Starting phenix.real_space_refine
on Wed Jun 25 01:50:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v4y_42977/06_2025/8v4y_42977.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v4y_42977/06_2025/8v4y_42977.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v4y_42977/06_2025/8v4y_42977.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v4y_42977/06_2025/8v4y_42977.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v4y_42977/06_2025/8v4y_42977.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v4y_42977/06_2025/8v4y_42977.cif"
  }
  resolution = 2.8
  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=   0.006 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic.
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: 9
    Type Number    sf(0)   Gaussians
     P     296      5.49       5
     Mg      1      5.21       5
     S      34      5.16       5
     Be      1      3.05       5
     C    9094      2.51       5
     N    2943      2.21       5
     O    3504      1.98       5
     F       3      1.80       5
     H   13550      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 29426
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1604
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "B"
      Number of atoms: 1468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 1468
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "C"
      Number of atoms: 1730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 1730
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 1542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1542
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1604
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 1371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 1371
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 1752
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 1542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1542
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "I"
      Number of atoms: 4680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 4680
          Classifications: {'DNA': 147}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 4646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 4646
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "W"
      Number of atoms: 7455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 7455
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 18, 'TRANS': 430}
          Chain breaks: 1
    Chain: "W"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 14.49, per 1000 atoms: 0.49
  Number of scatterers: 29426
  At special positions: 0
  Unit cell: (148.19, 128.714, 116.858, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     S      34     16.00
     P     296     15.00
     Mg      1     11.99
     F       3      9.00
     O    3504      8.00
     N    2943      7.00
     C    9094      6.00
     Be      1      4.00
     H   13550      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 7.04
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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:  2298

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 12 sheets defined
      65.3% alpha, 5.6% beta
      38 base pairs and 190 stacking pairs defined.
    Time for finding SS restraints: 12.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.581A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.502A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 113
      removed outlier: 3.645A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.653A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 19
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 3.666A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.554A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.600A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.868A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.691A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN C  84 " --> pdb=" O   PRO C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
      removed outlier: 3.732A  pdb=" N   GLN D  44 " --> pdb=" O   LYS D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.634A  pdb=" N   ALA D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 120
      removed outlier: 3.518A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
      removed outlier: 3.534A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.636A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.570A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.689A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.532A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.513A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.612A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.569A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.789A  pdb=" N   GLN H  44 " --> pdb=" O   LYS H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 122
    Processing helix  chain 'W' and resid 181 through 198
    Processing helix  chain 'W' and resid 210 through 225
    Processing helix  chain 'W' and resid 237 through 239
      No H-bonds generated for 'chain 'W' and resid 237 through 239'
    Processing helix  chain 'W' and resid 240 through 252
      removed outlier: 3.523A  pdb=" N   MET W 245 " --> pdb=" O   LEU W 241 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 263 through 274
    Processing helix  chain 'W' and resid 287 through 293
    Processing helix  chain 'W' and resid 293 through 298
    Processing helix  chain 'W' and resid 310 through 314
    Processing helix  chain 'W' and resid 318 through 325
      removed outlier: 3.575A  pdb=" N   ARG W 325 " --> pdb=" O   SER W 321 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 344 through 355
      removed outlier: 4.375A  pdb=" N   LEU W 350 " --> pdb=" O   GLU W 346 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE W 353 " --> pdb=" O   SER W 349 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 361 through 369
      removed outlier: 5.177A  pdb=" N   SER W 367 " --> pdb=" O   ASP W 363 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   TRP W 368 " --> pdb=" O   ASP W 364 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 387 through 391
      removed outlier: 4.443A  pdb=" N   PHE W 391 " --> pdb=" O   VAL W 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'W' and resid 387 through 391'
    Processing helix  chain 'W' and resid 396 through 401
    Processing helix  chain 'W' and resid 417 through 430
    Processing helix  chain 'W' and resid 438 through 442
    Processing helix  chain 'W' and resid 448 through 459
      removed outlier: 4.059A  pdb=" N   GLN W 452 " --> pdb=" O   ASN W 448 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 460 through 463
    Processing helix  chain 'W' and resid 475 through 481
      removed outlier: 3.662A  pdb=" N   VAL W 479 " --> pdb=" O   ASP W 475 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 482 through 489
      removed outlier: 3.613A  pdb=" N   ASP W 489 " --> pdb=" O   MET W 485 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 490 through 497
    Processing helix  chain 'W' and resid 508 through 523
      removed outlier: 3.724A  pdb=" N   LEU W 512 " --> pdb=" O   MET W 508 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 534 through 547
      removed outlier: 3.744A  pdb=" N   GLN W 539 " --> pdb=" O   HIS W 535 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP W 540 " --> pdb=" O   ASP W 536 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 559 through 563
    Processing helix  chain 'W' and resid 582 through 592
      removed outlier: 4.084A  pdb=" N   ASP W 586 " --> pdb=" O   ASN W 582 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 612 through 629
      removed outlier: 4.182A  pdb=" N   ARG W 616 " --> pdb=" O   THR W 612 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU W 627 " --> pdb=" O   MET W 623 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ASP W 628 " --> pdb=" O   LYS W 624 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.643A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.837A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.893A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.822A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.956A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'W' and resid 257 through 260
      removed outlier: 6.614A  pdb=" N   VAL W 258 " --> pdb=" O   VAL W 284 " (cutoff:3.500A)
      removed outlier: 8.812A  pdb=" N   SER W 286 " --> pdb=" O   VAL W 258 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   LEU W 260 " --> pdb=" O   SER W 286 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ILE W 202 " --> pdb=" O   LEU W 393 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'W' and resid 408 through 414
      removed outlier: 6.570A  pdb=" N   CYS W 527 " --> pdb=" O   MET W 556 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   SER W 558 " --> pdb=" O   CYS W 527 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   LEU W 529 " --> pdb=" O   SER W 558 " (cutoff:3.500A)

