Starting phenix.real_space_refine
on Fri Aug 22 20:20:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ilq_35540/08_2025/8ilq_35540.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ilq_35540/08_2025/8ilq_35540.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ilq_35540/08_2025/8ilq_35540.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ilq_35540/08_2025/8ilq_35540.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ilq_35540/08_2025/8ilq_35540.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ilq_35540/08_2025/8ilq_35540.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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: 4
    Type Number    sf(0)   Gaussians
     S      79      5.16       5
     C    4850      2.51       5
     N    1331      2.21       5
     O    1469      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7729
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 501, 3837
          Classifications: {'peptide': 501}
          Link IDs: {'PTRANS': 24, 'TRANS': 476}
    Chain: "B"
      Number of atoms: 3808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 3808
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 21, 'TRANS': 487}
    Chain: "C"
      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: "A"
      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
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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
  Time building chain proxies: 2.14, per 1000 atoms: 0.28
  Number of scatterers: 7729
  At special positions: 0
  Unit cell: (189, 128.52, 124.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      79     16.00
     O    1469      8.00
     N    1331      7.00
     C    4850      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 143 " - pdb=" SG  CYS A 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 206 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 258 " - pdb=" SG  CYS A 305 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 303 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 287 " - pdb=" SG  CYS A 292 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 352 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 356 " - pdb=" SG  CYS A 424 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 563 " - pdb=" SG  CYS B 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 644 " - pdb=" SG  CYS B 841 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 650 " - pdb=" SG  CYS B 698 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 691 " - pdb=" SG  CYS B 696 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 778 " - pdb=" SG  CYS B 793 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 809 " - pdb=" SG  CYS B 823 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 908 " - pdb=" SG  CYS B 978 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 918 " - pdb=" SG  CYS B 921 " distance=2.04

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A  33 "
      " NAG B1101 " - " ASN B 914 "
      " NAG B1102 " - " ASN B 853 "
      " NAG B1103 " - " ASN B 936 "
      " NAG C   1 " - " ASN A  63 "
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 446.6 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1820

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 17 sheets defined
      16.2% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 52
      removed outlier: 3.840A  pdb=" N   ASP A  52 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 65
      removed outlier: 4.043A  pdb=" N   HIS A  64 " --> pdb=" O   TRP A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 105
    Processing helix  chain 'A' and resid 188 through 200
      removed outlier: 3.973A  pdb=" N   GLU A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LEU A 194 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 275
      removed outlier: 3.936A  pdb=" N   LYS A 275 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 291
      removed outlier: 3.816A  pdb=" N   VAL A 289 " --> pdb=" O   GLN A 285 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY A 291 " --> pdb=" O   CYS A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 441
      removed outlier: 4.397A  pdb=" N   GLU A 440 " --> pdb=" O   THR A 436 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   PHE A 441 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 436 through 441'
    Processing helix  chain 'A' and resid 451 through 465
      removed outlier: 3.678A  pdb=" N   PHE A 455 " --> pdb=" O   LYS A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 476
      removed outlier: 3.638A  pdb=" N   THR A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASN A 472 " --> pdb=" O   MET A 468 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   VAL A 473 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 484
