Starting phenix.real_space_refine
on Thu Mar  5 04:12:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e5z_30995/03_2026/7e5z_30995.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e5z_30995/03_2026/7e5z_30995.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e5z_30995/03_2026/7e5z_30995.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e5z_30995/03_2026/7e5z_30995.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e5z_30995/03_2026/7e5z_30995.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e5z_30995/03_2026/7e5z_30995.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.034
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: 8
    Type Number    sf(0)   Gaussians
     W       1     12.54       5
     Fe     20      7.16       5
     P       5      5.49       5
     S      85      5.16       5
     C    6389      2.51       5
     N    1820      2.21       5
     O    1924      1.98       5
     H    8810      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19054
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 11141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 775, 11141
          Classifications: {'peptide': 775}
          Link IDs: {'PTRANS': 45, 'TRANS': 729}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 7747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 7747
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 27, 'TRANS': 509}
    Chain: "A"
      Number of atoms: 123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 123
          Unusual residues: {'  W': 1, 'FES': 1, 'MGD': 2, 'SF4': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 43
          Unusual residues: {'FES': 1, 'FMN': 1, 'SF4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    490  SG  CYS A 102      52.690  29.667  81.735  1.00 78.33           S
  ATOM    676  SG  CYS A 115      53.012  27.443  83.224  1.00 81.48           S
  ATOM    717  SG  CYS A 118      57.786  28.789  83.440  1.00 82.89           S
  ATOM    884  SG  CYS A 132      57.079  32.544  81.745  1.00 84.97           S
  ATOM   2092  SG  CYS A 216      45.893  27.696  77.991  1.00 82.89           S
  ATOM   2057  SG  CYS A 213      40.458  26.953  80.445  1.00 83.96           S
  ATOM   2740  SG  CYS A 266      42.889  24.929  74.851  1.00 80.21           S
  ATOM   2133  SG  CYS A 219      42.000  29.786  75.167  1.00 83.24           S
  ATOM   2191  SG  CYS A 223      39.836  35.677  69.737  1.00 81.05           S
  ATOM   2686  SG  CYS A 262      40.099  31.233  69.550  1.00 80.67           S
  ATOM   2639  SG  CYS A 256      35.005  33.064  66.998  1.00 83.00           S
  ATOM   2657  SG  CYS A 259      39.457  35.799  65.522  1.00 78.47           S
  ATOM   2191  SG  CYS A 223      39.836  35.677  69.737  1.00 81.05           S
  ATOM   2657  SG  CYS A 259      39.457  35.799  65.522  1.00 78.47           S
  ATOM   3176  SG  CYS A 295      45.936  34.087  52.188  1.00 86.22           S
  ATOM   3667  SG  CYS A 329      41.258  35.643  56.111  1.00 76.61           S
  ATOM   3219  SG  CYS A 298      41.732  38.713  51.901  1.00 88.24           S
  ATOM   3176  SG  CYS A 295      45.936  34.087  52.188  1.00 86.22           S
  ATOM   3257  SG  CYS A 302      47.040  36.431  55.411  1.00 80.77           S
  ATOM  18110  SG  CYS B 502      45.093  35.317  92.305  1.00 79.77           S
  ATOM  18610  SG  CYS B 542      48.649  35.148  95.664  1.00 83.44           S
  ATOM  18176  SG  CYS B 508      45.577  30.724  93.567  1.00 84.21           S
  ATOM  18140  SG  CYS B 505      48.800  31.120  92.714  1.00 84.95           S
  ATOM  18610  SG  CYS B 542      48.649  35.148  95.664  1.00 83.44           S
  ATOM  18110  SG  CYS B 502      45.093  35.317  92.305  1.00 79.77           S
  ATOM  18176  SG  CYS B 508      45.577  30.724  93.567  1.00 84.21           S
  ATOM  12410  SG  CYS B 113      31.884  36.456 110.142  1.00 78.16           S
  ATOM  12451  SG  CYS B 118      31.038  37.209 113.136  1.00 77.35           S
  ATOM  12874  SG  CYS B 146      35.767  39.161 109.530  1.00 80.98           S
  ATOM  12924  SG  CYS B 150      36.341  38.978 113.213  1.00 78.95           S

  Time building chain proxies: 3.34, per 1000 atoms: 0.18
  Number of scatterers: 19054
  At special positions: 0
  Unit cell: (88.81, 89.64, 142.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     W       1     73.95
     Fe     20     26.01
     S      85     16.00
     P       5     15.00
     O    1924      8.00
     N    1820      7.00
     C    6389      6.00
     H    8810      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.11
  Conformation dependent library (CDL) restraints added in 610.6 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" FES A1003 "
        pdb="FE2  FES A1003 " - pdb=" SG  CYS A 132 "
        pdb="FE2  FES A1003 " - pdb=" SG  CYS A 118 "
        pdb="FE1  FES A1003 " - pdb=" SG  CYS A 102 "
        pdb="FE1  FES A1003 " - pdb=" SG  CYS A 115 "
      pdb=" FES B1002 "
        pdb="FE2  FES B1002 " - pdb=" SG  CYS B 146 "
        pdb="FE1  FES B1002 " - pdb=" SG  CYS B 113 "
        pdb="FE2  FES B1002 " - pdb=" SG  CYS B 150 "
        pdb="FE1  FES B1002 " - pdb=" SG  CYS B 118 "
      pdb=" SF4 A1004 "
        pdb="FE3  SF4 A1004 " - pdb=" SG  CYS A 266 "
        pdb="FE1  SF4 A1004 " - pdb=" SG  CYS A 216 "
        pdb="FE2  SF4 A1004 " - pdb=" SG  CYS A 213 "
        pdb="FE4  SF4 A1004 " - pdb=" SG  CYS A 219 "
      pdb=" SF4 A1005 "
        pdb="FE4  SF4 A1005 " - pdb=" SG  CYS A 259 "
        pdb="FE4  SF4 A1005 " - pdb=" SG  CYS A 223 "
        pdb="FE2  SF4 A1005 " - pdb=" SG  CYS A 256 "
        pdb="FE1  SF4 A1005 " - pdb=" SG  CYS A 262 "
      pdb=" SF4 A1006 "
        pdb="FE2  SF4 A1006 " - pdb=" SG  CYS A 329 "
        pdb="FE4  SF4 A1006 " - pdb=" SG  CYS A 302 "
        pdb="FE1  SF4 A1006 " - pdb=" SG  CYS A 295 "
        pdb="FE3  SF4 A1006 " - pdb=" SG  CYS A 298 "
      pdb=" SF4 B1001 "
        pdb="FE1  SF4 B1001 " - pdb=" SG  CYS B 542 "
