Starting phenix.real_space_refine
on Tue Mar  3 17:41:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b5s_12050/03_2026/7b5s_12050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b5s_12050/03_2026/7b5s_12050.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/7b5s_12050/03_2026/7b5s_12050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b5s_12050/03_2026/7b5s_12050.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b5s_12050/03_2026/7b5s_12050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b5s_12050/03_2026/7b5s_12050.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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      5      6.06       5
     S      51      5.16       5
     C    4876      2.51       5
     N    1328      2.21       5
     O    1411      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 7671
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 5157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5157
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 10, 'TRANS': 623}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "H"
      Number of atoms: 1832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1832
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 210}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 677
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "H"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "R"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5289  SG  CYS H 276      74.246  18.842  51.812  1.00117.24           S
  ATOM   5322  SG  CYS H 281      72.428  16.447  54.367  1.00135.41           S
  ATOM   5453  SG  CYS H 297      70.707  18.082  51.435  1.00131.43           S
  ATOM   5468  SG  CYS H 299      71.810  20.100  54.558  1.00133.40           S
  ATOM   5509  SG  CYS H 304      76.310  26.245  41.910  1.00100.27           S
  ATOM   5534  SG  CYS H 307      79.658  25.355  41.531  1.00 95.27           S
  ATOM   5616  SG  CYS H 317      78.195  27.306  38.568  1.00 70.99           S
  ATOM   7177  SG  CYS R  42      69.077  57.905  32.569  1.00 46.85           S
  ATOM   7196  SG  CYS R  45      69.268  56.455  36.282  1.00 43.75           S
  ATOM   7444  SG  CYS R  83      71.090  59.547  35.358  1.00 53.09           S
  ATOM   7373  SG  CYS R  75      73.529  60.384  19.938  1.00 75.14           S
  ATOM   7540  SG  CYS R  94      75.023  58.860  23.232  1.00 70.69           S
  ATOM   7263  SG  CYS R  53      69.020  61.737  39.490  1.00 58.47           S
  ATOM   7286  SG  CYS R  56      67.332  64.720  41.123  1.00 61.71           S
  ATOM   7323  SG  CYS R  68      66.372  63.491  37.491  1.00 65.60           S

  Time building chain proxies: 1.66, per 1000 atoms: 0.22
  Number of scatterers: 7671
  At special positions: 0
  Unit cell: (111.18, 93.74, 163.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      5     29.99
     S      51     16.00
     O    1411      8.00
     N    1328      7.00
     C    4876      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 272.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN H 601 "
        pdb="ZN    ZN H 601 " - pdb=" SG  CYS H 297 "
        pdb="ZN    ZN H 601 " - pdb=" SG  CYS H 281 "
        pdb="ZN    ZN H 601 " - pdb=" SG  CYS H 299 "
        pdb="ZN    ZN H 601 " - pdb=" SG  CYS H 276 "
      pdb="  ZN H 602 "
        pdb="ZN    ZN H 602 " - pdb=" NE2 HIS H 312 "
        pdb="ZN    ZN H 602 " - pdb=" SG  CYS H 307 "
        pdb="ZN    ZN H 602 " - pdb=" SG  CYS H 304 "
        pdb="ZN    ZN H 602 " - pdb=" SG  CYS H 317 "
      pdb="  ZN R 201 "
        pdb="ZN    ZN R 201 " - pdb=" ND1 HIS R  80 "
        pdb="ZN    ZN R 201 " - pdb=" SG  CYS R  42 "
        pdb="ZN    ZN R 201 " - pdb=" SG  CYS R  45 "
        pdb="ZN    ZN R 201 " - pdb=" SG  CYS R  83 "
      pdb="  ZN R 202 "
        pdb="ZN    ZN R 202 " - pdb=" ND1 HIS R  77 "
        pdb="ZN    ZN R 202 " - pdb=" SG  CYS R  75 "
        pdb="ZN    ZN R 202 " - pdb=" SG  CYS R  94 "
      pdb="  ZN R 203 "
        pdb="ZN    ZN R 203 " - pdb=" ND1 HIS R  82 "
        pdb="ZN    ZN R 203 " - pdb=" SG  CYS R  53 "
        pdb="ZN    ZN R 203 " - pdb=" SG  CYS R  68 "
        pdb="ZN    ZN R 203 " - pdb=" SG  CYS R  56 "
      Number of angles added : 15


  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1808

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      64.9% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'C' and resid 20 through 32
    Processing helix  chain 'C' and resid 38 through 53
      removed outlier: 3.624A  pdb=" N   TYR C  42 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 105
    Processing helix  chain 'C' and resid 114 through 137
      removed outlier: 3.843A  pdb=" N   GLN C 121 " --> pdb=" O   LYS C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 144
      removed outlier: 3.566A  pdb=" N   HIS C 143 " --> pdb=" O   TYR C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 172
    Processing helix  chain 'C' and resid 174 through 188
    Processing helix  chain 'C' and resid 189 through 191
      No H-bonds generated for 'chain 'C' and resid 189 through 191'
    Processing helix  chain 'C' and resid 198 through 211
      removed outlier: 3.904A  pdb=" N   GLY C 203 " --> pdb=" O   ARG C 199 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   VAL C 204 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
    Processing helix  chain 'C' and resid 232 through 253
      removed outlier: 3.781A  pdb=" N   THR C 249 " --> pdb=" O   THR C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 275
      removed outlier: 3.730A  pdb=" N   TYR C 260 " --> pdb=" O   PRO C 256 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   VAL C 275 " --> pdb=" O   GLU C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 295
    Processing helix  chain 'C' and resid 299 through 313
    Processing helix  chain 'C' and resid 317 through 328