      removed outlier: 3.859A  pdb=" N   VAL A 484 " --> pdb=" O   GLY A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 500
      removed outlier: 3.955A  pdb=" N   ARG A 500 " --> pdb=" O   LYS A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 518
      removed outlier: 3.893A  pdb=" N   LYS A 508 " --> pdb=" O   CYS A 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1032 through 1054
      removed outlier: 3.771A  pdb=" N   ILE B1037 " --> pdb=" O   LEU B1033 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   GLY B1047 " --> pdb=" O   VAL B1043 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LEU B1048 " --> pdb=" O   LEU B1044 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ALA B1049 " --> pdb=" O   LEU B1045 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LEU B1050 " --> pdb=" O   GLY B1046 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE B1054 " --> pdb=" O   LEU B1050 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1054 through 1063
      removed outlier: 3.931A  pdb=" N   LYS B1059 " --> pdb=" O   MET B1055 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   LEU B1060 " --> pdb=" O   SER B1056 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY B1061 " --> pdb=" O   LEU B1057 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73
      removed outlier: 6.531A  pdb=" N   LEU A 167 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82
      removed outlier: 6.982A  pdb=" N   SER A  81 " --> pdb=" O   TRP A 174 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   PHE A 129 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 149
    Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180
      removed outlier: 3.626A  pdb=" N   CYS A 327 " --> pdb=" O   ASP A 231 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA A 335 " --> pdb=" O   GLN A 223 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA A 228 " --> pdb=" O   MET A 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208
    Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 248
    Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 356
    Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 383
      removed outlier: 3.510A  pdb=" N   SER A 372 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A 409 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   THR A 416 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 575 through 576
      removed outlier: 3.788A  pdb=" N   VAL B 587 " --> pdb=" O   SER B 575 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 602 through 603
      removed outlier: 4.002A  pdb=" N   LYS B 621 " --> pdb=" O   GLU B 735 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 635 through 637
      removed outlier: 3.799A  pdb=" N   SER B 723 " --> pdb=" O   GLU B 779 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLU B 779 " --> pdb=" O   SER B 723 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648
    Processing sheet with id=AB4, first strand: chain 'B' and resid 760 through 765
      removed outlier: 3.684A  pdb=" N   THR B 763 " --> pdb=" O   SER B 891 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 832 through 834
      removed outlier: 3.966A  pdb=" N   GLU B 833 " --> pdb=" O   VAL B 840 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL B 840 " --> pdb=" O   GLU B 833 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 908 through 917
      removed outlier: 3.824A  pdb=" N   THR B 909 " --> pdb=" O   HIS B 932 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   SER B 928 " --> pdb=" O   THR B 913 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   VAL B 915 " --> pdb=" O   LYS B 926 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LYS B 926 " --> pdb=" O   VAL B 915 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 938 through 939
      removed outlier: 3.888A  pdb=" N   PHE B 950 " --> pdb=" O   ALA B 939 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 973 through 974
      removed outlier: 3.520A  pdb=" N   CYS B 974 " --> pdb=" O   VAL B 985 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL B 985 " --> pdb=" O   CYS B 974 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8

    177 hydrogen bonds defined for protein.
    465 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: 1.17

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2503
        1.34 -     1.46: 1837
        1.46 -     1.59: 3454
        1.59 -     1.71: 0
        1.71 -     1.83: 103
  Bond restraints: 7897
  Sorted by residual:
  bond pdb=" CA  PRO A 449 "
       pdb=" C   PRO A 449 "
    ideal  model  delta    sigma   weight residual
    1.517  1.554 -0.037 1.46e-02 4.69e+03 6.32e+00
  bond pdb=" CA  PRO B 715 "
       pdb=" C   PRO B 715 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.033 1.42e-02 4.96e+03 5.39e+00
  bond pdb=" CD1 TYR A 448 "
