (m-40) cc_final: 0.7964 (m-40)
REVERT: B  148 THR cc_start: 0.7883 (p) cc_final: 0.7641 (p)
REVERT: B  182 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7098 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6214 (mmp80) cc_final: 0.5305 (tpt90)
REVERT: B  202 ASN cc_start: 0.8590 (m110) cc_final: 0.7925 (m110)
REVERT: C  177 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8245 (mm-30)
REVERT: D  124 MET cc_start: 0.5725 (tpp) cc_final: 0.5482 (tpp)
  outliers start: 27
  outliers final: 15
  residues processed: 222
  average time/residue: 0.2997
  time to fit residues: 94.6639
Evaluate side-chains
  206 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 189
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1311 ASP
Chi-restraints excluded: chain A residue 1326 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 147 optimal weight:    0.8980
   chunk 113 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 164 optimal weight:    5.9990
   chunk 158 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 44 optimal weight:    0.2980
   chunk 162 optimal weight:    3.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 ASN
** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 ASN
E 132 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.164711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.131451 restraints weight = 32083.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 3.55
r_work: 0.3278 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  13787  Z= 0.212
  Angle     :  0.606   8.770  18715  Z= 0.304
  Chirality :  0.043   0.221   2109
  Planarity :  0.004   0.043   2391
  Dihedral  :  4.345  24.761   1836
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.86 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.83 (0.21), residues: 1680
  helix:  1.11 (0.18), residues: 897
  sheet: -0.93 (0.49), residues: 105
  loop :  0.21 (0.25), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 191 
 HIS   0.007   0.001   HIS A 864 
 PHE   0.017   0.002   PHE A 411 
 TYR   0.013   0.002   TYR A 117 
 ARG   0.009   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  667)
  hydrogen bonds       : angle       4.61950 ( 1903)
  metal coordination   : bond        0.00755 (    4)
  metal coordination   : angle       3.48227 (    2)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       1.59698 (    2)
  covalent geometry    : bond        0.00526 (13782)
  covalent geometry    : angle       0.60493 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 1.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LYS cc_start: 0.8268 (mmmt) cc_final: 0.8016 (mmmt)
REVERT: A  119 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8575 (ttmm)
REVERT: A  178 ASP cc_start: 0.8019 (m-30) cc_final: 0.7219 (m-30)
REVERT: A  214 GLN cc_start: 0.8071 (tt0) cc_final: 0.7379 (mm-40)
REVERT: A  514 LYS cc_start: 0.7687 (ptpt) cc_final: 0.7141 (pttt)
REVERT: A  518 GLU cc_start: 0.7934 (tt0) cc_final: 0.7558 (mt-10)
REVERT: A  635 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7635 (mmtm)
REVERT: A  736 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7371 (mmt180)
REVERT: A  999 LYS cc_start: 0.8004 (tppt) cc_final: 0.7674 (mttm)
REVERT: A 1271 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5719 (t80)
REVERT: A 1280 PHE cc_start: 0.7494 (m-10) cc_final: 0.7139 (m-10)
REVERT: A 1375 ARG cc_start: 0.8437 (ttm110) cc_final: 0.7605 (ttt-90)
REVERT: A 1383 SER cc_start: 0.7868 (m) cc_final: 0.6977 (p)
REVERT: A 1384 ASN cc_start: 0.8411 (m-40) cc_final: 0.7864 (m-40)
REVERT: B  182 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7114 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6292 (mmp80) cc_final: 0.5315 (tpt90)
REVERT: B  202 ASN cc_start: 0.8723 (m110) cc_final: 0.8061 (m110)
REVERT: B  213 ASN cc_start: 0.8032 (t0) cc_final: 0.7780 (t0)
REVERT: C  177 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8256 (mm-30)
  outliers start: 28
  outliers final: 19
  residues processed: 208
  average time/residue: 0.2944
  time to fit residues: 86.7505
Evaluate side-chains
  206 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 1.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  663 ASN
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  822 MET
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1311 ASP
Chi-restraints excluded: chain A residue 1326 LEU
Chi-restraints excluded: chain A residue 1362 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0770
   chunk 79 optimal weight:    0.9990
   chunk 139 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   overall best weight:    0.7742