      removed outlier: 3.877A  pdb=" N   ARG C 321 " --> pdb=" O   GLU C 317 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 354
      removed outlier: 3.857A  pdb=" N   LYS C 338 " --> pdb=" O   GLY C 334 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS C 354 " --> pdb=" O   ALA C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 355 through 361
      removed outlier: 3.584A  pdb=" N   ALA C 359 " --> pdb=" O   GLY C 356 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASN C 361 " --> pdb=" O   ALA C 358 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 362 through 384
      removed outlier: 3.602A  pdb=" N   TYR C 366 " --> pdb=" O   ASP C 362 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 388 through 405
      removed outlier: 3.508A  pdb=" N   ASN C 405 " --> pdb=" O   ARG C 401 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 412
    Processing helix  chain 'C' and resid 417 through 431
    Processing helix  chain 'C' and resid 438 through 455
    Processing helix  chain 'C' and resid 458 through 476
      removed outlier: 4.016A  pdb=" N   PHE C 462 " --> pdb=" O   ASP C 458 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN C 463 " --> pdb=" O   LYS C 459 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 481 through 497
    Processing helix  chain 'C' and resid 501 through 525
      removed outlier: 3.558A  pdb=" N   GLN C 505 " --> pdb=" O   THR C 501 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE C 511 " --> pdb=" O   MET C 507 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU C 519 " --> pdb=" O   LYS C 515 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 526 through 528
      No H-bonds generated for 'chain 'C' and resid 526 through 528'
    Processing helix  chain 'C' and resid 559 through 574
      removed outlier: 3.628A  pdb=" N   ARG C 573 " --> pdb=" O   PHE C 569 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS C 574 " --> pdb=" O   TYR C 570 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 604 through 613
    Processing helix  chain 'C' and resid 622 through 630
      removed outlier: 3.765A  pdb=" N   SER C 628 " --> pdb=" O   GLN C 624 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 632 through 646
    Processing helix  chain 'H' and resid 316 through 326
      removed outlier: 4.237A  pdb=" N   LYS H 326 " --> pdb=" O   LYS H 322 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 408 through 430
      removed outlier: 3.641A  pdb=" N   GLN H 412 " --> pdb=" O   ARG H 408 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE H 430 " --> pdb=" O   GLN H 426 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 430 through 448
      removed outlier: 3.625A  pdb=" N   HIS H 448 " --> pdb=" O   GLU H 444 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 452 through 481
      removed outlier: 3.986A  pdb=" N   TYR H 474 " --> pdb=" O   ALA H 470 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL H 477 " --> pdb=" O   MET H 473 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   TYR H 481 " --> pdb=" O   VAL H 477 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 485 through 513
      removed outlier: 3.652A  pdb=" N   ILE H 490 " --> pdb=" O   ASN H 486 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   PHE H 491 " --> pdb=" O   GLN H 487 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA H 496 " --> pdb=" O   GLU H 492 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP H 497 " --> pdb=" O   ASN H 493 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU H 510 " --> pdb=" O   SER H 506 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ARG H 511 " --> pdb=" O   GLY H 507 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 517 through 550
      removed outlier: 4.251A  pdb=" N   GLN H 523 " --> pdb=" O   GLN H 519 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR H 531 " --> pdb=" O   ASP H 527 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 53 through 58
      removed outlier: 4.046A  pdb=" N   ALA R  58 " --> pdb=" O   ILE R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 91
      removed outlier: 4.162A  pdb=" N   ARG R  86 " --> pdb=" O   HIS R  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 540
      removed outlier: 5.931A  pdb=" N   ASP C 534 " --> pdb=" O   TRP R  27 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   ALA R  29 " --> pdb=" O   ASP C 534 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   SER C 536 " --> pdb=" O   ALA R  29 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   ALA R  31 " --> pdb=" O   SER C 536 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   GLN C 538 " --> pdb=" O   ALA R  31 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LYS R  26 " --> pdb=" O   GLU C 589 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS C 587 " --> pdb=" O   ASN R  28 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   VAL R  30 " --> pdb=" O   LEU C 585 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   LEU C 585 " --> pdb=" O   VAL R  30 " (cutoff:3.500A)
      removed outlier: 11.594A  pdb=" N   LEU R  32 " --> pdb=" O   TYR C 583 " (cutoff:3.500A)
      removed outlier: 10.888A  pdb=" N   TYR C 583 " --> pdb=" O   LEU R  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 601 through 602
    Processing sheet with id=AA3, first strand: chain 'C' and resid 619 through 621
      removed outlier: 3.885A  pdb=" N   TYR C 620 " --> pdb=" O   ILE C 669 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 104
    Processing sheet with id=AA5, first strand: chain 'H' and resid 294 through 296
    Processing sheet with id=AA6, first strand: chain 'R' and resid 70 through 72
      removed outlier: 3.507A  pdb=" N   PHE R  79 " --> pdb=" O   ALA R  71 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1281 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: 0.97

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2499
