Starting phenix.real_space_refine
on Thu Jan 16 18:46:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y6a_38983/01_2025/8y6a_38983.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y6a_38983/01_2025/8y6a_38983.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y6a_38983/01_2025/8y6a_38983.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y6a_38983/01_2025/8y6a_38983.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y6a_38983/01_2025/8y6a_38983.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y6a_38983/01_2025/8y6a_38983.cif"
  }
  resolution = 2.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      47      5.16       5
     C    6214      2.51       5
     N    1618      2.21       5
     O    1906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9786
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 4793
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 587, 4783
          Classifications: {'peptide': 587}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 560}
      Conformer: "B"
        Number of residues, atoms: 587, 4783
          Classifications: {'peptide': 587}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 560}
          bond proxies already assigned to first conformer: 4902
    Chain: "B"
      Number of atoms: 1478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1478
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 11, 'TRANS': 170}
    Chain: "C"
      Number of atoms: 1701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1701
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 212}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1615
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200}
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' ZN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 8.34, per 1000 atoms: 0.85
  Number of scatterers: 9786
  At special positions: 0
  Unit cell: (80.75, 96.05, 145.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      47     16.00
     O    1906      8.00
     N    1618      7.00
     C    6214      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 154 " - pdb=" SG  CYS C 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 134 " - pdb=" SG  CYS D 194 " distance=2.02

  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
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
    NAG-ASN
      " NAG A 801 " - " ASN A 103 "
      " NAG A 803 " - " ASN A 546 "
      " NAG B 601 " - " ASN B 354 "
      " NAG E   1 " - " ASN A  53 "
      " NAG F   1 " - " ASN A  90 "
      " NAG G   1 " - " ASN A 322 "
      " NAG H   1 " - " ASN B 343 "
  Time building additional restraints: 2.73
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 802 "
        pdb="ZN    ZN A 802 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 802 " - pdb=" NE2 HIS A 374 "


  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2252

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 15 sheets defined
      36.4% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 53
      removed outlier: 4.644A  pdb=" N   LYS A  26 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR A  27 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   PHE A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 109 through 128
    Processing helix  chain 'A' and resid 146 through 154
      removed outlier: 3.665A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.846A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 4.203A  pdb=" N   SER A 280 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.703A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.633A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.970A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
      removed outlier: 3.613A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 3.923A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
      removed outlier: 3.759A  pdb=" N   TRP A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LYS A 481 " --> pdb=" O   TRP A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.743A  pdb=" N   THR A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLU A 527 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ALA A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA A 532 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.560A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 4.133A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 589 through 599
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
      removed outlier: 3.677A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 421
      removed outlier: 4.318A  pdb=" N   TYR B 421 " --> pdb=" O   ASN B 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 31
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 4.292A  pdb=" N   THR C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 84
      removed outlier: 3.659A  pdb=" N   PHE D  84 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 126
    Processing helix  chain 'D' and resid 182 through 189
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352
      removed outlier: 3.531A  pdb=" N   GLY A 352 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.630A  pdb=" N   THR B 356 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 514 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60
      removed outlier: 5.450A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLY C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER C  35 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 134 through 138
      removed outlier: 3.865A  pdb=" N   SER C 194 " --> pdb=" O   CYS C 154 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 134 through 138
      removed outlier: 3.865A  pdb=" N   SER C 194 " --> pdb=" O   CYS C 154 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER C 191 " --> pdb=" O   VAL C 183 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL C 183 " --> pdb=" O   SER C 191 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168
      removed outlier: 4.073A  pdb=" N   TYR C 208 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.081A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   GLN D  38 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   LEU D  47 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.081A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 29
      removed outlier: 12.432A  pdb=" N   CYS D  23 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 11.416A  pdb=" N   THR D  75 " --> pdb=" O   CYS D  23 " (cutoff:3.500A)
      removed outlier: 11.757A  pdb=" N   ALA D  25 " --> pdb=" O   THR D  73 " (cutoff:3.500A)
      removed outlier: 11.405A  pdb=" N   THR D  73 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
      removed outlier: 11.133A  pdb=" N   GLN D  27 " --> pdb=" O   ASP D  71 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASP D  71 " --> pdb=" O   GLN D  27 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 139
      removed outlier: 3.593A  pdb=" N   LEU D 175 " --> pdb=" O   LEU D 136 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ASN D 138 " --> pdb=" O   TYR D 173 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   TYR D 173 " --> pdb=" O   ASN D 138 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR D 178 " --> pdb=" O   GLN D 160 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 153 through 154

    396 hydrogen bonds defined for protein.