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

Flipped N/Q/H residues before XYZ refinement:
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 ASN
A 671 GLN
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 ASN
E 132 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.167891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.131627 restraints weight = 28837.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 3.48
r_work: 0.3320 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13787  Z= 0.127
  Angle     :  0.572  13.264  18715  Z= 0.283
  Chirality :  0.040   0.187   2109
  Planarity :  0.004   0.044   2391
  Dihedral  :  4.245  24.866   1836
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.79 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.96 (0.21), residues: 1680
  helix:  1.20 (0.18), residues: 899
  sheet: -0.85 (0.49), residues: 105
  loop :  0.29 (0.25), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1019 
 HIS   0.005   0.001   HIS A 666 
 PHE   0.027   0.001   PHE A1011 
 TYR   0.011   0.001   TYR A 153 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  667)
  hydrogen bonds       : angle       4.52717 ( 1903)
  metal coordination   : bond        0.01184 (    4)
  metal coordination   : angle       3.09320 (    2)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       1.45794 (    2)
  covalent geometry    : bond        0.00305 (13782)
  covalent geometry    : angle       0.57140 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 194
  time to evaluate  : 1.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8043 (tpm170) cc_final: 0.7840 (tpm170)
REVERT: A   48 LYS cc_start: 0.8260 (mmmt) cc_final: 0.8008 (mmmt)
REVERT: A  119 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8589 (ttmm)
REVERT: A  178 ASP cc_start: 0.7965 (m-30) cc_final: 0.7174 (m-30)
REVERT: A  214 GLN cc_start: 0.8019 (tt0) cc_final: 0.7368 (mm-40)
REVERT: A  514 LYS cc_start: 0.7583 (ptpt) cc_final: 0.7053 (pttt)
REVERT: A  518 GLU cc_start: 0.7780 (tt0) cc_final: 0.7433 (mt-10)
REVERT: A  635 LYS cc_start: 0.7940 (mmmm) cc_final: 0.7583 (mmtm)
REVERT: A  736 ARG cc_start: 0.8117 (mmt90) cc_final: 0.7332 (mmt180)
REVERT: A  999 LYS cc_start: 0.7943 (tppt) cc_final: 0.7620 (mttm)
REVERT: A 1217 ARG cc_start: 0.7020 (ttm110) cc_final: 0.6635 (ttp80)
REVERT: A 1271 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5613 (t80)
REVERT: A 1280 PHE cc_start: 0.7374 (m-10) cc_final: 0.7060 (m-10)
REVERT: A 1375 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7612 (ttt-90)
REVERT: A 1383 SER cc_start: 0.7801 (m) cc_final: 0.6902 (p)
REVERT: A 1384 ASN cc_start: 0.8294 (m-40) cc_final: 0.7723 (m-40)
REVERT: B  182 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7089 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6393 (mmp80) cc_final: 0.5309 (tpt90)
REVERT: B  202 ASN cc_start: 0.8648 (m110) cc_final: 0.8022 (m110)
REVERT: B  213 ASN cc_start: 0.7940 (t0) cc_final: 0.7690 (t0)
REVERT: C  177 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8187 (mm-30)
  outliers start: 27
  outliers final: 20
  residues processed: 212
  average time/residue: 0.3309
  time to fit residues: 100.6400
Evaluate side-chains
  209 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 187
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  663 ASN
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1240 ILE
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1311 ASP
Chi-restraints excluded: chain A residue 1326 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 162 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 123 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 42 optimal weight:    7.9990
   chunk 95 optimal weight:    0.0170
   chunk 115 optimal weight:    0.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 ASN
A 663 ASN
** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 ASN
E 132 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.168261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.135974 restraints weight = 32835.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 3.64
r_work: 0.3373 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13787  Z= 0.120
  Angle     :  0.580  14.747  18715  Z= 0.283
  Chirality :  0.040   0.157   2109
  Planarity :  0.004   0.043   2391
  Dihedral  :  4.209  24.794   1836
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.33 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.21), residues: 1680
  helix:  1.28 (0.18), residues: 898
  sheet: -0.85 (0.49), residues: 105