        1.34 -     1.46: 1858
        1.46 -     1.59: 3391
        1.59 -     1.71: 0
        1.71 -     1.83: 72
  Bond restraints: 7820
  Sorted by residual:
  bond pdb=" N   VAL H 504 "
       pdb=" CA  VAL H 504 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.85e+00
  bond pdb=" N   ILE H 521 "
       pdb=" CA  ILE H 521 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.030 1.19e-02 7.06e+03 6.23e+00
  bond pdb=" N   LEU H 505 "
       pdb=" CA  LEU H 505 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.19e-02 7.06e+03 5.62e+00
  bond pdb=" N   LYS H 522 "
       pdb=" CA  LYS H 522 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.19e-02 7.06e+03 4.87e+00
  bond pdb=" CA  GLN H 487 "
       pdb=" C   GLN H 487 "
    ideal  model  delta    sigma   weight residual
    1.522  1.503  0.020 1.37e-02 5.33e+03 2.10e+00
  ... (remaining 7815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 10294
        2.16 -     4.32: 210
        4.32 -     6.49: 32
        6.49 -     8.65: 3
        8.65 -    10.81: 3
  Bond angle restraints: 10542
  Sorted by residual:
  angle pdb=" N   VAL C 145 "
        pdb=" CA  VAL C 145 "
        pdb=" C   VAL C 145 "
      ideal   model   delta    sigma   weight residual
     112.83  107.90    4.93 9.90e-01 1.02e+00 2.48e+01
  angle pdb=" N   ILE H 521 "
        pdb=" CA  ILE H 521 "
        pdb=" C   ILE H 521 "
      ideal   model   delta    sigma   weight residual
     110.62  105.69    4.93 1.02e+00 9.61e-01 2.34e+01
  angle pdb=" CA  PRO H 277 "
        pdb=" N   PRO H 277 "
        pdb=" CD  PRO H 277 "
      ideal   model   delta    sigma   weight residual
     112.00  105.98    6.02 1.40e+00 5.10e-01 1.85e+01
  angle pdb=" N   MET C 111 "
        pdb=" CA  MET C 111 "
        pdb=" CB  MET C 111 "
      ideal   model   delta    sigma   weight residual
     114.17  109.44    4.73 1.14e+00 7.69e-01 1.72e+01
  angle pdb=" N   TRP C 144 "
        pdb=" CA  TRP C 144 "
        pdb=" C   TRP C 144 "
      ideal   model   delta    sigma   weight residual
     114.56  109.77    4.79 1.27e+00 6.20e-01 1.42e+01
  ... (remaining 10537 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4163
       17.94 -    35.88: 472
       35.88 -    53.81: 70
       53.81 -    71.75: 15
       71.75 -    89.69: 9
  Dihedral angle restraints: 4729
    sinusoidal: 1950
      harmonic: 2779
  Sorted by residual:
  dihedral pdb=" CA  ASP C 217 "
           pdb=" C   ASP C 217 "
           pdb=" N   ALA C 218 "
           pdb=" CA  ALA C 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.72   25.28     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  LEU C 110 "
           pdb=" C   LEU C 110 "
           pdb=" N   MET C 111 "
           pdb=" CA  MET C 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.25   21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  PRO C 530 "
           pdb=" C   PRO C 530 "
           pdb=" N   LEU C 531 "
           pdb=" CA  LEU C 531 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.21  -20.79     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 4726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 949
       0.057 -    0.113: 171
       0.113 -    0.170: 18
       0.170 -    0.227: 3
       0.227 -    0.283: 1
  Chirality restraints: 1142
  Sorted by residual:
  chirality pdb=" CA  ILE H 521 "
            pdb=" N   ILE H 521 "
            pdb=" C   ILE H 521 "
            pdb=" CB  ILE H 521 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CB  THR C 580 "
            pdb=" CA  THR C 580 "
            pdb=" OG1 THR C 580 "
            pdb=" CG2 THR C 580 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  ILE H 513 "
            pdb=" CA  ILE H 513 "
            pdb=" CG1 ILE H 513 "
            pdb=" CG2 ILE H 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.38e-01
  ... (remaining 1139 not shown)

  Planarity restraints: 1342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS H 276 "   -0.103 5.00e-02 4.00e+02   1.54e-01 3.78e+01
        pdb=" N   PRO H 277 "    0.266 5.00e-02 4.00e+02
        pdb=" CA  PRO H 277 "   -0.086 5.00e-02 4.00e+02
        pdb=" CD  PRO H 277 "   -0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 173 "   -0.041 5.00e-02 4.00e+02   6.13e-02 6.00e+00
        pdb=" N   PRO C 174 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO C 174 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 174 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU H 509 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.40e+00
        pdb=" C   LEU H 509 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   LEU H 509 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU H 510 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1339 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 70
        2.58 -     3.16: 6525
        3.16 -     3.74: 11264
        3.74 -     4.32: 14710
        4.32 -     4.90: 24744
  Nonbonded interactions: 57313
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R  97 "
            pdb="ZN    ZN R 202 "
     model   vdw
     1.997 2.230
  nonbonded pdb=" O   LYS C 459 "
            pdb=" OH  TYR C 500 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" N   GLU H 454 "
            pdb=" OE1 GLU H 454 "
     model   vdw
     2.191 3.120
  nonbonded pdb=" OH  TYR C 244 "
            pdb=" OE2 GLU C 271 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OH  TYR C 260 "
            pdb=" O   LEU C 295 "
     model   vdw
     2.222 3.040
  ... (remaining 57308 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:             2.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.670
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.269   7839  Z= 0.289
  Angle     :  0.811  13.709  10557  Z= 0.462
  Chirality :  0.045   0.283   1142
  Planarity :  0.005   0.154   1342
  Dihedral  : 15.477  89.688   2921
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.24 %