       pdb=" CE1 TYR A 448 "
    ideal  model  delta    sigma   weight residual
    1.382  1.321  0.061 3.00e-02 1.11e+03 4.17e+00
  bond pdb=" C   ASN A 444 "
       pdb=" N   PRO A 445 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 2.34e-02 1.83e+03 3.03e+00
  bond pdb=" N   PRO A 449 "
       pdb=" CA  PRO A 449 "
    ideal  model  delta    sigma   weight residual
    1.472  1.494 -0.022 1.32e-02 5.74e+03 2.90e+00
  ... (remaining 7892 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 10402
        1.95 -     3.90: 229
        3.90 -     5.85: 31
        5.85 -     7.80: 6
        7.80 -     9.75: 4
  Bond angle restraints: 10672
  Sorted by residual:
  angle pdb=" N   GLU B 813 "
        pdb=" CA  GLU B 813 "
        pdb=" C   GLU B 813 "
      ideal   model   delta    sigma   weight residual
     114.62  107.68    6.94 1.14e+00 7.69e-01 3.71e+01
  angle pdb=" CA  GLN A 348 "
        pdb=" CB  GLN A 348 "
        pdb=" CG  GLN A 348 "
      ideal   model   delta    sigma   weight residual
     114.10  123.85   -9.75 2.00e+00 2.50e-01 2.38e+01
  angle pdb=" C   ALA B 596 "
        pdb=" N   VAL B 597 "
        pdb=" CA  VAL B 597 "
      ideal   model   delta    sigma   weight residual
     121.97  129.51   -7.54 1.80e+00 3.09e-01 1.76e+01
  angle pdb=" CA  GLU B 813 "
        pdb=" C   GLU B 813 "
        pdb=" N   SER B 814 "
      ideal   model   delta    sigma   weight residual
     119.71  115.60    4.11 1.17e+00 7.31e-01 1.23e+01
  angle pdb=" CA  VAL B 597 "
        pdb=" CB  VAL B 597 "
        pdb=" CG1 VAL B 597 "
      ideal   model   delta    sigma   weight residual
     110.40  115.75   -5.35 1.70e+00 3.46e-01 9.89e+00
  ... (remaining 10667 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4026
       17.92 -    35.83: 608
       35.83 -    53.75: 170
       53.75 -    71.67: 21
       71.67 -    89.59: 13
  Dihedral angle restraints: 4838
    sinusoidal: 1989
      harmonic: 2849
  Sorted by residual:
  dihedral pdb=" CB  CYS A 258 "
           pdb=" SG  CYS A 258 "
           pdb=" SG  CYS A 305 "
           pdb=" CB  CYS A 305 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.84  -80.16     1      1.00e+01 1.00e-02 7.96e+01
  dihedral pdb=" CB  CYS B 918 "
           pdb=" SG  CYS B 918 "
           pdb=" SG  CYS B 921 "
           pdb=" CB  CYS B 921 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.29  -68.71     1      1.00e+01 1.00e-02 6.11e+01
  dihedral pdb=" CA  CYS B 918 "
           pdb=" C   CYS B 918 "
           pdb=" N   TYR B 919 "
           pdb=" CA  TYR B 919 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 4835 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1095
       0.081 -    0.162: 97
       0.162 -    0.244: 3
       0.244 -    0.325: 1
       0.325 -    0.406: 1
  Chirality restraints: 1197
  Sorted by residual:
  chirality pdb=" CB  VAL B 597 "
            pdb=" CA  VAL B 597 "
            pdb=" CG1 VAL B 597 "
            pdb=" CG2 VAL B 597 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A  63 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CB  ILE B 625 "
            pdb=" CA  ILE B 625 "
            pdb=" CG1 ILE B 625 "
            pdb=" CG2 ILE B 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1194 not shown)

  Planarity restraints: 1362
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 853 "    0.020 2.00e-02 2.50e+03   1.86e-02 4.35e+00
        pdb=" CG  ASN B 853 "   -0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 853 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 853 "   -0.018 2.00e-02 2.50e+03
        pdb=" C1  NAG B1102 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 444 "   -0.034 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 445 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 445 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 445 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  83 "    0.034 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A  84 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A  84 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  84 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1359 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 794
        2.75 -     3.28: 7089
        3.28 -     3.82: 11126
        3.82 -     4.36: 11629
        4.36 -     4.90: 21365
  Nonbonded interactions: 52003
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 614 "
            pdb=" OG  SER B 902 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   SER B 934 "
            pdb=" OG  SER B 934 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   ASP B 639 "
            pdb=" ND2 ASN B 714 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" NE2 HIS A 243 "
            pdb=" OH  TYR A 328 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OG  SER A 152 "