        pdb="FE2  SF4 B1001 " - pdb=" SG  CYS B 508 "
        pdb="FE4  SF4 B1001 " - pdb=" SG  CYS B 502 "
        pdb="FE3  SF4 B1001 " - pdb=" SG  CYS B 505 "
      Number of angles added : 62


  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2394

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 12 sheets defined
      41.7% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 86 through 95
    Processing helix  chain 'A' and resid 147 through 163
    Processing helix  chain 'A' and resid 166 through 170
      removed outlier: 4.299A  pdb=" N   SER A 170 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 184
    Processing helix  chain 'A' and resid 217 through 224
    Processing helix  chain 'A' and resid 245 through 249
    Processing helix  chain 'A' and resid 329 through 334
    Processing helix  chain 'A' and resid 378 through 396
      removed outlier: 4.058A  pdb=" N   ALA A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLY A 387 " --> pdb=" O   ARG A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 424
      removed outlier: 3.634A  pdb=" N   TYR A 414 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU A 415 " --> pdb=" O   GLU A 411 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   VAL A 420 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 448
      removed outlier: 3.673A  pdb=" N   VAL A 441 " --> pdb=" O   HIS A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 477
    Processing helix  chain 'A' and resid 477 through 492
    Processing helix  chain 'A' and resid 503 through 509
    Processing helix  chain 'A' and resid 519 through 535
      removed outlier: 4.091A  pdb=" N   MET A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ILE A 531 " --> pdb=" O   MET A 527 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   VAL A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 545
      removed outlier: 3.528A  pdb=" N   ILE A 542 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLY A 544 " --> pdb=" O   GLN A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 559
    Processing helix  chain 'A' and resid 564 through 569
    Processing helix  chain 'A' and resid 571 through 585
      removed outlier: 3.847A  pdb=" N   LEU A 575 " --> pdb=" O   ASP A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 598
      removed outlier: 3.903A  pdb=" N   SER A 597 " --> pdb=" O   GLY A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 610
      removed outlier: 3.911A  pdb=" N   CYS A 608 " --> pdb=" O   ASP A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 617
      removed outlier: 4.629A  pdb=" N   LEU A 614 " --> pdb=" O   ILE A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 640
    Processing helix  chain 'A' and resid 658 through 663
    Processing helix  chain 'A' and resid 663 through 668
    Processing helix  chain 'A' and resid 678 through 687
    Processing helix  chain 'A' and resid 700 through 704
    Processing helix  chain 'A' and resid 711 through 717
      removed outlier: 4.270A  pdb=" N   LEU A 715 " --> pdb=" O   ALA A 711 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   MET A 717 " --> pdb=" O   HIS A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 785
      removed outlier: 3.827A  pdb=" N   ILE A 777 " --> pdb=" O   GLN A 773 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLN A 779 " --> pdb=" O   TRP A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 803
      removed outlier: 4.637A  pdb=" N   ALA A 799 " --> pdb=" O   ALA A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 809
    Processing helix  chain 'A' and resid 812 through 818
    Processing helix  chain 'B' and resid 35 through 43
      removed outlier: 3.706A  pdb=" N   GLU B  39 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU B  41 " --> pdb=" O   GLU B  37 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 63
    Processing helix  chain 'B' and resid 68 through 79
    Processing helix  chain 'B' and resid 81 through 89
      removed outlier: 3.733A  pdb=" N   VAL B  85 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 121
      removed outlier: 3.693A  pdb=" N   PHE B 121 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 131
    Processing helix  chain 'B' and resid 167 through 177
      removed outlier: 4.183A  pdb=" N   ALA B 173 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 196
      removed outlier: 4.042A  pdb=" N   GLY B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 207
      removed outlier: 3.645A  pdb=" N   GLU B 203 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   LEU B 205 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG B 206 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 222
      removed outlier: 3.533A  pdb=" N   LEU B 216 " --> pdb=" O   VAL B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 244
    Processing helix  chain 'B' and resid 263 through 269
    Processing helix  chain 'B' and resid 271 through 287
      removed outlier: 4.346A  pdb=" N   PHE B 275 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 310
      removed outlier: 3.983A  pdb=" N   ALA B 307 " --> pdb=" O   ARG B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 313
      No H-bonds generated for 'chain 'B' and resid 311 through 313'
    Processing helix  chain 'B' and resid 328 through 332
    Processing helix  chain 'B' and resid 333 through 342
    Processing helix  chain 'B' and resid 369 through 375
      removed outlier: 3.510A  pdb=" N   TRP B 375 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 383
      removed outlier: 3.571A  pdb=" N   ARG B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 388
    Processing helix  chain 'B' and resid 420 through 427
      removed outlier: 3.524A  pdb=" N   LEU B 424 " --> pdb=" O   THR B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 469