    Favored  : 99.52 %
  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: -0.49 (0.28), residues: 915
  helix:  1.05 (0.22), residues: 546
  sheet:  0.79 (1.67), residues: 10
  loop : -2.66 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 511 
 TYR   0.021   0.002   TYR C 377 
 PHE   0.020   0.002   PHE C 303 
 TRP   0.014   0.001   TRP R  33 
 HIS   0.003   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 7820)
  covalent geometry    : angle       0.78294 (10542)
  hydrogen bonds       : bond        0.12992 (  430)
  hydrogen bonds       : angle       5.33100 ( 1281)
  metal coordination   : bond        0.06390 (   19)
  metal coordination   : angle       5.68855 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: C  143 HIS cc_start: 0.7798 (m-70) cc_final: 0.7366 (m90)
REVERT: C  672 TYR cc_start: 0.8488 (t80) cc_final: 0.8021 (t80)
REVERT: H  521 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8071 (mt)
REVERT: R   54 ILE cc_start: 0.9197 (tp) cc_final: 0.8770 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0790
  time to fit residues: 11.7771
Evaluate side-chains
  86 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  521 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0570
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
C 304 HIS
** C 607 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.138329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.102869 restraints weight = 12591.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.105636 restraints weight = 8147.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107443 restraints weight = 6137.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.108663 restraints weight = 5125.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.109382 restraints weight = 4535.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7839  Z= 0.145
  Angle     :  0.594   9.026  10557  Z= 0.314
  Chirality :  0.038   0.204   1142
  Planarity :  0.004   0.096   1342
  Dihedral  :  4.713  22.854   1023
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.15 %
    Favored  : 90.77 %
  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:  0.21 (0.29), residues: 915
  helix:  1.59 (0.22), residues: 563
  sheet:  1.53 (1.84), residues: 10
  loop : -2.54 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 511 
 TYR   0.024   0.001   TYR H 529 
 PHE   0.029   0.001   PHE H 457 
 TRP   0.009   0.001   TRP H 452 
 HIS   0.005   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7820)
  covalent geometry    : angle       0.58020 (10542)
  hydrogen bonds       : bond        0.05819 (  430)
  hydrogen bonds       : angle       4.17048 ( 1281)
  metal coordination   : bond        0.00773 (   19)
  metal coordination   : angle       3.46183 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LYS cc_start: 0.8694 (tppt) cc_final: 0.8043 (tttm)
REVERT: C  143 HIS cc_start: 0.8069 (m-70) cc_final: 0.7682 (m90)
REVERT: C  488 MET cc_start: 0.8617 (tpt) cc_final: 0.8239 (tpt)
REVERT: C  589 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6801 (mm-30)
REVERT: H  275 TRP cc_start: 0.7235 (m100) cc_final: 0.7014 (m100)
REVERT: H  497 ASP cc_start: 0.7734 (t0) cc_final: 0.7464 (t0)
REVERT: R   54 ILE cc_start: 0.9059 (tp) cc_final: 0.8707 (tp)
  outliers start: 9
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0762
  time to fit residues: 11.8348
Evaluate side-chains
  94 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain R residue   38 VAL
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 63 optimal weight:    0.3980
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0970
   chunk 27 optimal weight:    0.0770
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
** C 607 GLN ** 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 = 0.3748 r_free = 0.3748 target = 0.142169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.106906 restraints weight = 12242.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.109498 restraints weight = 8252.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.111289 restraints weight = 6383.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.112500 restraints weight = 5363.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113278 restraints weight = 4759.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7839  Z= 0.125
  Angle     :  0.543   6.734  10557  Z= 0.288
  Chirality :  0.037   0.160   1142
  Planarity :  0.004   0.076   1342
  Dihedral  :  4.497  23.212   1021
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.27 %
    Favored  : 87.29 %
  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:  0.45 (0.29), residues: 915
  helix:  1.81 (0.22), residues: 567
  sheet:  1.59 (1.84), residues: 10
  loop : -2.56 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  41 
 TYR   0.021   0.001   TYR H 529 
 PHE   0.021   0.001   PHE H 457 
 TRP   0.008   0.001   TRP C 167 
 HIS   0.004   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7820)
  covalent geometry    : angle       0.53407 (10542)
  hydrogen bonds       : bond        0.05194 (  430)
  hydrogen bonds       : angle       3.88022 ( 1281)
  metal coordination   : bond        0.00531 (   19)
  metal coordination   : angle       2.67601 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LYS cc_start: 0.8631 (tppt) cc_final: 0.7942 (tttm)
REVERT: C  143 HIS cc_start: 0.7932 (m-70) cc_final: 0.7521 (m90)
REVERT: C  427 ASP cc_start: 0.8165 (t0) cc_final: 0.7949 (t0)
REVERT: C  488 MET cc_start: 0.8727 (tpt) cc_final: 0.8327 (tpt)
REVERT: C  589 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6831 (mm-30)
REVERT: C  620 TYR cc_start: 0.7384 (m-80) cc_final: 0.6982 (m-80)
REVERT: C  681 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7554 (ttm-80)
REVERT: H  449 ASN cc_start: 0.6674 (t0) cc_final: 0.6463 (p0)
REVERT: H  450 MET cc_start: 0.4323 (mmm) cc_final: 0.4046 (mmt)