            pdb=" OE1 GLU A 154 "
     model   vdw
     2.278 3.040
  ... (remaining 51998 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  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:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.650
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
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      :  0.003   0.061   7919  Z= 0.155
  Angle     :  0.686   9.747  10722  Z= 0.346
  Chirality :  0.047   0.406   1197
  Planarity :  0.004   0.052   1357
  Dihedral  : 18.132  89.585   2970
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 13.12 %
    Favored  : 86.68 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 35.99 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.25), residues: 1006
  helix:  0.21 (0.45), residues: 147
  sheet: -1.27 (0.36), residues: 228
  loop : -2.74 (0.22), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 332 
 TYR   0.019   0.002   TYR B 854 
 PHE   0.019   0.001   PHE A 330 
 TRP   0.008   0.001   TRP A 453 
 HIS   0.005   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7897)
  covalent geometry    : angle       0.67609 (10672)
  SS BOND              : bond        0.00364 (   16)
  SS BOND              : angle       1.41303 (   32)
  hydrogen bonds       : bond        0.15620 (  177)
  hydrogen bonds       : angle       6.86257 (  465)
  link_BETA1-4         : bond        0.00069 (    1)
  link_BETA1-4         : angle       1.86420 (    3)
  link_NAG-ASN         : bond        0.00720 (    5)
  link_NAG-ASN         : angle       2.58829 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 92
  average time/residue: 0.0817
  time to fit residues: 10.7659
Evaluate side-chains
  89 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 582 ASN
B 601 GLN
** B 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 808 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.202698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.140945 restraints weight = 88932.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.139444 restraints weight = 50458.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.135672 restraints weight = 43458.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.133807 restraints weight = 41382.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.133314 restraints weight = 38645.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   7919  Z= 0.244
  Angle     :  0.832   7.637  10722  Z= 0.424
  Chirality :  0.049   0.288   1197
  Planarity :  0.005   0.050   1357
  Dihedral  :  6.170  39.782   1198
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 16.30 %
    Favored  : 83.30 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.39 %
    Favored  : 94.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.17 (0.25), residues: 1006
  helix:  0.07 (0.43), residues: 157
  sheet: -1.55 (0.36), residues: 228
  loop : -3.10 (0.20), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 865 
 TYR   0.027   0.003   TYR B 635 
 PHE   0.026   0.002   PHE A 418 
 TRP   0.067   0.003   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 7897)
  covalent geometry    : angle       0.81446 (10672)
  SS BOND              : bond        0.00741 (   16)
  SS BOND              : angle       2.41357 (   32)
  hydrogen bonds       : bond        0.04413 (  177)
  hydrogen bonds       : angle       5.59736 (  465)
  link_BETA1-4         : bond        0.00045 (    1)
  link_BETA1-4         : angle       2.25897 (    3)
  link_NAG-ASN         : bond        0.00610 (    5)
  link_NAG-ASN         : angle       3.13998 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 TYR cc_start: 0.6685 (t80) cc_final: 0.6484 (t80)
REVERT: A  334 MET cc_start: 0.7826 (mmm) cc_final: 0.7626 (mmm)
REVERT: B  691 CYS cc_start: 0.7553 (t) cc_final: 0.7264 (t)
  outliers start: 4
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0952
  time to fit residues: 15.0626
Evaluate side-chains
  91 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0970
   chunk 64 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0870
   chunk 79 optimal weight:    0.3980
   chunk 32 optimal weight:    7.9990
   chunk 68 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.4156

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 601 GLN
B 626 ASN
B 747 HIS
B 808 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.210711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.159249 restraints weight = 84944.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.157442 restraints weight = 50380.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.152945 restraints weight = 41759.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.150339 restraints weight = 37581.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.148257 restraints weight = 36399.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7919  Z= 0.109