      removed outlier: 4.187A  pdb=" N   THR B 464 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   LEU B 465 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   GLU B 466 " --> pdb=" O   GLY B 463 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   LYS B 467 " --> pdb=" O   THR B 464 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY B 469 " --> pdb=" O   GLU B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 500
      removed outlier: 3.776A  pdb=" N   ALA B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 519
      removed outlier: 4.160A  pdb=" N   GLN B 513 " --> pdb=" O   ARG B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 539
    Processing helix  chain 'B' and resid 549 through 559
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74
      removed outlier: 6.923A  pdb=" N   GLU A  73 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208
      removed outlier: 3.566A  pdb=" N   MET A 272 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 294
      removed outlier: 3.786A  pdb=" N   ARG A 289 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL A 308 " --> pdb=" O   ARG A 289 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL A 291 " --> pdb=" O   TYR A 306 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   SER A 305 " --> pdb=" O   ALA A 316 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   ALA A 316 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   LYS A 307 " --> pdb=" O   VAL A 314 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 469
    Processing sheet with id=AA5, first strand: chain 'A' and resid 546 through 547
    Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.597A  pdb=" N   GLN A 652 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 752
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67
      removed outlier: 6.665A  pdb=" N   ILE B  66 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 144
      removed outlier: 6.892A  pdb=" N   ILE B 110 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   ALA B 144 " --> pdb=" O   ILE B 110 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   VAL B 112 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 249 through 251
      removed outlier: 3.942A  pdb=" N   LEU B 366 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA B 251 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 399 through 403
      removed outlier: 3.552A  pdb=" N   VAL B 403 " --> pdb=" O   GLY B 411 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY B 411 " --> pdb=" O   VAL B 403 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 451 through 452

    313 hydrogen bonds defined for protein.
    870 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: 3.71

  Time building geometry restraints manager: 2.62 seconds

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

  Histogram of bond lengths:
        0.84 -     1.13: 8800
        1.13 -     1.42: 4376
        1.42 -     1.71: 5978
        1.71 -     2.00: 94
        2.00 -     2.29: 56
  Bond restraints: 19304
  Sorted by residual:
  bond pdb=" C   LEU A 612 "
       pdb=" O   LEU A 612 "
    ideal  model  delta    sigma   weight residual
    1.236  1.305 -0.068 1.15e-02 7.56e+03 3.52e+01
  bond pdb=" C4  FMN B1000 "
       pdb=" C4A FMN B1000 "
    ideal  model  delta    sigma   weight residual
    1.485  1.388  0.097 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" N   LEU A 612 "
       pdb=" CA  LEU A 612 "
    ideal  model  delta    sigma   weight residual
    1.459  1.513 -0.054 1.19e-02 7.06e+03 2.07e+01
  bond pdb=" C10 MGD A1002 "
       pdb=" O3A MGD A1002 "
    ideal  model  delta    sigma   weight residual
    1.406  1.484 -0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" C4A FMN B1000 "
       pdb=" N5  FMN B1000 "
    ideal  model  delta    sigma   weight residual
    1.300  1.377 -0.077 2.00e-02 2.50e+03 1.48e+01
  ... (remaining 19299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.12: 34254
        4.12 -     8.25: 72
        8.25 -    12.37: 20
       12.37 -    16.49: 2
       16.49 -    20.62: 6
  Bond angle restraints: 34354
  Sorted by residual:
  angle pdb=" S1  FES A1003 "
        pdb="FE2  FES A1003 "
        pdb=" S2  FES A1003 "
      ideal   model   delta    sigma   weight residual
     104.33   86.51   17.82 1.14e+00 7.69e-01 2.44e+02
  angle pdb=" S1  FES B1002 "
        pdb="FE2  FES B1002 "
        pdb=" S2  FES B1002 "
      ideal   model   delta    sigma   weight residual
     104.33   87.36   16.97 1.14e+00 7.69e-01 2.21e+02
  angle pdb=" S1  FES A1003 "
        pdb="FE1  FES A1003 "
        pdb=" S2  FES A1003 "
      ideal   model   delta    sigma   weight residual
     104.33   86.48   17.85 1.20e+00 6.94e-01 2.21e+02
  angle pdb=" S1  FES B1002 "
        pdb="FE1  FES B1002 "
        pdb=" S2  FES B1002 "
      ideal   model   delta    sigma   weight residual
     104.33   87.36   16.97 1.20e+00 6.94e-01 2.00e+02
  angle pdb="FE1  FES A1003 "
        pdb=" S2  FES A1003 "
        pdb="FE2  FES A1003 "
      ideal   model   delta    sigma   weight residual
      75.66   85.97  -10.31 1.14e+00 7.69e-01 8.18e+01
  ... (remaining 34349 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 8188
       17.94 -    35.88: 817
       35.88 -    53.82: 225
       53.82 -    71.76: 55
       71.76 -    89.69: 21
  Dihedral angle restraints: 9306
    sinusoidal: 5053
      harmonic: 4253
  Sorted by residual:
  dihedral pdb=" CA  ARG A 237 "
           pdb=" C   ARG A 237 "
           pdb=" N   ALA A 238 "
           pdb=" CA  ALA A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.81  -23.19     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" C   ALA B 153 "
           pdb=" N   ALA B 153 "
           pdb=" CA  ALA B 153 "
           pdb=" CB  ALA B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.15   11.55     0      2.50e+00 1.60e-01 2.13e+01
  dihedral pdb=" CA  ASN A 209 "
           pdb=" C   ASN A 209 "
           pdb=" N   LEU A 210 "
           pdb=" CA  LEU A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.32  -20.68     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 9303 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1412