REVERT: H  458 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7959 (mp)
REVERT: H  473 MET cc_start: 0.7972 (tpp) cc_final: 0.7305 (tpp)
REVERT: H  497 ASP cc_start: 0.7806 (t0) cc_final: 0.7529 (t0)
REVERT: H  499 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7394 (tt0)
REVERT: R   54 ILE cc_start: 0.9058 (tp) cc_final: 0.8743 (tp)
  outliers start: 12
  outliers final: 6
  residues processed: 103
  average time/residue: 0.0764
  time to fit residues: 11.3338
Evaluate side-chains
  98 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  601 LEU
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 33 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C 607 GLN ** 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 = 0.3718 r_free = 0.3718 target = 0.139652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.103731 restraints weight = 12330.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.106308 restraints weight = 8428.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.108056 restraints weight = 6554.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.109136 restraints weight = 5538.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.109985 restraints weight = 4971.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7839  Z= 0.156
  Angle     :  0.562   9.377  10557  Z= 0.297
  Chirality :  0.038   0.169   1142
  Planarity :  0.004   0.066   1342
  Dihedral  :  4.510  23.137   1021
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 12.95 %
    Favored  : 84.41 %
  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:  0.47 (0.29), residues: 915
  helix:  1.84 (0.22), residues: 565
  sheet:  1.43 (1.87), residues: 10
  loop : -2.55 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 511 
 TYR   0.023   0.001   TYR H 529 
 PHE   0.023   0.001   PHE H 457 
 TRP   0.006   0.001   TRP R  35 
 HIS   0.003   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7820)
  covalent geometry    : angle       0.55112 (10542)
  hydrogen bonds       : bond        0.05895 (  430)
  hydrogen bonds       : angle       3.94943 ( 1281)
  metal coordination   : bond        0.00588 (   19)
  metal coordination   : angle       3.00938 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LYS cc_start: 0.8653 (tppt) cc_final: 0.7957 (tttm)
REVERT: C  143 HIS cc_start: 0.8046 (m-70) cc_final: 0.7635 (m90)
REVERT: C  488 MET cc_start: 0.8626 (tpt) cc_final: 0.8331 (tpt)
REVERT: C  558 GLU cc_start: 0.7974 (tp30) cc_final: 0.7754 (tp30)
REVERT: C  589 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6746 (mm-30)
REVERT: C  620 TYR cc_start: 0.7435 (m-80) cc_final: 0.6887 (m-80)
REVERT: C  681 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7460 (ttm-80)
REVERT: H  455 VAL cc_start: 0.6281 (OUTLIER) cc_final: 0.6018 (m)
REVERT: H  458 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7907 (mp)
REVERT: H  473 MET cc_start: 0.7958 (tpp) cc_final: 0.7197 (tpp)
REVERT: H  497 ASP cc_start: 0.7924 (t0) cc_final: 0.7651 (t0)
REVERT: H  499 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7340 (tt0)
REVERT: R   54 ILE cc_start: 0.9093 (tp) cc_final: 0.8825 (tp)
  outliers start: 22
  outliers final: 15
  residues processed: 104
  average time/residue: 0.0747
  time to fit residues: 11.1206
Evaluate side-chains
  105 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   35 GLN
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  585 LEU
Chi-restraints excluded: chain C residue  601 LEU
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  427 SER
Chi-restraints excluded: chain H residue  443 GLU
Chi-restraints excluded: chain H residue  455 VAL
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain H residue  471 THR
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 15 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 519 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.140992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.105301 restraints weight = 12312.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.107914 restraints weight = 8321.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.109712 restraints weight = 6426.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.110855 restraints weight = 5416.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111359 restraints weight = 4847.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7839  Z= 0.134
  Angle     :  0.533   7.303  10557  Z= 0.285
  Chirality :  0.037   0.191   1142
  Planarity :  0.003   0.059   1342
  Dihedral  :  4.381  23.914   1021
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.11 %
    Favored  : 82.37 %
  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:  0.61 (0.29), residues: 915
  helix:  1.96 (0.22), residues: 567
  sheet:  1.49 (1.88), residues: 10
  loop : -2.53 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 173 
 TYR   0.022   0.001   TYR H 529 
 PHE   0.022   0.001   PHE H 457 
 TRP   0.006   0.001   TRP H 452 
 HIS   0.004   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7820)
  covalent geometry    : angle       0.52430 (10542)
  hydrogen bonds       : bond        0.05389 (  430)
  hydrogen bonds       : angle       3.81780 ( 1281)
  metal coordination   : bond        0.00545 (   19)
  metal coordination   : angle       2.57544 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LYS cc_start: 0.8584 (tppt) cc_final: 0.8307 (mmtm)
REVERT: C  143 HIS cc_start: 0.8047 (m-70) cc_final: 0.7775 (m-70)
REVERT: C  458 ASP cc_start: 0.7796 (p0) cc_final: 0.7521 (p0)
REVERT: C  589 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6612 (mm-30)
REVERT: C  620 TYR cc_start: 0.7439 (m-80) cc_final: 0.6848 (m-80)
REVERT: H  449 ASN cc_start: 0.6641 (p0) cc_final: 0.6431 (p0)
REVERT: H  450 MET cc_start: 0.4692 (mmm) cc_final: 0.4397 (mmt)
REVERT: H  473 MET cc_start: 0.7954 (tpp) cc_final: 0.7186 (tpp)
REVERT: H  497 ASP cc_start: 0.7917 (t0) cc_final: 0.7642 (t0)