    1081 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.07

  Time building geometry restraints manager: 3.05 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2095
        1.33 -     1.45: 2493
        1.45 -     1.57: 5383
        1.57 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 10042
  Sorted by residual:
  bond pdb=" N   ASN A  33 "
       pdb=" CA  ASN A  33 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.28e-02 6.10e+03 8.21e+00
  bond pdb=" N   VAL C 164 "
       pdb=" CA  VAL C 164 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.53e+00
  bond pdb=" N   TYR C 159 "
       pdb=" CA  TYR C 159 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.032 1.27e-02 6.20e+03 6.41e+00
  bond pdb=" N   GLN A  24 "
       pdb=" CA  GLN A  24 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.31e+00
  bond pdb=" N   CYS A 498 "
       pdb=" CA  CYS A 498 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.16e-02 7.43e+03 6.30e+00
  ... (remaining 10037 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 12928
        1.49 -     2.98: 570
        2.98 -     4.47: 122
        4.47 -     5.96: 21
        5.96 -     7.45: 5
  Bond angle restraints: 13646
  Sorted by residual:
  angle pdb=" CA  PHE A 588 "
        pdb=" C   PHE A 588 "
        pdb=" O   PHE A 588 "
      ideal   model   delta    sigma   weight residual
     122.63  116.65    5.98 1.29e+00 6.01e-01 2.15e+01
  angle pdb=" O   PHE B 342 "
        pdb=" C   PHE B 342 "
        pdb=" N   ASN B 343 "
      ideal   model   delta    sigma   weight residual
     122.09  126.46   -4.37 1.08e+00 8.57e-01 1.64e+01
  angle pdb=" N   PHE A 588 "
        pdb=" CA  PHE A 588 "
        pdb=" C   PHE A 588 "
      ideal   model   delta    sigma   weight residual
     109.62  103.59    6.03 1.50e+00 4.44e-01 1.62e+01
  angle pdb=" CA  CYS A 498 "
        pdb=" C   CYS A 498 "
        pdb=" O   CYS A 498 "
      ideal   model   delta    sigma   weight residual
     121.38  117.21    4.17 1.06e+00 8.90e-01 1.55e+01
  angle pdb=" N   LYS A  31 "
        pdb=" CA  LYS A  31 "
        pdb=" C   LYS A  31 "
      ideal   model   delta    sigma   weight residual
     111.07  107.32    3.75 1.07e+00 8.73e-01 1.23e+01
  ... (remaining 13641 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.26: 5671
       21.26 -    42.53: 370
       42.53 -    63.79: 52
       63.79 -    85.05: 32
       85.05 -   106.31: 14
  Dihedral angle restraints: 6139
    sinusoidal: 2623
      harmonic: 3516
  Sorted by residual:
  dihedral pdb=" CA  ALA A 501 "
           pdb=" C   ALA A 501 "
           pdb=" N   SER A 502 "
           pdb=" CA  SER A 502 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.53   29.47     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -35.96  -50.04     1      1.00e+01 1.00e-02 3.43e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.62   49.62     1      1.00e+01 1.00e-02 3.38e+01
  ... (remaining 6136 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.172: 1493
       0.172 -    0.344: 8
       0.344 -    0.516: 0
       0.516 -    0.688: 2
       0.688 -    0.860: 2
  Chirality restraints: 1505
  Sorted by residual:
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-02 2.50e+03 1.10e+03
  chirality pdb=" C1  NAG H   2 "
            pdb=" O4  NAG H   1 "
            pdb=" C2  NAG H   2 "
            pdb=" O5  NAG H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-02 2.50e+03 5.98e+01
  chirality pdb=" C1  MAN E   4 "
            pdb=" O3  BMA E   3 "
            pdb=" C2  MAN E   4 "
            pdb=" O5  MAN E   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.27    0.13 2.00e-02 2.50e+03 4.27e+01
  ... (remaining 1502 not shown)

  Planarity restraints: 1745
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "    0.194 2.00e-02 2.50e+03   1.67e-01 3.49e+02
        pdb=" C7  NAG E   2 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "   -0.028 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "   -0.279 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "    0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG H   1 "   -0.152 2.00e-02 2.50e+03   1.28e-01 2.04e+02
        pdb=" C7  NAG H   1 "    0.029 2.00e-02 2.50e+03
        pdb=" C8  NAG H   1 "    0.039 2.00e-02 2.50e+03
        pdb=" N2  NAG H   1 "    0.204 2.00e-02 2.50e+03
        pdb=" O7  NAG H   1 "   -0.120 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 601 "    0.148 2.00e-02 2.50e+03   1.22e-01 1.87e+02
        pdb=" C7  NAG B 601 "   -0.043 2.00e-02 2.50e+03
        pdb=" C8  NAG B 601 "    0.111 2.00e-02 2.50e+03
        pdb=" N2  NAG B 601 "   -0.196 2.00e-02 2.50e+03
        pdb=" O7  NAG B 601 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1742 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1094