       0.077 -    0.154: 146
       0.154 -    0.232: 6
       0.232 -    0.309: 3
       0.309 -    0.386: 2
  Chirality restraints: 1569
  Sorted by residual:
  chirality pdb=" CA  ALA B 153 "
            pdb=" N   ALA B 153 "
            pdb=" C   ALA B 153 "
            pdb=" CB  ALA B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.10    0.39 2.00e-01 2.50e+01 3.72e+00
  chirality pdb=" C11 MGD A1001 "
            pdb=" C10 MGD A1001 "
            pdb=" C12 MGD A1001 "
            pdb=" O11 MGD A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.11    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C23 MGD A1002 "
            pdb=" C14 MGD A1002 "
            pdb=" N22 MGD A1002 "
            pdb=" O11 MGD A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.33    2.59   -0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 1566 not shown)

  Planarity restraints: 3009
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C16 MGD A1002 "   -0.078 2.00e-02 2.50e+03   1.70e-01 7.96e+02
        pdb=" C17 MGD A1002 "    0.016 2.00e-02 2.50e+03
        pdb=" C19 MGD A1002 "    0.025 2.00e-02 2.50e+03
        pdb=" C21 MGD A1002 "   -0.152 2.00e-02 2.50e+03
        pdb=" C23 MGD A1002 "    0.438 2.00e-02 2.50e+03
        pdb=" N15 MGD A1002 "   -0.173 2.00e-02 2.50e+03
        pdb=" N18 MGD A1002 "    0.071 2.00e-02 2.50e+03
        pdb=" N19 MGD A1002 "    0.087 2.00e-02 2.50e+03
        pdb=" N20 MGD A1002 "   -0.079 2.00e-02 2.50e+03
        pdb=" N22 MGD A1002 "   -0.212 2.00e-02 2.50e+03
        pdb=" O17 MGD A1002 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C16 MGD A1001 "    0.062 2.00e-02 2.50e+03   1.42e-01 5.55e+02
        pdb=" C17 MGD A1001 "   -0.014 2.00e-02 2.50e+03
        pdb=" C19 MGD A1001 "   -0.020 2.00e-02 2.50e+03
        pdb=" C21 MGD A1001 "    0.121 2.00e-02 2.50e+03
        pdb=" C23 MGD A1001 "   -0.363 2.00e-02 2.50e+03
        pdb=" N15 MGD A1001 "    0.139 2.00e-02 2.50e+03
        pdb=" N18 MGD A1001 "   -0.059 2.00e-02 2.50e+03
        pdb=" N19 MGD A1001 "   -0.074 2.00e-02 2.50e+03
        pdb=" N20 MGD A1001 "    0.064 2.00e-02 2.50e+03
        pdb=" N22 MGD A1001 "    0.191 2.00e-02 2.50e+03
        pdb=" O17 MGD A1001 "   -0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 529 "    0.071 2.00e-02 2.50e+03   7.53e-02 8.51e+01
        pdb=" CG  ASN A 529 "   -0.006 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 529 "   -0.068 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 529 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN A 529 "   -0.109 2.00e-02 2.50e+03
        pdb="HD22 ASN A 529 "    0.111 2.00e-02 2.50e+03
  ... (remaining 3006 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 289
        2.05 -     2.69: 28461
        2.69 -     3.33: 51198
        3.33 -     3.96: 63230
        3.96 -     4.60: 99934
  Nonbonded interactions: 243112
  Sorted by model distance:
  nonbonded pdb="HD13 LEU A 536 "
            pdb="HH22 ARG A 584 "
     model   vdw
     1.419 2.270
  nonbonded pdb=" OG1 THR A 454 "
            pdb=" H   LEU A 626 "
     model   vdw
     1.579 2.450
  nonbonded pdb=" HB3 PHE A 457 "
            pdb=" HE1 HIS A 627 "
     model   vdw
     1.599 2.270
  nonbonded pdb=" H   GLN A  82 "
            pdb=" OE1 GLU A  85 "
     model   vdw
     1.621 2.450
  nonbonded pdb=" O   GLN A 503 "
            pdb=" HG  SER A 506 "
     model   vdw
     1.622 2.450
  ... (remaining 243107 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  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:             0.070
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     21.090
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
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   0.895  10519  Z= 0.936
  Angle     :  2.621  78.218  14365  Z= 0.587
  Chirality :  0.048   0.386   1569
  Planarity :  0.007   0.170   1866
  Dihedral  : 15.025  89.695   3909
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 21.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.18 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  3.33 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.25 (0.16), residues: 1306
  helix: -3.41 (0.18), residues: 446
  sheet: -4.61 (0.35), residues: 95
  loop : -4.82 (0.15), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 815 
 TYR   0.009   0.001   TYR A 582 
 PHE   0.009   0.001   PHE A 744 
 TRP   0.015   0.001   TRP B 524 
 HIS   0.008   0.001   HIS B  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (10494)
  covalent geometry    : angle       0.92682 (14303)
  hydrogen bonds       : bond        0.21262 (  313)
  hydrogen bonds       : angle       8.57260 (  870)
  metal coordination   : bond        0.13301 (   24)
  metal coordination   : angle      37.33690 (   62)
  Misc. bond           : bond        0.89514 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  194 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 188
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.8120 (tpp) cc_final: 0.7902 (tpt)
REVERT: A  472 ASN cc_start: 0.7922 (t0) cc_final: 0.7629 (t0)
REVERT: A  545 TYR cc_start: 0.7907 (m-80) cc_final: 0.7474 (m-10)
REVERT: B  129 THR cc_start: 0.7611 (m) cc_final: 0.7261 (m)
REVERT: B  256 GLU cc_start: 0.7253 (pt0) cc_final: 0.6432 (pt0)
REVERT: B  264 ASP cc_start: 0.7306 (m-30) cc_final: 0.7098 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 192
  average time/residue: 0.2299
  time to fit residues: 60.2380
Evaluate side-chains
  126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain B residue  154 PRO
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 129 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 176 HIS
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 HIS
A 540 GLN
A 618 GLN
A 636 GLN
A 669 GLN
A 779 GLN