REVERT: H  499 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7384 (tt0)
REVERT: R   50 MET cc_start: 0.8612 (mmm) cc_final: 0.8270 (mmm)
REVERT: R   54 ILE cc_start: 0.9070 (tp) cc_final: 0.8807 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0772
  time to fit residues: 11.9901
Evaluate side-chains
  108 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  585 LEU
Chi-restraints excluded: chain C residue  601 LEU
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  427 SER
Chi-restraints excluded: chain H residue  443 GLU
Chi-restraints excluded: chain H residue  457 PHE
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain R residue   33 TRP
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0030
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 519 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.140739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.104997 restraints weight = 12326.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107605 restraints weight = 8363.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109356 restraints weight = 6483.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.110446 restraints weight = 5472.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111266 restraints weight = 4906.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7839  Z= 0.136
  Angle     :  0.553  14.086  10557  Z= 0.289
  Chirality :  0.037   0.194   1142
  Planarity :  0.003   0.057   1342
  Dihedral  :  4.327  24.177   1021
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.35 %
    Favored  : 82.01 %
  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:  0.67 (0.29), residues: 915
  helix:  1.99 (0.22), residues: 567
  sheet:  1.48 (1.88), residues: 10
  loop : -2.48 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 173 
 TYR   0.022   0.001   TYR H 529 
 PHE   0.022   0.001   PHE H 457 
 TRP   0.006   0.001   TRP H 452 
 HIS   0.003   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7820)
  covalent geometry    : angle       0.54460 (10542)
  hydrogen bonds       : bond        0.05422 (  430)
  hydrogen bonds       : angle       3.81716 ( 1281)
  metal coordination   : bond        0.00560 (   19)
  metal coordination   : angle       2.56613 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: C   90 LYS cc_start: 0.8534 (tppt) cc_final: 0.8324 (mmtm)
REVERT: C  143 HIS cc_start: 0.8025 (m-70) cc_final: 0.7762 (m-70)
REVERT: C  589 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6597 (mm-30)
REVERT: C  620 TYR cc_start: 0.7451 (m-80) cc_final: 0.6791 (m-80)
REVERT: C  672 TYR cc_start: 0.8452 (t80) cc_final: 0.8146 (t80)
REVERT: H  458 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7881 (mp)
REVERT: H  473 MET cc_start: 0.7969 (tpp) cc_final: 0.7140 (tpp)
REVERT: H  497 ASP cc_start: 0.7972 (t0) cc_final: 0.7659 (t0)
REVERT: H  499 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7359 (tt0)
REVERT: R   50 MET cc_start: 0.8622 (mmm) cc_final: 0.8270 (mmm)
REVERT: R   54 ILE cc_start: 0.9068 (tp) cc_final: 0.8811 (tp)
  outliers start: 22
  outliers final: 18
  residues processed: 107
  average time/residue: 0.0733
  time to fit residues: 11.1359
Evaluate side-chains
  107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   35 GLN
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  585 LEU
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  427 SER
Chi-restraints excluded: chain H residue  443 GLU
Chi-restraints excluded: chain H residue  457 PHE
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain H residue  471 THR
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain R residue   33 TRP
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 254 GLN
** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 519 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.140654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.104891 restraints weight = 12245.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.107485 restraints weight = 8323.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.109275 restraints weight = 6457.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.110384 restraints weight = 5449.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111118 restraints weight = 4873.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7839  Z= 0.142
  Angle     :  0.575  14.250  10557  Z= 0.298
  Chirality :  0.038   0.192   1142
  Planarity :  0.003   0.058   1342
  Dihedral  :  4.376  25.131   1021
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.31 %
    Favored  : 80.94 %
  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:  0.69 (0.29), residues: 915
  helix:  2.00 (0.22), residues: 567
  sheet:  1.56 (1.88), residues: 10
  loop : -2.48 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 173 
 TYR   0.022   0.001   TYR H 529 
 PHE   0.021   0.001   PHE H 457 
 TRP   0.006   0.001   TRP R  35 
 HIS   0.003   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7820)
  covalent geometry    : angle       0.56659 (10542)
  hydrogen bonds       : bond        0.05483 (  430)
  hydrogen bonds       : angle       3.82741 ( 1281)
  metal coordination   : bond        0.00582 (   19)
  metal coordination   : angle       2.58924 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: C  143 HIS cc_start: 0.8005 (m-70) cc_final: 0.7611 (m90)
REVERT: C  589 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6606 (mm-30)
REVERT: C  620 TYR cc_start: 0.7463 (m-80) cc_final: 0.6764 (m-80)
REVERT: H  458 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7775 (mp)
REVERT: H  473 MET cc_start: 0.7972 (tpp) cc_final: 0.7711 (tpp)
REVERT: H  499 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7355 (tt0)
REVERT: R   54 ILE cc_start: 0.9072 (tp) cc_final: 0.8870 (tp)
  outliers start: 23
  outliers final: 20
  residues processed: 105
  average time/residue: 0.0753
  time to fit residues: 11.3783
Evaluate side-chains