  Angle     :  0.645   7.822  10722  Z= 0.322
  Chirality :  0.044   0.227   1197
  Planarity :  0.004   0.047   1357
  Dihedral  :  5.309  36.027   1198
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 11.73 %
    Favored  : 87.87 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.17 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.25), residues: 1006
  helix:  0.40 (0.45), residues: 156
  sheet: -1.71 (0.35), residues: 230
  loop : -2.94 (0.21), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 865 
 TYR   0.018   0.001   TYR B 919 
 PHE   0.014   0.001   PHE A 135 
 TRP   0.021   0.001   TRP A 480 
 HIS   0.008   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7897)
  covalent geometry    : angle       0.63194 (10672)
  SS BOND              : bond        0.00493 (   16)
  SS BOND              : angle       1.82536 (   32)
  hydrogen bonds       : bond        0.02989 (  177)
  hydrogen bonds       : angle       5.13000 (  465)
  link_BETA1-4         : bond        0.00467 (    1)
  link_BETA1-4         : angle       1.38059 (    3)
  link_NAG-ASN         : bond        0.00603 (    5)
  link_NAG-ASN         : angle       2.43955 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.8280 (ppp) cc_final: 0.7835 (ppp)
REVERT: A  318 TYR cc_start: 0.6998 (t80) cc_final: 0.6615 (t80)
REVERT: A  333 MET cc_start: 0.7313 (mtt) cc_final: 0.6519 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0766
  time to fit residues: 13.2204
Evaluate side-chains
  95 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0670
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0870
   chunk 93 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 71 optimal weight:    0.1980
   chunk 45 optimal weight:    0.0970
   overall best weight:    0.1894

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.213687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.163422 restraints weight = 84833.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.162322 restraints weight = 49521.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.155491 restraints weight = 41644.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.155002 restraints weight = 42978.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.153015 restraints weight = 39372.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056   7919  Z= 0.101
  Angle     :  0.608   6.509  10722  Z= 0.305
  Chirality :  0.043   0.217   1197
  Planarity :  0.004   0.047   1357
  Dihedral  :  4.837  32.444   1198
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 11.83 %
    Favored  : 87.67 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.46 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.25), residues: 1006
  helix:  0.40 (0.45), residues: 157
  sheet: -1.66 (0.35), residues: 226
  loop : -2.78 (0.21), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 865 
 TYR   0.017   0.001   TYR B 919 
 PHE   0.011   0.001   PHE B 746 
 TRP   0.052   0.001   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7897)
  covalent geometry    : angle       0.59633 (10672)
  SS BOND              : bond        0.00410 (   16)
  SS BOND              : angle       1.63439 (   32)
  hydrogen bonds       : bond        0.02719 (  177)
  hydrogen bonds       : angle       4.85915 (  465)
  link_BETA1-4         : bond        0.00302 (    1)
  link_BETA1-4         : angle       1.33990 (    3)
  link_NAG-ASN         : bond        0.00535 (    5)
  link_NAG-ASN         : angle       2.35963 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.6905 (mtt) cc_final: 0.6474 (mtt)
REVERT: A  446 GLN cc_start: 0.7440 (tp40) cc_final: 0.6853 (tp-100)
REVERT: B  651 ARG cc_start: 0.8113 (mtp85) cc_final: 0.6980 (mtt180)
REVERT: B  691 CYS cc_start: 0.7370 (t) cc_final: 0.7054 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0816
  time to fit residues: 12.9958
Evaluate side-chains
  94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0470
   chunk 81 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0670
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.211662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.163860 restraints weight = 85735.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.161812 restraints weight = 49398.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.158354 restraints weight = 41531.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.153376 restraints weight = 40263.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.151554 restraints weight = 37214.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   7919  Z= 0.105
  Angle     :  0.620   9.022  10722  Z= 0.307
  Chirality :  0.043   0.224   1197
  Planarity :  0.004   0.048   1357
  Dihedral  :  4.731  32.647   1198