        2.75 -     3.29: 9830
        3.29 -     3.82: 16559
        3.82 -     4.36: 19254
        4.36 -     4.90: 32540
  Nonbonded interactions: 79277
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 137 "
            pdb=" N   ASN D 138 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 802 "
     model   vdw
     2.213 2.230
  nonbonded pdb=" CG  PRO C 163 "
            pdb=" NE2 HIS C 214 "
     model   vdw
     2.215 3.520
  nonbonded pdb=" NH1 ARG B 346 "
            pdb=" O   PHE B 347 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" NH2 ARG B 346 "
            pdb=" OD2 ASP B 450 "
     model   vdw
     2.229 3.120
  ... (remaining 79272 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
Found NCS groups:
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     30.040
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6316
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      :  0.004   0.075  10042  Z= 0.254
  Angle     :  0.731   7.454  13646  Z= 0.418
  Chirality :  0.061   0.860   1505
  Planarity :  0.008   0.167   1738
  Dihedral  : 15.694 106.313   3857
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.52 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.76 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.23), residues: 1199
  helix: -0.63 (0.25), residues: 409
  sheet: -0.76 (0.37), residues: 199
  loop : -1.88 (0.24), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 459 
 HIS   0.007   0.001   HIS A 374 
 PHE   0.035   0.001   PHE A 464 
 TYR   0.021   0.002   TYR B 501 
 ARG   0.007   0.000   ARG B 454 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 269
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.1196 (OUTLIER) cc_final: -0.0169 (mm110)
REVERT: A   31 LYS cc_start: 0.5644 (OUTLIER) cc_final: 0.4484 (tptm)
REVERT: A  111 ASP cc_start: 0.9017 (t70) cc_final: 0.8805 (p0)
REVERT: A  117 ASN cc_start: 0.7759 (m-40) cc_final: 0.7535 (t0)
REVERT: A  179 LEU cc_start: 0.8778 (mm) cc_final: 0.8378 (mm)
REVERT: A  196 TYR cc_start: 0.7583 (m-80) cc_final: 0.7170 (m-10)
REVERT: A  429 GLN cc_start: 0.8218 (mt0) cc_final: 0.7949 (pp30)
REVERT: A  577 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7240 (pttt)
REVERT: B  366 SER cc_start: 0.9254 (m) cc_final: 0.8996 (p)
REVERT: C   80 TYR cc_start: 0.6027 (m-80) cc_final: 0.5343 (m-80)
REVERT: D  162 SER cc_start: 0.7972 (t) cc_final: 0.7699 (m)
  outliers start: 5
  outliers final: 2
  residues processed: 272
  average time/residue: 1.3437
  time to fit residues: 389.9089
Evaluate side-chains
  138 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain C residue   99 ASP
Chi-restraints excluded: chain C residue  165 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 90 optimal weight:   30.0000
   chunk 50 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
A  98 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN
A 508 ASN
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 ASN
B 422 ASN
B 474 GLN
C  57 ASN
C  62 GLN
C  65 GLN
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 GLN
D 189 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.142247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.117276 restraints weight = 56379.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 5.94
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4207 r_free = 0.4207    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  10042  Z= 0.281
  Angle     :  0.845  14.059  13646  Z= 0.425
  Chirality :  0.047   0.237   1505
  Planarity :  0.005   0.047   1738
  Dihedral  : 10.450  76.871   1623
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.11 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.76 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.23), residues: 1199
  helix: -0.70 (0.24), residues: 410
  sheet: -0.94 (0.37), residues: 204
  loop : -1.86 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 168 
 HIS   0.009   0.002   HIS C 214 
 PHE   0.031   0.002   PHE A 523 
 TYR   0.030   0.002   TYR A 587 
 ARG   0.007   0.001   ARG A 518 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0605 (OUTLIER) cc_final: -0.0718 (mm110)
REVERT: A   31 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4623 (tptm)
REVERT: A  111 ASP cc_start: 0.9048 (t70) cc_final: 0.8828 (p0)
REVERT: A  162 LEU cc_start: 0.9335 (tm) cc_final: 0.9014 (mt)
REVERT: A  195 HIS cc_start: 0.7320 (t-90) cc_final: 0.7045 (t70)
REVERT: A  196 TYR cc_start: 0.7376 (m-80) cc_final: 0.7167 (m-10)
REVERT: A  248 LEU cc_start: 0.6799 (mt) cc_final: 0.6360 (tt)
REVERT: A  376 MET cc_start: 0.8862 (mmt) cc_final: 0.8568 (mmt)
REVERT: A  429 GLN cc_start: 0.8310 (mt0) cc_final: 0.8077 (pp30)
REVERT: B  386 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8970 (tptp)