  loop :  0.32 (0.25), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1019 
 HIS   0.004   0.001   HIS A 864 
 PHE   0.017   0.001   PHE A 411 
 TYR   0.013   0.001   TYR A 667 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  667)
  hydrogen bonds       : angle       4.49537 ( 1903)
  metal coordination   : bond        0.01152 (    4)
  metal coordination   : angle       2.87753 (    2)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       1.33170 (    2)
  covalent geometry    : bond        0.00283 (13782)
  covalent geometry    : angle       0.57961 (18711)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 195
  time to evaluate  : 1.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LYS cc_start: 0.8258 (mmmt) cc_final: 0.8047 (mmmt)
REVERT: A  119 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8618 (ttmm)
REVERT: A  178 ASP cc_start: 0.7961 (m-30) cc_final: 0.7166 (m-30)
REVERT: A  214 GLN cc_start: 0.8038 (tt0) cc_final: 0.7443 (mm-40)
REVERT: A  514 LYS cc_start: 0.7564 (ptpt) cc_final: 0.7076 (pttt)
REVERT: A  518 GLU cc_start: 0.7886 (tt0) cc_final: 0.7566 (mt-10)
REVERT: A  635 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7639 (mmtm)
REVERT: A  665 MET cc_start: 0.8716 (ttm) cc_final: 0.8447 (ttm)
REVERT: A  736 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7445 (mmt180)
REVERT: A  999 LYS cc_start: 0.7993 (tppt) cc_final: 0.7687 (mttm)
REVERT: A 1217 ARG cc_start: 0.7050 (ttm110) cc_final: 0.6715 (ttp80)
REVERT: A 1271 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.5586 (t80)
REVERT: A 1375 ARG cc_start: 0.8433 (ttm110) cc_final: 0.7673 (ttt-90)
REVERT: A 1383 SER cc_start: 0.7805 (m) cc_final: 0.6924 (p)
REVERT: A 1384 ASN cc_start: 0.8309 (m-40) cc_final: 0.7720 (m-40)
REVERT: B  148 THR cc_start: 0.7840 (p) cc_final: 0.7600 (p)
REVERT: B  182 ARG cc_start: 0.7772 (tpp80) cc_final: 0.7141 (ttm-80)
REVERT: B  188 ARG cc_start: 0.6390 (mmp80) cc_final: 0.5340 (tpt90)
REVERT: B  202 ASN cc_start: 0.8650 (m110) cc_final: 0.8020 (m110)
REVERT: B  213 ASN cc_start: 0.7964 (t0) cc_final: 0.7731 (t0)
REVERT: C  177 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8152 (mm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 213
  average time/residue: 0.3311
  time to fit residues: 101.0986
Evaluate side-chains
  209 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 189
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  119 LYS
Chi-restraints excluded: chain A residue  165 ASN
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  663 ASN
Chi-restraints excluded: chain A residue  678 ASP
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  947 ASP
Chi-restraints excluded: chain A residue 1028 SER
Chi-restraints excluded: chain A residue 1240 ILE
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1311 ASP
Chi-restraints excluded: chain A residue 1326 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 142 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   chunk 119 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 111 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 ASN
A 671 GLN
** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 ASN
E 132 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.170053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.134049 restraints weight = 25095.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.72
r_work: 0.3379 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13787  Z= 0.136
  Angle     :  0.590  14.944  18715  Z= 0.286
  Chirality :  0.040   0.164   2109
  Planarity :  0.004   0.043   2391
  Dihedral  :  4.214  24.808   1836
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.46 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.21), residues: 1680
  helix:  1.26 (0.18), residues: 897
  sheet: -0.87 (0.49), residues: 105
  loop :  0.31 (0.25), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1019 
 HIS   0.005   0.001   HIS A 864 
 PHE   0.024   0.001   PHE A1011 
 TYR   0.012   0.001   TYR A 656 
 ARG   0.011   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03466 (  667)
  hydrogen bonds       : angle       4.52897 ( 1903)
  metal coordination   : bond        0.01039 (    4)
  metal coordination   : angle       2.95340 (    2)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       1.29406 (    2)
  covalent geometry    : bond        0.00329 (13782)
  covalent geometry    : angle       0.58912 (18711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7687.31 seconds
wall clock time: 136 minutes 15.35 seconds (8175.35 seconds total)