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 12.03 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.99 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.25), residues: 1006
  helix:  0.46 (0.45), residues: 157
  sheet: -1.56 (0.34), residues: 238
  loop : -2.76 (0.21), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 865 
 TYR   0.015   0.001   TYR B 919 
 PHE   0.009   0.001   PHE A 225 
 TRP   0.030   0.001   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7897)
  covalent geometry    : angle       0.60901 (10672)
  SS BOND              : bond        0.00422 (   16)
  SS BOND              : angle       1.61860 (   32)
  hydrogen bonds       : bond        0.02736 (  177)
  hydrogen bonds       : angle       4.74326 (  465)
  link_BETA1-4         : bond        0.00399 (    1)
  link_BETA1-4         : angle       1.34659 (    3)
  link_NAG-ASN         : bond        0.00466 (    5)
  link_NAG-ASN         : angle       2.25383 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 MET cc_start: 0.5444 (ttm) cc_final: 0.5136 (ttp)
REVERT: A  333 MET cc_start: 0.7284 (mtt) cc_final: 0.6465 (mtt)
REVERT: B  691 CYS cc_start: 0.7365 (t) cc_final: 0.7105 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0697
  time to fit residues: 11.3553
Evaluate side-chains
  92 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0050
   chunk 85 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 78 optimal weight:    0.0470
   chunk 63 optimal weight:   20.0000
   overall best weight:    0.9896

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.208485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.146947 restraints weight = 89298.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.146046 restraints weight = 51608.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.141415 restraints weight = 43673.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.140294 restraints weight = 41459.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.139812 restraints weight = 40392.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7919  Z= 0.125
  Angle     :  0.638   7.431  10722  Z= 0.319
  Chirality :  0.043   0.239   1197
  Planarity :  0.004   0.049   1357
  Dihedral  :  4.889  35.443   1198
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 12.82 %
    Favored  : 86.78 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.76 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.25), residues: 1006
  helix:  0.49 (0.45), residues: 158
  sheet: -1.41 (0.35), residues: 238
  loop : -2.81 (0.21), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  62 
 TYR   0.015   0.002   TYR B 764 
 PHE   0.010   0.001   PHE A 455 
 TRP   0.024   0.001   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7897)
  covalent geometry    : angle       0.62420 (10672)
  SS BOND              : bond        0.00410 (   16)
  SS BOND              : angle       1.66857 (   32)
  hydrogen bonds       : bond        0.03037 (  177)
  hydrogen bonds       : angle       4.82010 (  465)
  link_BETA1-4         : bond        0.00356 (    1)
  link_BETA1-4         : angle       1.80043 (    3)
  link_NAG-ASN         : bond        0.00434 (    5)
  link_NAG-ASN         : angle       2.60998 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.6404 (mtt) cc_final: 0.6021 (mtt)
REVERT: B  691 CYS cc_start: 0.7467 (t) cc_final: 0.7168 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0701
  time to fit residues: 11.1710
Evaluate side-chains
  94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 93 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:   20.0000
   chunk 72 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.208919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.149519 restraints weight = 89660.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.151869 restraints weight = 52334.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.144794 restraints weight = 39673.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.141324 restraints weight = 36865.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.140763 restraints weight = 36249.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7919  Z= 0.117
  Angle     :  0.639   7.472  10722  Z= 0.317
  Chirality :  0.044   0.245   1197
  Planarity :  0.004   0.047   1357
  Dihedral  :  4.921  36.959   1198
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 12.03 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.76 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.25), residues: 1006
  helix:  0.52 (0.44), residues: 157
  sheet: -1.38 (0.35), residues: 238
  loop : -2.83 (0.21), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 241 
 TYR   0.014   0.002   TYR B 764 
 PHE   0.012   0.001   PHE A 225 
 TRP   0.021   0.001   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7897)
  covalent geometry    : angle       0.62745 (10672)