  112 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  382 MET
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  585 LEU
Chi-restraints excluded: chain C residue  653 ASP
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  427 SER
Chi-restraints excluded: chain H residue  457 PHE
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain H residue  471 THR
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain H residue  514 SER
Chi-restraints excluded: chain R residue   33 TRP
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    7.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 519 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.139718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.103812 restraints weight = 12246.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106402 restraints weight = 8392.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.108165 restraints weight = 6535.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.109343 restraints weight = 5535.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.110001 restraints weight = 4934.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7839  Z= 0.154
  Angle     :  0.583  13.347  10557  Z= 0.304
  Chirality :  0.038   0.190   1142
  Planarity :  0.003   0.058   1342
  Dihedral  :  4.392  25.209   1021
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.19 %
    Favored  : 80.34 %
  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:  0.70 (0.29), residues: 915
  helix:  2.04 (0.22), residues: 564
  sheet:  1.62 (1.88), residues: 10
  loop : -2.48 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 173 
 TYR   0.022   0.001   TYR H 529 
 PHE   0.022   0.001   PHE H 457 
 TRP   0.006   0.001   TRP R  35 
 HIS   0.003   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 7820)
  covalent geometry    : angle       0.57373 (10542)
  hydrogen bonds       : bond        0.05719 (  430)
  hydrogen bonds       : angle       3.88489 ( 1281)
  metal coordination   : bond        0.00671 (   19)
  metal coordination   : angle       2.81128 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: C  143 HIS cc_start: 0.8010 (m-70) cc_final: 0.7616 (m90)
REVERT: C  261 MET cc_start: 0.8895 (mtp) cc_final: 0.8610 (mtm)
REVERT: C  589 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6577 (mm-30)
REVERT: C  620 TYR cc_start: 0.7472 (m-80) cc_final: 0.6757 (m-80)
REVERT: C  672 TYR cc_start: 0.8436 (t80) cc_final: 0.8188 (t80)
REVERT: H  458 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: H  473 MET cc_start: 0.7963 (tpp) cc_final: 0.7691 (tpp)
REVERT: H  497 ASP cc_start: 0.7975 (t0) cc_final: 0.7638 (t0)
REVERT: H  499 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7405 (tt0)
REVERT: R   50 MET cc_start: 0.8650 (mmm) cc_final: 0.8326 (mmm)
REVERT: R   54 ILE cc_start: 0.9080 (tp) cc_final: 0.8877 (tp)
  outliers start: 29
  outliers final: 24
  residues processed: 107
  average time/residue: 0.0720
  time to fit residues: 11.0334
Evaluate side-chains
  113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  111 MET
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  382 MET
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  601 LEU
Chi-restraints excluded: chain C residue  653 ASP
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  427 SER
Chi-restraints excluded: chain H residue  443 GLU
Chi-restraints excluded: chain H residue  457 PHE
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain H residue  471 THR
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain H residue  514 SER
Chi-restraints excluded: chain R residue   33 TRP
Chi-restraints excluded: chain R residue   37 ILE
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue   96 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 77 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0870
   chunk 60 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 65 optimal weight:    9.9990
   chunk 74 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
C  30 GLN
** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 519 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.140828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.105091 restraints weight = 12250.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.107675 restraints weight = 8312.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.109227 restraints weight = 6459.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.110584 restraints weight = 5498.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.111315 restraints weight = 4892.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7839  Z= 0.139
  Angle     :  0.584  12.812  10557  Z= 0.301
  Chirality :  0.038   0.185   1142
  Planarity :  0.003   0.056   1342
  Dihedral  :  4.379  25.006   1021
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.15 %
    Favored  : 79.86 %
  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:  0.75 (0.29), residues: 915
  helix:  2.07 (0.22), residues: 565
  sheet:  1.79 (1.96), residues: 10
  loop : -2.47 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 173 
 TYR   0.022   0.001   TYR H 529 
 PHE   0.021   0.001   PHE H 457 
 TRP   0.007   0.001   TRP H 452 
 HIS   0.004   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7820)
  covalent geometry    : angle       0.57668 (10542)
  hydrogen bonds       : bond        0.05432 (  430)
  hydrogen bonds       : angle       3.84649 ( 1281)
  metal coordination   : bond        0.00581 (   19)
  metal coordination   : angle       2.46938 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: C  143 HIS cc_start: 0.7971 (m-70) cc_final: 0.7618 (m90)
REVERT: C  322 MET cc_start: 0.8441 (ttm) cc_final: 0.8092 (ttm)
REVERT: C  531 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5869 (pt)
REVERT: C  589 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6636 (mm-30)
REVERT: C  620 TYR cc_start: 0.7464 (m-80) cc_final: 0.6743 (m-80)