A 831 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.097578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.089432 restraints weight = 49913.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.091890 restraints weight = 19892.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.093272 restraints weight = 9590.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.094163 restraints weight = 5443.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.094687 restraints weight = 3356.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10519  Z= 0.121
  Angle     :  2.037  72.887  14365  Z= 0.346
  Chirality :  0.043   0.153   1569
  Planarity :  0.004   0.039   1866
  Dihedral  :  9.945  80.236   1577
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.81 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  8.47 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.87 (0.19), residues: 1306
  helix: -2.12 (0.22), residues: 472
  sheet: -4.01 (0.39), residues: 98
  loop : -4.09 (0.18), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 507 
 TYR   0.011   0.001   TYR A 791 
 PHE   0.015   0.001   PHE A 744 
 TRP   0.010   0.001   TRP B 524 
 HIS   0.007   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10494)
  covalent geometry    : angle       0.58828 (14303)
  hydrogen bonds       : bond        0.04638 (  313)
  hydrogen bonds       : angle       6.38929 (  870)
  metal coordination   : bond        0.01887 (   24)
  metal coordination   : angle      29.69037 (   62)
  Misc. bond           : bond        0.00420 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  139 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  176 GLU cc_start: 0.7713 (tp30) cc_final: 0.7371 (tp30)
REVERT: B  256 GLU cc_start: 0.7758 (pt0) cc_final: 0.6931 (pt0)
REVERT: B  264 ASP cc_start: 0.7226 (m-30) cc_final: 0.6908 (m-30)
REVERT: B  549 SER cc_start: 0.8692 (m) cc_final: 0.8237 (p)
  outliers start: 7
  outliers final: 3
  residues processed: 137
  average time/residue: 0.1750
  time to fit residues: 35.3373
Evaluate side-chains
  115 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 326 ASN
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 HIS
A 710 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.095218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.086733 restraints weight = 54949.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.089258 restraints weight = 21632.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.090699 restraints weight = 10462.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.091595 restraints weight = 5969.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.092156 restraints weight = 3745.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10519  Z= 0.130
  Angle     :  1.805  81.068  14365  Z= 0.321
  Chirality :  0.042   0.135   1569
  Planarity :  0.004   0.038   1866
  Dihedral  :  8.514  82.373   1570
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.19 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.90 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.06 (0.21), residues: 1306
  helix: -1.44 (0.23), residues: 483
  sheet: -3.41 (0.45), residues: 105
  loop : -3.64 (0.19), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  47 
 TYR   0.011   0.001   TYR A 315 
 PHE   0.017   0.001   PHE A 744 
 TRP   0.013   0.001   TRP B 524 
 HIS   0.007   0.001   HIS A 601 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10494)
  covalent geometry    : angle       0.54917 (14303)
  hydrogen bonds       : bond        0.04166 (  313)
  hydrogen bonds       : angle       5.83728 (  870)
  metal coordination   : bond        0.01678 (   24)
  metal coordination   : angle      26.17575 (   62)
  Misc. bond           : bond        0.00171 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 ASP cc_start: 0.7769 (t0) cc_final: 0.7556 (t70)
REVERT: A  189 SER cc_start: 0.8745 (t) cc_final: 0.8478 (p)
REVERT: A  251 MET cc_start: 0.8326 (tmm) cc_final: 0.8050 (tmm)
REVERT: A  594 MET cc_start: 0.7026 (mmp) cc_final: 0.6655 (mmt)
REVERT: B   54 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7361 (mm-30)
REVERT: B  256 GLU cc_start: 0.7921 (pt0) cc_final: 0.7145 (pt0)
REVERT: B  264 ASP cc_start: 0.7154 (m-30) cc_final: 0.6893 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1899
  time to fit residues: 34.2669
Evaluate side-chains
  116 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain A residue  437 HIS
Chi-restraints excluded: chain A residue  527 MET
Chi-restraints excluded: chain B residue   33 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 118 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 68 optimal weight:    0.1980
   chunk 16 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    2.6388

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.091721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.082942 restraints weight = 58348.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.085457 restraints weight = 23174.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.086954 restraints weight = 11348.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.087866 restraints weight = 6475.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088445 restraints weight = 4127.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10519  Z= 0.187
  Angle     :  1.724  75.928  14365  Z= 0.337
  Chirality :  0.044   0.144   1569
  Planarity :  0.004   0.040   1866
  Dihedral  :  8.331  84.936   1570
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.57 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.51 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.62 (0.22), residues: 1306
  helix: -1.10 (0.24), residues: 479
  sheet: -2.98 (0.52), residues: 94
  loop : -3.39 (0.20), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  47 
 TYR   0.011   0.001   TYR A 824 
 PHE   0.016   0.001   PHE A 744 
 TRP   0.020   0.001   TRP B 524 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (10494)
  covalent geometry    : angle       0.58600 (14303)
  hydrogen bonds       : bond        0.04363 (  313)
  hydrogen bonds       : angle       5.72132 (  870)