REVERT: C   64 PHE cc_start: 0.7910 (m-80) cc_final: 0.7607 (m-80)
REVERT: C   65 GLN cc_start: 0.8572 (mm110) cc_final: 0.8321 (mm-40)
REVERT: C   80 TYR cc_start: 0.6100 (m-80) cc_final: 0.5324 (m-80)
REVERT: C  105 TRP cc_start: 0.8262 (m-10) cc_final: 0.7954 (m-10)
REVERT: C  158 ASP cc_start: 0.8348 (t0) cc_final: 0.7928 (t0)
REVERT: C  190 TYR cc_start: 0.8367 (m-80) cc_final: 0.8150 (m-80)
REVERT: C  193 SER cc_start: 0.9165 (m) cc_final: 0.8722 (p)
  outliers start: 24
  outliers final: 9
  residues processed: 176
  average time/residue: 1.1527
  time to fit residues: 220.8078
Evaluate side-chains
  135 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 46 optimal weight:    0.3980
   chunk 86 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 76 optimal weight:    8.9990
   chunk 77 optimal weight:   20.0000
   chunk 103 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 GLN
A 508 ASN
C  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.139575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.114479 restraints weight = 65652.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 7.29
r_work: 0.3969 rms_B_bonded: 7.08 restraints_weight: 2.0000
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4001 r_free = 0.4001    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4001 r_free = 0.4001    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.116  10042  Z= 0.302
  Angle     :  0.841  15.748  13646  Z= 0.419
  Chirality :  0.047   0.224   1505
  Planarity :  0.005   0.053   1738
  Dihedral  :  8.651  51.922   1620
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.69 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 16.38 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.23), residues: 1199
  helix: -0.76 (0.24), residues: 404
  sheet: -1.09 (0.36), residues: 201
  loop : -1.88 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 163 
 HIS   0.009   0.002   HIS C 214 
 PHE   0.028   0.002   PHE A 464 
 TYR   0.041   0.002   TYR A 202 
 ARG   0.009   0.001   ARG D  78 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 137
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0978 (OUTLIER) cc_final: -0.0823 (mm-40)
REVERT: A   31 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4966 (tttp)
REVERT: A  111 ASP cc_start: 0.9128 (t70) cc_final: 0.8873 (p0)
REVERT: A  162 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9063 (mt)
REVERT: A  195 HIS cc_start: 0.6972 (t-90) cc_final: 0.6746 (t70)
REVERT: A  196 TYR cc_start: 0.7524 (m-80) cc_final: 0.7249 (m-10)
REVERT: A  248 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6401 (tt)
REVERT: A  376 MET cc_start: 0.9161 (mmt) cc_final: 0.8932 (mmt)
REVERT: A  429 GLN cc_start: 0.8346 (mt0) cc_final: 0.8113 (pp30)
REVERT: B  386 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8984 (tptp)
REVERT: B  421 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.3287 (p90)
REVERT: C   64 PHE cc_start: 0.7883 (m-80) cc_final: 0.7568 (m-80)
REVERT: C   65 GLN cc_start: 0.8812 (mm110) cc_final: 0.8539 (mm-40)
REVERT: C   80 TYR cc_start: 0.6289 (m-80) cc_final: 0.5341 (m-80)
REVERT: C   95 TYR cc_start: 0.6201 (m-10) cc_final: 0.5942 (m-10)
REVERT: C  105 TRP cc_start: 0.8658 (m-10) cc_final: 0.8382 (m-10)
REVERT: C  158 ASP cc_start: 0.8436 (t0) cc_final: 0.7962 (t0)
REVERT: C  166 VAL cc_start: 0.9234 (t) cc_final: 0.8963 (p)
REVERT: C  193 SER cc_start: 0.9217 (m) cc_final: 0.8584 (p)
REVERT: D  137 ASN cc_start: 0.7766 (t0) cc_final: 0.6783 (p0)
  outliers start: 41
  outliers final: 12
  residues processed: 158
  average time/residue: 1.0299
  time to fit residues: 177.4371
Evaluate side-chains
  133 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   31 LYS
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0170
   chunk 74 optimal weight:    0.3980
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 80 optimal weight:    0.1980
   chunk 104 optimal weight:    7.9990
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.142189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.117571 restraints weight = 65290.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 7.43
r_work: 0.4052 rms_B_bonded: 7.01 restraints_weight: 2.0000
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  10042  Z= 0.228
  Angle     :  0.792  16.990  13646  Z= 0.391
  Chirality :  0.046   0.265   1505
  Planarity :  0.005   0.045   1738
  Dihedral  :  7.136  46.433   1620
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.36 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.57 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.23), residues: 1199
  helix: -0.42 (0.25), residues: 398
  sheet: -1.13 (0.34), residues: 210
  loop : -1.71 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 163 