REVERT: C  672 TYR cc_start: 0.8467 (t80) cc_final: 0.8197 (t80)
REVERT: H  458 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7761 (mp)
REVERT: H  473 MET cc_start: 0.7955 (tpp) cc_final: 0.7077 (tpp)
REVERT: H  499 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7333 (tt0)
REVERT: R   50 MET cc_start: 0.8632 (mmm) cc_final: 0.8293 (mmm)
REVERT: R   54 ILE cc_start: 0.9052 (tp) cc_final: 0.8819 (tp)
  outliers start: 25
  outliers final: 18
  residues processed: 103
  average time/residue: 0.0730
  time to fit residues: 10.6159
Evaluate side-chains
  107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  382 MET
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  653 ASP
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  427 SER
Chi-restraints excluded: chain H residue  443 GLU
Chi-restraints excluded: chain H residue  457 PHE
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain H residue  471 THR
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain H residue  514 SER
Chi-restraints excluded: chain R residue   33 TRP
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0370
   chunk 39 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
C  30 GLN
** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 519 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.139574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.104010 restraints weight = 12256.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.106518 restraints weight = 8491.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.108194 restraints weight = 6660.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.109172 restraints weight = 5661.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.109995 restraints weight = 5104.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7839  Z= 0.144
  Angle     :  0.594  12.489  10557  Z= 0.306
  Chirality :  0.038   0.203   1142
  Planarity :  0.003   0.057   1342
  Dihedral  :  4.418  25.304   1021
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.15 %
    Favored  : 79.74 %
  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:  0.75 (0.29), residues: 915
  helix:  2.05 (0.22), residues: 565
  sheet:  1.77 (1.98), residues: 10
  loop : -2.43 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 173 
 TYR   0.022   0.001   TYR H 529 
 PHE   0.020   0.001   PHE H 457 
 TRP   0.006   0.001   TRP R  35 
 HIS   0.003   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7820)
  covalent geometry    : angle       0.58657 (10542)
  hydrogen bonds       : bond        0.05491 (  430)
  hydrogen bonds       : angle       3.86287 ( 1281)
  metal coordination   : bond        0.00563 (   19)
  metal coordination   : angle       2.51920 (   15)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: C  143 HIS cc_start: 0.8027 (m-70) cc_final: 0.7662 (m90)
REVERT: C  322 MET cc_start: 0.8471 (ttm) cc_final: 0.8210 (ttm)
REVERT: C  531 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5817 (pt)
REVERT: C  589 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6575 (mm-30)
REVERT: C  620 TYR cc_start: 0.7507 (m-80) cc_final: 0.6758 (m-80)
REVERT: C  672 TYR cc_start: 0.8437 (t80) cc_final: 0.8142 (t80)
REVERT: H  458 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7630 (mp)
REVERT: H  473 MET cc_start: 0.7983 (tpp) cc_final: 0.7054 (tpp)
REVERT: H  499 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7358 (tt0)
REVERT: R   50 MET cc_start: 0.8637 (mmm) cc_final: 0.8275 (mmm)
  outliers start: 26
  outliers final: 19
  residues processed: 101
  average time/residue: 0.0745
  time to fit residues: 10.7374
Evaluate side-chains
  107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  382 MET
Chi-restraints excluded: chain C residue  475 VAL
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  653 ASP
Chi-restraints excluded: chain H residue  273 LEU
Chi-restraints excluded: chain H residue  427 SER
Chi-restraints excluded: chain H residue  443 GLU
Chi-restraints excluded: chain H residue  457 PHE
Chi-restraints excluded: chain H residue  458 LEU
Chi-restraints excluded: chain H residue  471 THR
Chi-restraints excluded: chain H residue  499 GLU
Chi-restraints excluded: chain R residue   33 TRP
Chi-restraints excluded: chain R residue   37 ILE
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 519 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.138953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.103451 restraints weight = 12252.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.105921 restraints weight = 8447.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107582 restraints weight = 6630.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.108698 restraints weight = 5636.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109349 restraints weight = 5066.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7839  Z= 0.157
  Angle     :  0.623  14.684  10557  Z= 0.320
  Chirality :  0.039   0.240   1142
  Planarity :  0.004   0.057   1342
  Dihedral  :  4.475  25.126   1021
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.75 %
    Favored  : 79.26 %
  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:  0.65 (0.29), residues: 915
  helix:  1.95 (0.22), residues: 569
  sheet:  1.70 (1.96), residues: 10
  loop : -2.48 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 561 
 TYR   0.023   0.001   TYR H 529 
 PHE   0.020   0.001   PHE H 457 
 TRP   0.007   0.001   TRP R  35 
 HIS   0.003   0.001   HIS C 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7820)
  covalent geometry    : angle       0.61285 (10542)
  hydrogen bonds       : bond        0.05749 (  430)
  hydrogen bonds       : angle       3.91999 ( 1281)
  metal coordination   : bond        0.00637 (   19)
  metal coordination   : angle       2.97242 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1375.04 seconds
wall clock time: 24 minutes 21.29 seconds (1461.29 seconds total)