  metal coordination   : bond        0.02350 (   24)
  metal coordination   : angle      24.69031 (   62)
  Misc. bond           : bond        0.00155 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  594 MET cc_start: 0.7045 (mmp) cc_final: 0.6519 (mmt)
REVERT: A  624 THR cc_start: 0.9003 (p) cc_final: 0.8753 (p)
REVERT: B   54 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7547 (mm-30)
REVERT: B  264 ASP cc_start: 0.7241 (m-30) cc_final: 0.6933 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1772
  time to fit residues: 32.9143
Evaluate side-chains
  114 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain A residue  437 HIS
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain B residue   33 HIS
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  561 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 126 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 ASN
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.094566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.085807 restraints weight = 55875.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.088333 restraints weight = 22069.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.089823 restraints weight = 10764.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.090780 restraints weight = 6128.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.091315 restraints weight = 3830.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10519  Z= 0.098
  Angle     :  1.588  67.070  14365  Z= 0.292
  Chirality :  0.041   0.137   1569
  Planarity :  0.004   0.047   1866
  Dihedral  :  7.169  80.005   1570
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.97 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.94 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.07 (0.23), residues: 1306
  helix: -0.66 (0.25), residues: 476
  sheet: -2.72 (0.53), residues: 92
  loop : -3.05 (0.21), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 584 
 TYR   0.009   0.001   TYR A 315 
 PHE   0.015   0.001   PHE A 744 
 TRP   0.008   0.001   TRP B 524 
 HIS   0.003   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (10494)
  covalent geometry    : angle       0.50723 (14303)
  hydrogen bonds       : bond        0.03362 (  313)
  hydrogen bonds       : angle       5.34795 (  870)
  metal coordination   : bond        0.01121 (   24)
  metal coordination   : angle      22.91674 (   62)
  Misc. bond           : bond        0.00084 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  127 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 CYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7693 (p)
REVERT: A  523 MET cc_start: 0.7546 (ptm) cc_final: 0.7227 (ptm)
REVERT: A  594 MET cc_start: 0.6733 (mmp) cc_final: 0.6286 (mmp)
REVERT: B   54 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: B  264 ASP cc_start: 0.7188 (m-30) cc_final: 0.6897 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 121
  average time/residue: 0.1612
  time to fit residues: 29.7290
Evaluate side-chains
  118 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 112 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 65 optimal weight:    0.2980
   chunk 7 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   overall best weight:    3.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 GLN
B 131 GLN
B 504 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.089266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.080461 restraints weight = 58055.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.082901 restraints weight = 23518.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.084371 restraints weight = 11749.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.085293 restraints weight = 6863.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.085876 restraints weight = 4437.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10519  Z= 0.233
  Angle     :  1.736  66.194  14365  Z= 0.354
  Chirality :  0.045   0.155   1569
  Planarity :  0.005   0.048   1866
  Dihedral  :  8.397  87.790   1570
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.18 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.18 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.30 (0.22), residues: 1306
  helix: -0.81 (0.24), residues: 479
  sheet: -3.03 (0.49), residues: 102
  loop : -3.17 (0.20), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 237 
 TYR   0.013   0.002   TYR A 824 
 PHE   0.018   0.002   PHE A 744 
 TRP   0.027   0.002   TRP B 524 
 HIS   0.005   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (10494)
  covalent geometry    : angle       0.62133 (14303)
  hydrogen bonds       : bond        0.04678 (  313)
  hydrogen bonds       : angle       5.60090 (  870)
  metal coordination   : bond        0.02583 (   24)
  metal coordination   : angle      24.68226 (   62)
  Misc. bond           : bond        0.00154 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7811 (p)
REVERT: A  251 MET cc_start: 0.8238 (tmm) cc_final: 0.7987 (tmm)
REVERT: A  523 MET cc_start: 0.7671 (ptm) cc_final: 0.7446 (ptm)
REVERT: A  594 MET cc_start: 0.6907 (mmp) cc_final: 0.6349 (mmt)
REVERT: B  264 ASP cc_start: 0.7383 (m-30) cc_final: 0.7040 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 117
  average time/residue: 0.1647
  time to fit residues: 28.9767
Evaluate side-chains
  113 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain B residue   33 HIS
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  561 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0050
   chunk 48 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.7800

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.091276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.082662 restraints weight = 50556.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.085022 restraints weight = 21002.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.086414 restraints weight = 10659.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.087311 restraints weight = 6313.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.087879 restraints weight = 4113.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10519  Z= 0.130