 HIS   0.006   0.001   HIS C 214 
 PHE   0.023   0.001   PHE A 464 
 TYR   0.021   0.002   TYR B 365 
 ARG   0.003   0.000   ARG A 582 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0716 (OUTLIER) cc_final: -0.0991 (mm-40)
REVERT: A  111 ASP cc_start: 0.9102 (t70) cc_final: 0.8851 (p0)
REVERT: A  148 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6863 (tp)
REVERT: A  162 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8977 (mt)
REVERT: A  195 HIS cc_start: 0.6918 (t-90) cc_final: 0.6685 (t70)
REVERT: A  196 TYR cc_start: 0.7503 (m-80) cc_final: 0.7260 (m-10)
REVERT: A  248 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6222 (tt)
REVERT: A  255 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.4305 (m-10)
REVERT: A  297 MET cc_start: 0.5599 (mmp) cc_final: 0.4557 (tpp)
REVERT: A  429 GLN cc_start: 0.8361 (mt0) cc_final: 0.8159 (pp30)
REVERT: B  335 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8142 (mm)
REVERT: B  421 TYR cc_start: 0.5869 (OUTLIER) cc_final: 0.3651 (p90)
REVERT: C   64 PHE cc_start: 0.7733 (m-80) cc_final: 0.7364 (m-80)
REVERT: C   73 ASP cc_start: 0.8684 (t0) cc_final: 0.8468 (t0)
REVERT: C   80 TYR cc_start: 0.6206 (m-80) cc_final: 0.5405 (m-80)
REVERT: C   95 TYR cc_start: 0.6104 (m-10) cc_final: 0.5840 (m-10)
REVERT: C  105 TRP cc_start: 0.8557 (m-10) cc_final: 0.8284 (m-10)
REVERT: C  158 ASP cc_start: 0.8386 (t0) cc_final: 0.7847 (t0)
REVERT: C  193 SER cc_start: 0.9114 (m) cc_final: 0.8818 (p)
REVERT: D  137 ASN cc_start: 0.7849 (t0) cc_final: 0.6933 (p0)
  outliers start: 34
  outliers final: 13
  residues processed: 154
  average time/residue: 1.0326
  time to fit residues: 173.3624
Evaluate side-chains
  133 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  133 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN
D  90 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.140338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.115828 restraints weight = 54082.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.4185 rms_B_bonded: 6.59
r_work: 0.4033 rms_B_bonded: 6.52 restraints_weight: 2.0000
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4030 r_free = 0.4030    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4030 r_free = 0.4030    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096  10042  Z= 0.286
  Angle     :  0.807  16.344  13646  Z= 0.401
  Chirality :  0.046   0.281   1505
  Planarity :  0.006   0.111   1738
  Dihedral  :  6.500  43.937   1616
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.11 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.05 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.24), residues: 1199
  helix: -0.37 (0.25), residues: 397
  sheet: -1.13 (0.34), residues: 206
  loop : -1.63 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 163 
 HIS   0.015   0.002   HIS A 345 
 PHE   0.024   0.002   PHE A 464 
 TYR   0.026   0.002   TYR C  27 
 ARG   0.013   0.001   ARG D  24 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.1024 (OUTLIER) cc_final: -0.1038 (mm110)
REVERT: A  111 ASP cc_start: 0.9068 (t70) cc_final: 0.8817 (p0)
REVERT: A  162 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8984 (mt)
REVERT: A  195 HIS cc_start: 0.6804 (t-90) cc_final: 0.6601 (t70)
REVERT: A  196 TYR cc_start: 0.7567 (m-80) cc_final: 0.7294 (m-10)
REVERT: A  248 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6103 (tt)
REVERT: A  255 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.4267 (m-10)
REVERT: A  287 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6847 (pm20)
REVERT: A  297 MET cc_start: 0.5661 (mmp) cc_final: 0.4550 (tpp)
REVERT: A  376 MET cc_start: 0.9017 (mmt) cc_final: 0.8803 (mmt)
REVERT: A  429 GLN cc_start: 0.8313 (mt0) cc_final: 0.8074 (pp30)
REVERT: B  421 TYR cc_start: 0.5852 (OUTLIER) cc_final: 0.3405 (p90)
REVERT: C   27 TYR cc_start: 0.3252 (p90) cc_final: 0.2988 (p90)
REVERT: C   64 PHE cc_start: 0.7804 (m-80) cc_final: 0.7412 (m-80)
REVERT: C   73 ASP cc_start: 0.8749 (t0) cc_final: 0.8515 (t0)
REVERT: C   80 TYR cc_start: 0.6234 (m-80) cc_final: 0.5383 (m-80)
REVERT: C   95 TYR cc_start: 0.6141 (m-10) cc_final: 0.5883 (m-10)
REVERT: C  105 TRP cc_start: 0.8590 (m-10) cc_final: 0.8333 (m-10)
REVERT: C  158 ASP cc_start: 0.8458 (t0) cc_final: 0.7891 (t0)
REVERT: C  193 SER cc_start: 0.9179 (m) cc_final: 0.8495 (p)
REVERT: D  137 ASN cc_start: 0.7982 (t0) cc_final: 0.7117 (p0)
  outliers start: 33
  outliers final: 14
  residues processed: 145
  average time/residue: 1.0655
  time to fit residues: 168.1102
Evaluate side-chains
  134 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 115 optimal weight:   10.0000
   chunk 105 optimal weight:    0.2980
   chunk 89 optimal weight:   20.0000