    547 hydrogen bonds defined for protein.
    1599 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      84 hydrogen bonds
      168 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      190 stacking parallelities
  Total time for adding SS restraints: 12.15

  Time building geometry restraints manager: 8.62 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 13544
        1.02 -     1.22: 290
        1.22 -     1.42: 6691
        1.42 -     1.62: 9728
        1.62 -     1.82: 65
  Bond restraints: 30318
  Sorted by residual:
  bond pdb=" F1  BEF W1103 "
       pdb="BE   BEF W1103 "
    ideal  model  delta    sigma   weight residual
    1.476  1.761 -0.285 2.00e-02 2.50e+03 2.03e+02
  bond pdb=" F2  BEF W1103 "
       pdb="BE   BEF W1103 "
    ideal  model  delta    sigma   weight residual
    1.476  1.760 -0.284 2.00e-02 2.50e+03 2.02e+02
  bond pdb=" F3  BEF W1103 "
       pdb="BE   BEF W1103 "
    ideal  model  delta    sigma   weight residual
    1.476  1.759 -0.283 2.00e-02 2.50e+03 2.01e+02
  bond pdb=" ND2 ASN W 567 "
       pdb="HD22 ASN W 567 "
    ideal  model  delta    sigma   weight residual
    0.860  0.982 -0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" ND2 ASN W 436 "
       pdb="HD21 ASN W 436 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.67e+01
  ... (remaining 30313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 51305
        2.71 -     5.41: 3028
        5.41 -     8.12: 581
        8.12 -    10.82: 22
       10.82 -    13.53: 6
  Bond angle restraints: 54942
  Sorted by residual:
  angle pdb=" N   VAL W 502 "
        pdb=" CA  VAL W 502 "
        pdb=" C   VAL W 502 "
      ideal   model   delta    sigma   weight residual
     108.48  122.01  -13.53 1.44e+00 4.82e-01 8.83e+01
  angle pdb=" N   TRP W 177 "
        pdb=" CA  TRP W 177 "
        pdb=" C   TRP W 177 "
      ideal   model   delta    sigma   weight residual
     111.71  121.63   -9.92 1.15e+00 7.56e-01 7.44e+01
  angle pdb=" N   GLY D 101 "
        pdb=" CA  GLY D 101 "
        pdb=" C   GLY D 101 "
      ideal   model   delta    sigma   weight residual
     112.73  122.47   -9.74 1.20e+00 6.94e-01 6.59e+01
  angle pdb=" N   ARG E  83 "
        pdb=" CA  ARG E  83 "
        pdb=" C   ARG E  83 "
      ideal   model   delta    sigma   weight residual
     109.95   98.74   11.21 1.44e+00 4.82e-01 6.06e+01
  angle pdb=" N   GLY W 201 "
        pdb=" CA  GLY W 201 "
        pdb=" C   GLY W 201 "
      ideal   model   delta    sigma   weight residual
     112.61  124.64  -12.03 1.60e+00 3.91e-01 5.65e+01
  ... (remaining 54937 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.81: 11691
       29.81 -    59.62: 1199
       59.62 -    89.44: 44
       89.44 -   119.25: 1