  SS BOND              : bond        0.00426 (   16)
  SS BOND              : angle       1.60153 (   32)
  hydrogen bonds       : bond        0.02857 (  177)
  hydrogen bonds       : angle       4.78794 (  465)
  link_BETA1-4         : bond        0.00625 (    1)
  link_BETA1-4         : angle       1.14290 (    3)
  link_NAG-ASN         : bond        0.00550 (    5)
  link_NAG-ASN         : angle       2.45891 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 MET cc_start: 0.5563 (ttp) cc_final: 0.5327 (ttm)
REVERT: A  333 MET cc_start: 0.6865 (mtt) cc_final: 0.5914 (mtt)
REVERT: B  691 CYS cc_start: 0.7410 (t) cc_final: 0.7151 (t)
REVERT: B  894 TYR cc_start: 0.8867 (p90) cc_final: 0.8663 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0668
  time to fit residues: 10.8025
Evaluate side-chains
  98 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0370
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.3864

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 808 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.204422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.142874 restraints weight = 87603.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.146002 restraints weight = 50984.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.137083 restraints weight = 42530.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.134483 restraints weight = 39272.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.133857 restraints weight = 35853.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7919  Z= 0.152
  Angle     :  0.690  11.227  10722  Z= 0.342
  Chirality :  0.045   0.254   1197
  Planarity :  0.005   0.071   1357
  Dihedral  :  5.191  39.851   1198
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 13.42 %
    Favored  : 85.98 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.17 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.85 (0.25), residues: 1006
  helix:  0.48 (0.44), residues: 160
  sheet: -1.39 (0.36), residues: 216
  loop : -2.90 (0.21), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 332 
 TYR   0.018   0.002   TYR B 764 
 PHE   0.012   0.002   PHE A 418 
 TRP   0.021   0.002   TRP B1024 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7897)
  covalent geometry    : angle       0.67767 (10672)
  SS BOND              : bond        0.00516 (   16)
  SS BOND              : angle       1.79370 (   32)
  hydrogen bonds       : bond        0.03267 (  177)
  hydrogen bonds       : angle       4.92750 (  465)
  link_BETA1-4         : bond        0.00410 (    1)
  link_BETA1-4         : angle       1.19143 (    3)
  link_NAG-ASN         : bond        0.00395 (    5)
  link_NAG-ASN         : angle       2.49485 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.7255 (mtt) cc_final: 0.6911 (mtt)
REVERT: B  691 CYS cc_start: 0.7551 (t) cc_final: 0.7292 (t)
REVERT: B  894 TYR cc_start: 0.8941 (p90) cc_final: 0.8306 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0663
  time to fit residues: 10.5489
Evaluate side-chains
  91 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 77 optimal weight:    0.3980
   chunk 75 optimal weight:    0.0870
   chunk 36 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 808 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.207414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.145166 restraints weight = 87078.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.143553 restraints weight = 51257.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.140181 restraints weight = 44901.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.138712 restraints weight = 42416.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.137851 restraints weight = 39302.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7919  Z= 0.112
  Angle     :  0.665   9.954  10722  Z= 0.325
  Chirality :  0.044   0.247   1197
  Planarity :  0.004   0.062   1357
  Dihedral  :  5.046  38.539   1198
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 11.73 %
    Favored  : 87.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.06 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.84 (0.25), residues: 1006
  helix:  0.51 (0.44), residues: 161
  sheet: -1.47 (0.36), residues: 218
  loop : -2.87 (0.21), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 651 
 TYR   0.011   0.001   TYR B 764 
 PHE   0.009   0.001   PHE A 197 
 TRP   0.058   0.002   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7897)
  covalent geometry    : angle       0.65349 (10672)
  SS BOND              : bond        0.00450 (   16)
  SS BOND              : angle       1.65456 (   32)
  hydrogen bonds       : bond        0.02834 (  177)
  hydrogen bonds       : angle       4.74819 (  465)
  link_BETA1-4         : bond        0.00539 (    1)