   chunk 86 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 116 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
A  42 GLN
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN
C  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.137553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.112586 restraints weight = 57833.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.4127 rms_B_bonded: 6.57
r_work: 0.3976 rms_B_bonded: 6.49 restraints_weight: 2.0000
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3971 r_free = 0.3971    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3971 r_free = 0.3971    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.146  10042  Z= 0.380
  Angle     :  0.888  17.068  13646  Z= 0.442
  Chirality :  0.048   0.294   1505
  Planarity :  0.006   0.054   1738
  Dihedral  :  6.462  43.676   1616
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.61 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.10 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.23), residues: 1199
  helix: -0.51 (0.25), residues: 393
  sheet: -1.13 (0.34), residues: 212
  loop : -1.67 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 163 
 HIS   0.008   0.002   HIS A 401 
 PHE   0.028   0.002   PHE A 464 
 TYR   0.032   0.003   TYR A 381 
 ARG   0.006   0.001   ARG D  24 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0530 (OUTLIER) cc_final: -0.1444 (mm110)
REVERT: A  111 ASP cc_start: 0.9038 (t70) cc_final: 0.8758 (p0)
REVERT: A  162 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9037 (mt)
REVERT: A  196 TYR cc_start: 0.7442 (m-80) cc_final: 0.7240 (m-10)
REVERT: A  255 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.4310 (m-10)
REVERT: A  429 GLN cc_start: 0.8272 (mt0) cc_final: 0.8055 (pp30)
REVERT: B  421 TYR cc_start: 0.5670 (OUTLIER) cc_final: 0.3295 (p90)
REVERT: C   43 GLN cc_start: 0.8936 (mt0) cc_final: 0.8716 (mt0)
REVERT: C   64 PHE cc_start: 0.7948 (m-80) cc_final: 0.7626 (m-80)
REVERT: C   73 ASP cc_start: 0.8766 (t0) cc_final: 0.8499 (t0)
REVERT: C   80 TYR cc_start: 0.6408 (m-80) cc_final: 0.5486 (m-80)
REVERT: C   95 TYR cc_start: 0.6338 (m-10) cc_final: 0.6026 (m-10)
REVERT: C  105 TRP cc_start: 0.8767 (m-10) cc_final: 0.8521 (m-10)
REVERT: C  158 ASP cc_start: 0.8491 (t0) cc_final: 0.7934 (t0)
REVERT: C  193 SER cc_start: 0.9207 (m) cc_final: 0.8731 (p)
REVERT: D   90 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7497 (tm130)
  outliers start: 34
  outliers final: 17
  residues processed: 146
  average time/residue: 0.9938
  time to fit residues: 159.1688
Evaluate side-chains
  135 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  209 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 111 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** 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 = 0.4590 r_free = 0.4590 target = 0.140041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.117335 restraints weight = 34823.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.4210 rms_B_bonded: 5.55
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4174 r_free = 0.4174    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4174 r_free = 0.4174    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.4660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086  10042  Z= 0.266
  Angle     :  0.853  17.947  13646  Z= 0.418
  Chirality :  0.046   0.283   1505
  Planarity :  0.005   0.043   1738
  Dihedral  :  6.174  37.297   1616
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.61 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 22.00 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.23), residues: 1199
  helix: -0.36 (0.25), residues: 394
  sheet: -1.16 (0.35), residues: 214
  loop : -1.63 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 163 
 HIS   0.005   0.001   HIS C 214 
 PHE   0.041   0.002   PHE D 209 
 TYR   0.021   0.002   TYR A 385 
 ARG   0.008   0.001   ARG D  78 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0403 (OUTLIER) cc_final: -0.1384 (mm110)
REVERT: A  111 ASP cc_start: 0.8921 (t70) cc_final: 0.8668 (p0)
REVERT: A  127 TYR cc_start: 0.3983 (t80) cc_final: 0.3768 (t80)
REVERT: A  196 TYR cc_start: 0.7528 (m-80) cc_final: 0.7305 (m-10)
REVERT: A  255 TYR cc_start: 0.5979 (OUTLIER) cc_final: 0.4378 (m-10)
REVERT: A  287 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6647 (pm20)
REVERT: A  429 GLN cc_start: 0.8325 (mt0) cc_final: 0.8042 (pp30)
REVERT: B  421 TYR cc_start: 0.5516 (OUTLIER) cc_final: 0.2761 (p90)
REVERT: C   64 PHE cc_start: 0.7994 (m-80) cc_final: 0.7650 (m-80)
REVERT: C   73 ASP cc_start: 0.8713 (t0) cc_final: 0.8458 (t0)
REVERT: C   80 TYR cc_start: 0.6207 (m-80) cc_final: 0.5332 (m-80)
REVERT: C   95 TYR cc_start: 0.5969 (m-10) cc_final: 0.5651 (m-10)