      119.25 -   149.06: 1
  Dihedral angle restraints: 12936
    sinusoidal: 8882
      harmonic: 4054
  Sorted by residual:
  dihedral pdb=" O1B ADP W1101 "
           pdb=" O3A ADP W1101 "
           pdb=" PB  ADP W1101 "
           pdb=" PA  ADP W1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -164.12  104.11     1      2.00e+01 2.50e-03 2.99e+01
  dihedral pdb=" CA  THR W 609 "
           pdb=" C   THR W 609 "
           pdb=" N   ASP W 610 "
           pdb=" CA  ASP W 610 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.56  -24.44     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.71  -21.29     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 12933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 2320
       0.103 -    0.205: 318
       0.205 -    0.308: 59
       0.308 -    0.411: 5
       0.411 -    0.514: 2
  Chirality restraints: 2704
  Sorted by residual:
  chirality pdb=" CA  ARG E  40 "
            pdb=" N   ARG E  40 "
            pdb=" C   ARG E  40 "
            pdb=" CB  ARG E  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.59e+00
  chirality pdb=" CA  LYS D  82 "
            pdb=" N   LYS D  82 "
            pdb=" C   LYS D  82 "
            pdb=" CB  LYS D  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.25e+00
  chirality pdb=" CA  ASP W 281 "
            pdb=" N   ASP W 281 "
            pdb=" C   ASP W 281 "
            pdb=" CB  ASP W 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.02e+00
  ... (remaining 2701 not shown)

  Planarity restraints: 3394
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C  38 "   -0.087 2.00e-02 2.50e+03   4.88e-01 3.58e+03
        pdb=" CG  ASN C  38 "    0.002 2.00e-02 2.50e+03
        pdb=" OD1 ASN C  38 "    0.085 2.00e-02 2.50e+03
        pdb=" ND2 ASN C  38 "    0.000 2.00e-02 2.50e+03
        pdb="HD21 ASN C  38 "   -0.842 2.00e-02 2.50e+03
        pdb="HD22 ASN C  38 "    0.841 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN W 342 "    0.292 2.00e-02 2.50e+03   4.39e-01 2.89e+03
        pdb=" CG  ASN W 342 "   -0.022 2.00e-02 2.50e+03
        pdb=" OD1 ASN W 342 "   -0.287 2.00e-02 2.50e+03
        pdb=" ND2 ASN W 342 "    0.003 2.00e-02 2.50e+03
        pdb="HD21 ASN W 342 "    0.709 2.00e-02 2.50e+03
        pdb="HD22 ASN W 342 "   -0.695 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN W 360 "   -0.301 2.00e-02 2.50e+03   4.29e-01 2.76e+03
        pdb=" CG  ASN W 360 "    0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN W 360 "    0.291 2.00e-02 2.50e+03
        pdb=" ND2 ASN W 360 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN W 360 "   -0.692 2.00e-02 2.50e+03
        pdb="HD22 ASN W 360 "    0.670 2.00e-02 2.50e+03
  ... (remaining 3391 not shown)