  Angle     :  1.637  65.298  14365  Z= 0.307
  Chirality :  0.042   0.133   1569
  Planarity :  0.004   0.048   1866
  Dihedral  :  7.510  83.238   1570
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.89 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.65 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.23), residues: 1306
  helix: -0.53 (0.25), residues: 477
  sheet: -2.86 (0.50), residues: 102
  loop : -2.96 (0.21), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 584 
 TYR   0.010   0.001   TYR A 824 
 PHE   0.017   0.001   PHE A 744 
 TRP   0.015   0.001   TRP B 524 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10494)
  covalent geometry    : angle       0.53460 (14303)
  hydrogen bonds       : bond        0.03717 (  313)
  hydrogen bonds       : angle       5.34712 (  870)
  metal coordination   : bond        0.01563 (   24)
  metal coordination   : angle      23.55622 (   62)
  Misc. bond           : bond        0.00074 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7708 (p)
REVERT: A  131 SER cc_start: 0.9425 (t) cc_final: 0.8905 (p)
REVERT: A  188 GLU cc_start: 0.7526 (pp20) cc_final: 0.7094 (pp20)
REVERT: A  251 MET cc_start: 0.8216 (tmm) cc_final: 0.7950 (tmm)
REVERT: A  560 THR cc_start: 0.8402 (t) cc_final: 0.8125 (m)
REVERT: A  594 MET cc_start: 0.6703 (mmp) cc_final: 0.6341 (mmp)
REVERT: B  264 ASP cc_start: 0.7327 (m-30) cc_final: 0.6979 (m-30)
REVERT: B  368 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8227 (m110)
  outliers start: 17
  outliers final: 10
  residues processed: 118
  average time/residue: 0.1720
  time to fit residues: 30.5561
Evaluate side-chains
  114 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  368 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 55 optimal weight:    9.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.089138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.080587 restraints weight = 51066.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.082884 restraints weight = 21667.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.084266 restraints weight = 11170.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.085155 restraints weight = 6660.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.085703 restraints weight = 4368.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10519  Z= 0.207
  Angle     :  1.722  63.847  14365  Z= 0.342
  Chirality :  0.044   0.150   1569
  Planarity :  0.004   0.047   1866
  Dihedral  :  8.079  85.995   1570
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.87 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.41 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.22), residues: 1306
  helix: -0.54 (0.24), residues: 472
  sheet: -2.94 (0.48), residues: 104
  loop : -2.99 (0.21), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 224 
 TYR   0.014   0.001   TYR A 824 
 PHE   0.017   0.001   PHE A 744 
 TRP   0.024   0.001   TRP B 524 
 HIS   0.005   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (10494)
  covalent geometry    : angle       0.59760 (14303)
  hydrogen bonds       : bond        0.04386 (  313)
  hydrogen bonds       : angle       5.49186 (  870)
  metal coordination   : bond        0.02222 (   24)
  metal coordination   : angle      24.59615 (   62)
  Misc. bond           : bond        0.00143 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 CYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7735 (p)
REVERT: A  131 SER cc_start: 0.9480 (t) cc_final: 0.8915 (p)
REVERT: A  251 MET cc_start: 0.8300 (tmm) cc_final: 0.8030 (tmm)
REVERT: A  560 THR cc_start: 0.8453 (t) cc_final: 0.8202 (m)
REVERT: A  594 MET cc_start: 0.6773 (mmp) cc_final: 0.6330 (mmp)
REVERT: B  264 ASP cc_start: 0.7417 (m-30) cc_final: 0.7065 (m-30)
REVERT: B  368 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8315 (m110)
  outliers start: 18
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1517
  time to fit residues: 27.4616
Evaluate side-chains
  120 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain A residue  791 TYR
Chi-restraints excluded: chain B residue   33 HIS
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  561 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 92 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.090109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.081604 restraints weight = 49932.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.083883 restraints weight = 21113.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.085234 restraints weight = 10879.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.086080 restraints weight = 6499.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.086614 restraints weight = 4315.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10519  Z= 0.149
  Angle     :  1.667  63.611  14365  Z= 0.317
  Chirality :  0.042   0.133   1569
  Planarity :  0.004   0.048   1866
  Dihedral  :  7.587  82.930   1570
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.96 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.70 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.23), residues: 1306
  helix: -0.44 (0.25), residues: 474
  sheet: -2.88 (0.48), residues: 99
  loop : -2.89 (0.21), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 584 
 TYR   0.011   0.001   TYR A 824 
 PHE   0.017   0.001   PHE A 744 
 TRP   0.017   0.001   TRP B 524 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10494)
  covalent geometry    : angle       0.55132 (14303)
  hydrogen bonds       : bond        0.03871 (  313)
  hydrogen bonds       : angle       5.32734 (  870)
  metal coordination   : bond        0.01795 (   24)
  metal coordination   : angle      23.94814 (   62)