REVERT: C  158 ASP cc_start: 0.8364 (t0) cc_final: 0.7812 (t0)
REVERT: C  193 SER cc_start: 0.9315 (m) cc_final: 0.8886 (p)
  outliers start: 24
  outliers final: 14
  residues processed: 142
  average time/residue: 0.9984
  time to fit residues: 155.1021
Evaluate side-chains
  128 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 83 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 103 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
C  62 GLN
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.141267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.116757 restraints weight = 63138.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.4201 rms_B_bonded: 7.02
r_work: 0.4038 rms_B_bonded: 6.97 restraints_weight: 2.0000
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4037 r_free = 0.4037    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4037 r_free = 0.4037    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6719
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  10042  Z= 0.239
  Angle     :  0.835  17.649  13646  Z= 0.409
  Chirality :  0.045   0.251   1505
  Planarity :  0.005   0.045   1738
  Dihedral  :  5.874  41.160   1616
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.02 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.14 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.24), residues: 1199
  helix: -0.31 (0.25), residues: 398
  sheet: -1.06 (0.34), residues: 221
  loop : -1.58 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 163 
 HIS   0.005   0.001   HIS C 214 
 PHE   0.021   0.001   PHE A 464 
 TYR   0.028   0.002   TYR C  54 
 ARG   0.014   0.001   ARG A 518 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0888 (OUTLIER) cc_final: -0.1022 (mm-40)
REVERT: A  111 ASP cc_start: 0.9007 (t70) cc_final: 0.8731 (p0)
REVERT: A  127 TYR cc_start: 0.4726 (t80) cc_final: 0.4264 (t80)
REVERT: A  196 TYR cc_start: 0.7560 (m-80) cc_final: 0.7293 (m-10)
REVERT: A  277 ASN cc_start: 0.7925 (m-40) cc_final: 0.7704 (m110)
REVERT: A  287 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6814 (pm20)
REVERT: A  429 GLN cc_start: 0.8249 (mt0) cc_final: 0.8022 (pp30)
REVERT: B  421 TYR cc_start: 0.5813 (OUTLIER) cc_final: 0.3452 (p90)
REVERT: C   64 PHE cc_start: 0.7786 (m-80) cc_final: 0.7433 (m-80)
REVERT: C   73 ASP cc_start: 0.8817 (t0) cc_final: 0.8560 (t0)
REVERT: C   80 TYR cc_start: 0.6209 (m-80) cc_final: 0.5307 (m-80)
REVERT: C   95 TYR cc_start: 0.6207 (m-10) cc_final: 0.5882 (m-10)
REVERT: C   99 ASP cc_start: 0.7419 (t0) cc_final: 0.7194 (t0)
REVERT: C  105 TRP cc_start: 0.8538 (m-10) cc_final: 0.8223 (m-10)
REVERT: C  158 ASP cc_start: 0.8412 (t0) cc_final: 0.7829 (t0)
REVERT: C  193 SER cc_start: 0.9204 (m) cc_final: 0.8745 (p)
  outliers start: 23
  outliers final: 15
  residues processed: 142
  average time/residue: 0.9698
  time to fit residues: 151.0384
Evaluate side-chains
  128 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 111 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** 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 = 0.4528 r_free = 0.4528 target = 0.136882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.111095 restraints weight = 76018.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 7.78
r_work: 0.3971 rms_B_bonded: 7.29 restraints_weight: 2.0000
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3971 r_free = 0.3971    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3971 r_free = 0.3971    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  10042  Z= 0.315
  Angle     :  0.888  20.483  13646  Z= 0.437
  Chirality :  0.047   0.261   1505
  Planarity :  0.005   0.084   1738
  Dihedral  :  6.009  41.222   1616
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 19.16
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.28 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 23.43 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.24), residues: 1199
  helix: -0.46 (0.25), residues: 399
  sheet: -0.98 (0.36), residues: 214
  loop : -1.64 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 163 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.031   0.002   PHE D 209 
 TYR   0.024   0.002   TYR C  54 
 ARG   0.021   0.001   ARG A 518 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0950 (OUTLIER) cc_final: -0.0861 (mm110)
REVERT: A  127 TYR cc_start: 0.4921 (t80) cc_final: 0.4495 (t80)
REVERT: A  196 TYR cc_start: 0.7518 (m-80) cc_final: 0.7293 (m-10)
REVERT: A  249 MET cc_start: 0.6822 (ptp) cc_final: 0.5477 (pp-130)
REVERT: A  277 ASN cc_start: 0.7922 (m-40) cc_final: 0.7653 (m110)
REVERT: A  429 GLN cc_start: 0.8295 (mt0) cc_final: 0.8015 (pp30)
REVERT: B  421 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.3471 (p90)