  Histogram of nonbonded interaction distances:
        1.01 -     1.73: 14
        1.73 -     2.44: 13051
        2.44 -     3.16: 83161
        3.16 -     3.88: 111052
        3.88 -     4.60: 180703
  Nonbonded interactions: 387981
  Sorted by model distance:
  nonbonded pdb=" HB  THR W 474 "
            pdb=" HE1 HIS W 477 "
     model   vdw
     1.007 2.270
  nonbonded pdb=" HH  TYR W 461 "
            pdb=" HD2 HIS W 477 "
     model   vdw
     1.154 2.100
  nonbonded pdb="HH22 ARG A  72 "
            pdb=" OP1  DC J  51 "
     model   vdw
     1.161 2.450
  nonbonded pdb="HH12 ARG C  11 "
            pdb=" H1'  DT I 178 "
     model   vdw
     1.192 2.270
  nonbonded pdb=" HB  THR W 474 "
            pdb=" CE1 HIS W 477 "
     model   vdw
     1.283 2.970
  ... (remaining 387976 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 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 20 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = chain 'D'
  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=1.00 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:             3.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.150
  Construct map_model_manager:             0.410
  Extract box with map and model:          1.090
  Check model and map are aligned:         0.190
  Set scattering table:                    0.250
  Process input model:                     69.950
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.090
  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:12.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   88.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
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      :  0.011   0.285  16768  Z= 0.741
  Angle     :  1.331  13.529  23904  Z= 0.893
  Chirality :  0.077   0.514   2704
  Planarity :  0.011   0.111   1995
  Dihedral  : 20.030 149.062   7056
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.67 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  2.85 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.09 (0.22), residues: 1199
  helix: -0.52 (0.17), residues: 721
  sheet:  0.43 (0.57), residues: 73
  loop : -1.05 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.078   0.008   TRP W 348 
 HIS   0.011   0.003   HIS H 106 
 PHE   0.043   0.008   PHE W 297 
 TYR   0.116   0.011   TYR G  57 
 ARG   0.009   0.001   ARG C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25185 (  631)
  hydrogen bonds       : angle       7.83905 ( 1767)
  covalent geometry    : bond        0.01100 (16768)
  covalent geometry    : angle       1.33100 (23904)

*********************** 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
  233 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 226
  time to evaluate  : 1.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8637 (tmtt)
REVERT: E   79 LYS cc_start: 0.8754 (tttt) cc_final: 0.8507 (tttp)
REVERT: E  105 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7521 (mt-10)
REVERT: E  115 LYS cc_start: 0.8840 (mttt) cc_final: 0.8520 (mtmp)
REVERT: F   68 ASP cc_start: 0.8292 (m-30) cc_final: 0.8015 (m-30)
REVERT: H  117 LYS cc_start: 0.9076 (tttt) cc_final: 0.8866 (tttm)
  outliers start: 7
  outliers final: 2
  residues processed: 233
  average time/residue: 4.4292
  time to fit residues: 1096.0233
Evaluate side-chains
  136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain W residue  432 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    0.8980
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 112 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
W 477 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.097181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.077192 restraints weight = 90492.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.49
r_work: 0.3213 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  16768  Z= 0.181
  Angle     :  0.662   6.105  23904  Z= 0.391
  Chirality :  0.042   0.149   2704
  Planarity :  0.006   0.063   1995
  Dihedral  : 23.053 166.130   4579
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.34 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.84 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.23), residues: 1199
  helix:  1.48 (0.19), residues: 730
  sheet:  0.76 (0.58), residues: 72
  loop : -1.35 (0.27), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP W 280 
 HIS   0.023   0.001   HIS W 477 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.014   0.001   TYR W 195 
 ARG   0.008   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06661 (  631)
  hydrogen bonds       : angle       4.11844 ( 1767)
  covalent geometry    : bond        0.00381 (16768)
  covalent geometry    : angle       0.66161 (23904)

*********************** 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
  164 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 1.780 
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
  outliers start: 16
  outliers final: 2
  residues processed: 155
  average time/residue: 3.4281
  time to fit residues: 575.2319
Evaluate side-chains
  133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 2.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  432 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   chunk 140 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 132 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
W 341 GLN
W 598 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.087362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.066395 restraints weight = 88997.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 1.48
r_work: 0.2959 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  16768  Z= 0.218
  Angle     :  0.648   6.631  23904  Z= 0.385
  Chirality :  0.043   0.154   2704
  Planarity :  0.005   0.049   1995
  Dihedral  : 24.508 168.307   4578
  Min Nonbonded Distance : 1.770