  link_BETA1-4         : angle       1.17284 (    3)
  link_NAG-ASN         : bond        0.00488 (    5)
  link_NAG-ASN         : angle       2.45043 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.6747 (mtt) cc_final: 0.5954 (mtt)
REVERT: A  414 ASP cc_start: 0.8010 (m-30) cc_final: 0.7807 (m-30)
REVERT: B  691 CYS cc_start: 0.7504 (t) cc_final: 0.7247 (t)
REVERT: B  894 TYR cc_start: 0.8915 (p90) cc_final: 0.8278 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0733
  time to fit residues: 11.1099
Evaluate side-chains
  94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 73 optimal weight:    0.0570
   chunk 30 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   overall best weight:    0.8302

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
** B 794 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 = 0.4093 r_free = 0.4093 target = 0.207274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.146134 restraints weight = 88538.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.143859 restraints weight = 51520.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.140539 restraints weight = 44878.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.139240 restraints weight = 42687.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.139004 restraints weight = 40588.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7919  Z= 0.119
  Angle     :  0.665   9.616  10722  Z= 0.327
  Chirality :  0.044   0.262   1197
  Planarity :  0.004   0.058   1357
  Dihedral  :  5.034  38.738   1198
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 12.72 %
    Favored  : 86.68 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.12 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.25), residues: 1006
  helix:  0.54 (0.44), residues: 161
  sheet: -1.30 (0.36), residues: 224
  loop : -2.90 (0.21), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 651 
 TYR   0.013   0.001   TYR B 764 
 PHE   0.010   0.001   PHE A 225 
 TRP   0.057   0.002   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7897)
  covalent geometry    : angle       0.65217 (10672)
  SS BOND              : bond        0.00463 (   16)
  SS BOND              : angle       1.78085 (   32)
  hydrogen bonds       : bond        0.02851 (  177)
  hydrogen bonds       : angle       4.74689 (  465)
  link_BETA1-4         : bond        0.00519 (    1)
  link_BETA1-4         : angle       1.17418 (    3)
  link_NAG-ASN         : bond        0.00462 (    5)
  link_NAG-ASN         : angle       2.44780 (   15)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.6756 (mtt) cc_final: 0.6338 (mtt)
REVERT: B  691 CYS cc_start: 0.7495 (t) cc_final: 0.7242 (t)
REVERT: B  894 TYR cc_start: 0.8902 (p90) cc_final: 0.8311 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0855
  time to fit residues: 12.7381
Evaluate side-chains
  93 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 86 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 808 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.203997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.148818 restraints weight = 88002.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.147367 restraints weight = 51801.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.143470 restraints weight = 44530.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.140869 restraints weight = 40703.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.140174 restraints weight = 39476.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7919  Z= 0.164
  Angle     :  0.726   9.274  10722  Z= 0.361
  Chirality :  0.046   0.276   1197
  Planarity :  0.005   0.055   1357
  Dihedral  :  5.375  40.527   1198
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 13.82 %
    Favored  : 85.59 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.59 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (0.25), residues: 1006
  helix:  0.45 (0.44), residues: 160
  sheet: -1.42 (0.36), residues: 221
  loop : -2.94 (0.21), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 624 
 TYR   0.020   0.002   TYR B 764 
 PHE   0.012   0.002   PHE A 418 
 TRP   0.055   0.002   TRP A 480 
 HIS   0.006   0.001   HIS B 967 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7897)
  covalent geometry    : angle       0.71326 (10672)
  SS BOND              : bond        0.00582 (   16)
  SS BOND              : angle       1.99092 (   32)
  hydrogen bonds       : bond        0.03353 (  177)
  hydrogen bonds       : angle       4.85339 (  465)
  link_BETA1-4         : bond        0.00495 (    1)
  link_BETA1-4         : angle       1.16036 (    3)
  link_NAG-ASN         : bond        0.00397 (    5)
  link_NAG-ASN         : angle       2.47855 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1417.25 seconds
wall clock time: 25 minutes 7.07 seconds (1507.07 seconds total)