REVERT: C   43 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8390 (mp10)
REVERT: C   64 PHE cc_start: 0.7954 (m-80) cc_final: 0.7611 (m-80)
REVERT: C   73 ASP cc_start: 0.8795 (t0) cc_final: 0.8519 (t0)
REVERT: C   80 TYR cc_start: 0.6362 (m-80) cc_final: 0.5477 (m-80)
REVERT: C   95 TYR cc_start: 0.6402 (m-10) cc_final: 0.6023 (m-10)
REVERT: C  158 ASP cc_start: 0.8495 (t0) cc_final: 0.7942 (t0)
REVERT: C  193 SER cc_start: 0.9321 (m) cc_final: 0.8870 (p)
REVERT: C  225 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7766 (p)
  outliers start: 25
  outliers final: 14
  residues processed: 129
  average time/residue: 0.9447
  time to fit residues: 133.8411
Evaluate side-chains
  120 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain C residue   43 GLN
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   chunk 118 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 74 optimal weight:    0.1980
   chunk 65 optimal weight:    0.0980
   chunk 27 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN
** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** 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 = 0.4612 r_free = 0.4612 target = 0.141639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.117385 restraints weight = 50307.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 5.58
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4216 r_free = 0.4216    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4216 r_free = 0.4216    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10042  Z= 0.236
  Angle     :  0.856  18.300  13646  Z= 0.419
  Chirality :  0.046   0.270   1505
  Planarity :  0.005   0.059   1738
  Dihedral  :  5.817  44.765   1616
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.86 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 24.10 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.24), residues: 1199
  helix: -0.31 (0.25), residues: 397
  sheet: -1.00 (0.35), residues: 222
  loop : -1.58 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 163 
 HIS   0.005   0.001   HIS C 214 
 PHE   0.020   0.001   PHE A 464 
 TYR   0.029   0.002   TYR C  54 
 ARG   0.009   0.001   ARG A 518 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.0326 (OUTLIER) cc_final: -0.1242 (mm-40)
REVERT: A  127 TYR cc_start: 0.4272 (t80) cc_final: 0.3670 (t80)
REVERT: A  302 TRP cc_start: 0.6904 (m-10) cc_final: 0.6286 (m100)
REVERT: A  518 ARG cc_start: 0.6646 (ppt170) cc_final: 0.6438 (ppt90)
REVERT: B  421 TYR cc_start: 0.5469 (OUTLIER) cc_final: 0.2856 (p90)
REVERT: C   64 PHE cc_start: 0.7797 (m-80) cc_final: 0.7488 (m-80)
REVERT: C   73 ASP cc_start: 0.8680 (t0) cc_final: 0.8436 (t0)
REVERT: C   80 TYR cc_start: 0.6148 (m-80) cc_final: 0.5243 (m-80)
REVERT: C   95 TYR cc_start: 0.5947 (m-10) cc_final: 0.5716 (m-10)
REVERT: C  158 ASP cc_start: 0.8463 (t0) cc_final: 0.8082 (t0)
REVERT: C  193 SER cc_start: 0.9271 (m) cc_final: 0.8812 (p)
  outliers start: 20
  outliers final: 13
  residues processed: 125
  average time/residue: 1.0394
  time to fit residues: 142.4712
Evaluate side-chains
  116 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  421 TYR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain C residue   43 GLN
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain D residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 89 optimal weight:   30.0000
   chunk 74 optimal weight:    0.0060
   chunk 111 optimal weight:   20.0000
   chunk 61 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
C  62 GLN
** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.141610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.119123 restraints weight = 41145.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.4249 rms_B_bonded: 5.75
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4248 r_free = 0.4248    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4248 r_free = 0.4248    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.4248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10042  Z= 0.238
  Angle     :  0.871  19.815  13646  Z= 0.423
  Chirality :  0.046   0.254   1505
  Planarity :  0.005   0.048   1738
  Dihedral  :  5.733  44.132   1616
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.36 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 24.76 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.24), residues: 1199
  helix: -0.27 (0.25), residues: 398
  sheet: -0.96 (0.35), residues: 217
  loop : -1.51 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 163 
 HIS   0.005   0.001   HIS C 214 
 PHE   0.034   0.002   PHE D 209 
 TYR   0.028   0.002   TYR C  54 
 ARG   0.009   0.001   ARG A 518 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9883.76 seconds
wall clock time: 174 minutes 45.48 seconds (10485.48 seconds total)