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.17 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.32 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.39 (0.24), residues: 1199
  helix:  2.14 (0.20), residues: 725
  sheet:  0.47 (0.61), residues: 74
  loop : -1.36 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP W 348 
 HIS   0.005   0.001   HIS W 477 
 PHE   0.009   0.001   PHE E  84 
 TYR   0.010   0.001   TYR G  57 
 ARG   0.005   0.001   ARG E  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06599 (  631)
  hydrogen bonds       : angle       3.92467 ( 1767)
  covalent geometry    : bond        0.00478 (16768)
  covalent geometry    : angle       0.64837 (23904)

*********************** 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
  156 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 1.858 
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: E   94 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7954 (mp0)
REVERT: G   74 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8499 (mmmt)
REVERT: H   31 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7952 (mptt)
REVERT: H   90 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8853 (mp0)
REVERT: W  620 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7534 (mmm160)
  outliers start: 20
  outliers final: 5
  residues processed: 147
  average time/residue: 3.8995
  time to fit residues: 614.5828
Evaluate side-chains
  136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 2.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain W residue  367 SER
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  620 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 78 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 141 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.087088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.066383 restraints weight = 88465.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.47
r_work: 0.2981 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.4654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16768  Z= 0.196
  Angle     :  0.609   6.028  23904  Z= 0.363
  Chirality :  0.042   0.145   2704
  Planarity :  0.005   0.055   1995
  Dihedral  : 25.077 162.653   4576
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 1.29
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.25 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.27 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1199
  helix:  2.36 (0.20), residues: 726
  sheet:  0.49 (0.62), residues: 76
  loop : -1.39 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP W 348 
 HIS   0.003   0.001   HIS W 477 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.007   0.001   TYR W 183 
 ARG   0.009   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05627 (  631)
  hydrogen bonds       : angle       3.72863 ( 1767)
  covalent geometry    : bond        0.00431 (16768)
  covalent geometry    : angle       0.60925 (23904)

*********************** 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
  153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 1.839 
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: W  620 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7516 (mmm160)
  outliers start: 13
  outliers final: 3
  residues processed: 147
  average time/residue: 3.6766
  time to fit residues: 585.7087
Evaluate side-chains
  133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 1.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  620 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.085402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.064943 restraints weight = 87625.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.40
r_work: 0.2942 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.4988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  16768  Z= 0.219
  Angle     :  0.602   6.076  23904  Z= 0.359
  Chirality :  0.043   0.155   2704
  Planarity :  0.005   0.058   1995
  Dihedral  : 25.544 159.790   4576
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.09 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.13 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.64 (0.25), residues: 1199
  helix:  2.39 (0.20), residues: 726
  sheet:  0.57 (0.62), residues: 76
  loop : -1.39 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP W 348 
 HIS   0.003   0.001   HIS W 535 
 PHE   0.018   0.001   PHE W 391 
 TYR   0.018   0.001   TYR W 195 
 ARG   0.012   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05987 (  631)
  hydrogen bonds       : angle       3.73026 ( 1767)
  covalent geometry    : bond        0.00484 (16768)
  covalent geometry    : angle       0.60231 (23904)

*********************** 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
  144 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 1.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   42 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7590 (mtp180)
REVERT: W  368 TRP cc_start: 0.6489 (m-10) cc_final: 0.6271 (m-10)
REVERT: W  620 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7527 (mmm160)
  outliers start: 10
  outliers final: 4
  residues processed: 140
  average time/residue: 3.8049
  time to fit residues: 571.2421
Evaluate side-chains
  132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 1.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  620 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 85 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 126 optimal weight:    0.5980
   chunk 136 optimal weight:    5.9990
   chunk 121 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
D  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.086424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.066091 restraints weight = 87723.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.41
r_work: 0.2967 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.5163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16768  Z= 0.166
  Angle     :  0.582   6.162  23904  Z= 0.347
  Chirality :  0.040   0.146   2704
  Planarity :  0.004   0.050   1995
  Dihedral  : 25.721 159.125   4576
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.34 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 16.08 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.83 (0.25), residues: 1199
  helix:  2.57 (0.20), residues: 726
  sheet:  0.51 (0.61), residues: 76
  loop : -1.33 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP W 348 
 HIS   0.002   0.001   HIS W 535 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.011   0.001   TYR W 195 
 ARG   0.007   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05049 (  631)
  hydrogen bonds       : angle       3.58036 ( 1767)
  covalent geometry    : bond        0.00360 (16768)
  covalent geometry    : angle       0.58198 (23904)