  Misc. bond           : bond        0.00081 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  124 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7740 (p)
REVERT: A  131 SER cc_start: 0.9472 (t) cc_final: 0.8933 (p)
REVERT: A  251 MET cc_start: 0.8292 (tmm) cc_final: 0.8021 (tmm)
REVERT: A  560 THR cc_start: 0.8401 (t) cc_final: 0.8183 (m)
REVERT: A  594 MET cc_start: 0.6725 (mmp) cc_final: 0.6279 (mmp)
REVERT: B  264 ASP cc_start: 0.7379 (m-30) cc_final: 0.7021 (m-30)
  outliers start: 16
  outliers final: 13
  residues processed: 119
  average time/residue: 0.1693
  time to fit residues: 30.1563
Evaluate side-chains
  120 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain B residue   33 HIS
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  561 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 109 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.091884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.083404 restraints weight = 49078.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.085662 restraints weight = 20593.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.087069 restraints weight = 10623.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.087931 restraints weight = 6223.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.088445 restraints weight = 4074.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10519  Z= 0.114
  Angle     :  1.622  62.638  14365  Z= 0.306
  Chirality :  0.041   0.134   1569
  Planarity :  0.004   0.048   1866
  Dihedral  :  7.122  78.991   1570
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.88 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 16.27 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.23), residues: 1306
  helix: -0.17 (0.25), residues: 469
  sheet: -2.55 (0.53), residues: 86
  loop : -2.67 (0.22), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 511 
 TYR   0.009   0.001   TYR A 824 
 PHE   0.016   0.001   PHE A 744 
 TRP   0.011   0.001   TRP B 524 
 HIS   0.002   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10494)
  covalent geometry    : angle       0.53974 (14303)
  hydrogen bonds       : bond        0.03414 (  313)
  hydrogen bonds       : angle       5.15089 (  870)
  metal coordination   : bond        0.01357 (   24)
  metal coordination   : angle      23.29108 (   62)
  Misc. bond           : bond        0.00065 (    1)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   96 is missing expected H atoms. Skipping.
Residue VAL  127 is missing expected H atoms. Skipping.
Residue LEU  128 is missing expected H atoms. Skipping.
Residue VAL  142 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue THR  187 is missing expected H atoms. Skipping.
Residue SER  189 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue SER  405 is missing expected H atoms. Skipping.
Residue LYS  485 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue ILE  691 is missing expected H atoms. Skipping.
Residue ALA   34 is missing expected H atoms. Skipping.
Residue THR  117 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue THR  270 is missing expected H atoms. Skipping.
Residue LEU  313 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue SER  400 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue TYR  468 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue MET  519 is missing expected H atoms. Skipping.
Evaluate side-chains
  125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7668 (p)
REVERT: A  131 SER cc_start: 0.9444 (t) cc_final: 0.8966 (p)
REVERT: A  135 THR cc_start: 0.9330 (t) cc_final: 0.8906 (m)
REVERT: A  155 MET cc_start: 0.8661 (tpp) cc_final: 0.8448 (tpp)
REVERT: A  251 MET cc_start: 0.8205 (tmm) cc_final: 0.7969 (tmm)
REVERT: A  594 MET cc_start: 0.6602 (mmp) cc_final: 0.6163 (mmp)
REVERT: B  264 ASP cc_start: 0.7357 (m-30) cc_final: 0.7009 (m-30)
  outliers start: 13
  outliers final: 12
  residues processed: 122
  average time/residue: 0.1642
  time to fit residues: 29.8388
Evaluate side-chains
  121 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  223 CYS
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  410 ASN
Chi-restraints excluded: chain B residue   33 HIS
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  277 GLU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  501 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.092410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.083891 restraints weight = 49858.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.086209 restraints weight = 20707.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.087627 restraints weight = 10522.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.088451 restraints weight = 6127.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.088982 restraints weight = 4055.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.4707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10519  Z= 0.108
  Angle     :  1.599  61.349  14365  Z= 0.299
  Chirality :  0.041   0.134   1569
  Planarity :  0.004   0.047   1866
  Dihedral  :  6.904  76.128   1570
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.35 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 16.27 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.23), residues: 1306
  helix: -0.09 (0.25), residues: 475
  sheet: -2.24 (0.51), residues: 94
  loop : -2.55 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 607 
 TYR   0.009   0.001   TYR A 315 
 PHE   0.015   0.001   PHE A 744 
 TRP   0.010   0.001   TRP B 524 
 HIS   0.002   0.001   HIS A 720 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10494)
  covalent geometry    : angle       0.52601 (14303)
  hydrogen bonds       : bond        0.03258 (  313)
  hydrogen bonds       : angle       5.03971 (  870)
  metal coordination   : bond        0.01256 (   24)
  metal coordination   : angle      22.98482 (   62)
  Misc. bond           : bond        0.00061 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2474.72 seconds
wall clock time: 43 minutes 40.99 seconds (2620.99 seconds total)