*********************** 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
  136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 1.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   42 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7798 (ttm110)
REVERT: W  620 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7464 (mmm160)
REVERT: W  623 MET cc_start: 0.8458 (mmm) cc_final: 0.8208 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 134
  average time/residue: 3.9445
  time to fit residues: 569.2327
Evaluate side-chains
  130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 3.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain W residue  367 SER
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  620 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 142 optimal weight:    0.0770
   chunk 26 optimal weight:    0.0970
   overall best weight:    0.4336

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.087764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.067488 restraints weight = 88472.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 1.43
r_work: 0.2992 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.5327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16768  Z= 0.134
  Angle     :  0.572   6.355  23904  Z= 0.340
  Chirality :  0.038   0.154   2704
  Planarity :  0.004   0.044   1995
  Dihedral  : 25.764 159.337   4576
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.34 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 16.08 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.10 (0.25), residues: 1199
  helix:  2.76 (0.20), residues: 731
  sheet:  0.92 (0.62), residues: 66
  loop : -1.25 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP W 368 
 HIS   0.003   0.000   HIS W 535 
 PHE   0.025   0.001   PHE W 391 
 TYR   0.013   0.001   TYR W 195 
 ARG   0.006   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  631)
  hydrogen bonds       : angle       3.38703 ( 1767)
  covalent geometry    : bond        0.00291 (16768)
  covalent geometry    : angle       0.57247 (23904)

*********************** 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
  141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 1.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   42 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7704 (ttm110)
REVERT: W  620 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7456 (mmm160)
  outliers start: 8
  outliers final: 4
  residues processed: 139
  average time/residue: 3.7347
  time to fit residues: 566.2491
Evaluate side-chains
  132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 1.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain W residue  367 SER
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  620 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 143 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 122 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   chunk 120 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 132 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.084730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.063930 restraints weight = 89305.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.49
r_work: 0.2888 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.5375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16768  Z= 0.195
  Angle     :  0.581   7.731  23904  Z= 0.345
  Chirality :  0.041   0.148   2704
  Planarity :  0.004   0.047   1995
  Dihedral  : 25.926 158.647   4576
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.92 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.89 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.95 (0.25), residues: 1199
  helix:  2.65 (0.20), residues: 726
  sheet:  0.87 (0.62), residues: 66
  loop : -1.28 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP W 280 
 HIS   0.002   0.001   HIS H 106 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.009   0.001   TYR W 195 
 ARG   0.005   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05398 (  631)
  hydrogen bonds       : angle       3.55701 ( 1767)
  covalent geometry    : bond        0.00428 (16768)
  covalent geometry    : angle       0.58110 (23904)

*********************** 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
  138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 1.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.6814 (tttt) cc_final: 0.6555 (pmmt)
REVERT: E   42 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7725 (ttm110)
REVERT: W  620 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7453 (mmm160)
  outliers start: 9
  outliers final: 8
  residues processed: 136
  average time/residue: 3.6570
  time to fit residues: 536.2349
Evaluate side-chains
  135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 1.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain W residue  304 TYR
Chi-restraints excluded: chain W residue  367 SER
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  535 HIS
Chi-restraints excluded: chain W residue  620 ARG
Chi-restraints excluded: chain W residue  628 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.083753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.062772 restraints weight = 88416.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.50
r_work: 0.2875 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.5438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  16768  Z= 0.222
  Angle     :  0.595   7.808  23904  Z= 0.351
  Chirality :  0.042   0.151   2704
  Planarity :  0.004   0.045   1995
  Dihedral  : 26.100 159.029   4576
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.92 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 15.89 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.83 (0.25), residues: 1199
  helix:  2.56 (0.20), residues: 726
  sheet:  0.77 (0.63), residues: 67
  loop : -1.34 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP W 368 
 HIS   0.002   0.001   HIS H 106 
 PHE   0.029   0.001   PHE W 391 
 TYR   0.008   0.001   TYR W 195 
 ARG   0.005   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05624 (  631)
  hydrogen bonds       : angle       3.61434 ( 1767)
  covalent geometry    : bond        0.00493 (16768)
  covalent geometry    : angle       0.59515 (23904)

*********************** 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
  138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 1.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   28 LYS cc_start: 0.6771 (tttt) cc_final: 0.6515 (pmmt)
REVERT: E   42 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7596 (mtm180)
REVERT: W  233 MET cc_start: 0.8555 (tpp) cc_final: 0.8072 (tpp)
REVERT: W  620 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7468 (mmm160)
  outliers start: 10
  outliers final: 7
  residues processed: 135
  average time/residue: 3.5281
  time to fit residues: 513.7062
Evaluate side-chains
  136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 1.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain W residue  367 SER
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  535 HIS
Chi-restraints excluded: chain W residue  620 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 127 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
W 385 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.084829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.064061 restraints weight = 88809.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.49
r_work: 0.2905 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.5497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16768  Z= 0.160
  Angle     :  0.578   7.307  23904  Z= 0.341
  Chirality :  0.039   0.152   2704
  Planarity :  0.004   0.044   1995
  Dihedral  : 26.145 159.542   4576
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.84 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.89 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.96 (0.25), residues: 1199
  helix:  2.65 (0.20), residues: 731
  sheet:  0.77 (0.63), residues: 67
  loop : -1.29 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP W 348 
 HIS   0.004   0.001   HIS W 385 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.010   0.001   TYR W 195 
 ARG   0.005   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04901 (  631)
  hydrogen bonds       : angle       3.51608 ( 1767)
  covalent geometry    : bond        0.00347 (16768)
  covalent geometry    : angle       0.57841 (23904)

********************** 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
  141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 1.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  104 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8689 (mt0)
REVERT: D   28 LYS cc_start: 0.6786 (tttt) cc_final: 0.6533 (pmmt)
REVERT: E   42 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7616 (mtm180)
REVERT: H   31 LYS cc_start: 0.8592 (mppt) cc_final: 0.8300 (mptm)
REVERT: W  233 MET cc_start: 0.8549 (tpp) cc_final: 0.8094 (tpp)
REVERT: W  620 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7443 (mmm160)
  outliers start: 9
  outliers final: 7
  residues processed: 138
  average time/residue: 3.6303
  time to fit residues: 541.1843
Evaluate side-chains
  137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 1.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain W residue  367 SER
Chi-restraints excluded: chain W residue  429 MET
Chi-restraints excluded: chain W residue  535 HIS
Chi-restraints excluded: chain W residue  620 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.084755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.064040 restraints weight = 88814.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.48
r_work: 0.2903 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  16768  Z= 0.179
  Angle     :  0.762  59.185  23904  Z= 0.457
  Chirality :  0.040   0.152   2704
  Planarity :  0.004   0.044   1995
  Dihedral  : 26.144 159.507   4576
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.92 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.98 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.96 (0.25), residues: 1199
  helix:  2.66 (0.20), residues: 730
  sheet:  0.78 (0.63), residues: 67
  loop : -1.29 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP W 348 
 HIS   0.003   0.001   HIS W 385 
 PHE   0.009   0.001   PHE W 391 
 TYR   0.010   0.001   TYR W 195 
 ARG   0.004   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04968 (  631)
  hydrogen bonds       : angle       3.51633 ( 1767)
  covalent geometry    : bond        0.00385 (16768)
  covalent geometry    : angle       0.76238 (23904)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 23726.42 seconds
wall clock time: 411 minutes 9.62 seconds (24669.62 seconds total)