Starting phenix.real_space_refine
on Mon Apr 28 14:13:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ilq_35540/04_2025/8ilq_35540.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ilq_35540/04_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_35540/04_2025/8ilq_35540.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ilq_35540/04_2025/8ilq_35540.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ilq_35540/04_2025/8ilq_35540.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ilq_35540/04_2025/8ilq_35540.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.12, per 1000 atoms: 0.66
  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: 2.09
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.88
  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: 2.23

  Time building geometry restraints manager: 2.34 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:             1.360
  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:          0.410
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.890
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.860
-------------------------------------------------------------------------------
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 : 9.06
  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 (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: -2.78 (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
 TRP   0.008   0.001   TRP A 453 
 HIS   0.005   0.001   HIS B 967 
 PHE   0.019   0.001   PHE A 330 
 TYR   0.019   0.002   TYR B 854 
 ARG   0.002   0.000   ARG A 332 

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

*********************** 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  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 92
  average time/residue: 0.1753
  time to fit residues: 23.0916
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  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0050
   chunk 25 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0470
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.4496

-------------------------------------------------------------------------------
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 626 ASN
** B 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1006 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.216898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.161408 restraints weight = 85103.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.162200 restraints weight = 47830.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.156149 restraints weight = 38197.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7919  Z= 0.118
  Angle     :  0.669   6.798  10722  Z= 0.334
  Chirality :  0.044   0.248   1197
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.478  44.128   1198
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.33 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.17 %
    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: -2.75 (0.25), residues: 1006
  helix:  0.50 (0.45), residues: 150
  sheet: -1.43 (0.35), residues: 230
  loop : -2.74 (0.22), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.001   TRP A 480 
 HIS   0.008   0.001   HIS B 967 
 PHE   0.024   0.001   PHE B 699 
 TYR   0.014   0.001   TYR B 919 
 ARG   0.003   0.000   ARG B 835 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00611 (    5)
  link_NAG-ASN         : angle       2.82480 (   15)
  link_BETA1-4         : bond        0.00245 (    1)
  link_BETA1-4         : angle       1.62916 (    3)
  hydrogen bonds       : bond        0.03220 (  177)
  hydrogen bonds       : angle       5.34650 (  465)
  SS BOND              : bond        0.00433 (   16)
  SS BOND              : angle       1.93888 (   32)
  covalent geometry    : bond        0.00267 ( 7897)
  covalent geometry    : angle       0.65334 (10672)

*********************** 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
  121 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  691 CYS cc_start: 0.7432 (t) cc_final: 0.7152 (t)
REVERT: B  865 ARG cc_start: 0.8315 (tpt-90) cc_final: 0.8020 (ttm-80)
  outliers start: 3
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2290
  time to fit residues: 36.7658
Evaluate side-chains
  90 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0370
   overall best weight:    2.1864

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.203127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.140930 restraints weight = 88747.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.139579 restraints weight = 52040.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.135520 restraints weight = 44173.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   7919  Z= 0.210
  Angle     :  0.760   8.442  10722  Z= 0.388
  Chirality :  0.047   0.288   1197
  Planarity :  0.005   0.049   1357
  Dihedral  :  5.801  39.792   1198
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 15.21 %
    Favored  : 84.39 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  5.51 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.03 (0.25), residues: 1006
  helix:  0.14 (0.43), residues: 157
  sheet: -1.39 (0.37), residues: 222
  loop : -3.01 (0.21), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 480 
 HIS   0.007   0.001   HIS B 967 
 PHE   0.023   0.002   PHE A 418 
 TYR   0.025   0.002   TYR B 764 
 ARG   0.008   0.001   ARG A  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00415 (    5)
  link_NAG-ASN         : angle       2.57638 (   15)
  link_BETA1-4         : bond        0.00442 (    1)
  link_BETA1-4         : angle       1.42062 (    3)
  hydrogen bonds       : bond        0.04235 (  177)
  hydrogen bonds       : angle       5.37576 (  465)
  SS BOND              : bond        0.00952 (   16)
  SS BOND              : angle       2.13277 (   32)
  covalent geometry    : bond        0.00498 ( 7897)
  covalent geometry    : angle       0.74637 (10672)

*********************** 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
  104 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 TYR cc_start: 0.7090 (t80) cc_final: 0.6833 (t80)
REVERT: A  333 MET cc_start: 0.6209 (mtp) cc_final: 0.5744 (mtt)
REVERT: B  807 ILE cc_start: 0.8418 (mm) cc_final: 0.8170 (mt)
REVERT: B  895 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7758 (ttm-80)
  outliers start: 2
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1900
  time to fit residues: 27.7912
Evaluate side-chains
  85 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 61 optimal weight:   20.0000
   chunk 91 optimal weight:    0.8980
   chunk 96 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 26 optimal weight:   20.0000
   chunk 80 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.207654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.149582 restraints weight = 87618.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.148960 restraints weight = 52378.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.142675 restraints weight = 42763.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7919  Z= 0.115
  Angle     :  0.650   8.453  10722  Z= 0.326
  Chirality :  0.044   0.263   1197
  Planarity :  0.004   0.058   1357
  Dihedral  :  5.280  36.874   1198
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 11.63 %
    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 (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: -2.94 (0.25), residues: 1006
  helix:  0.25 (0.44), residues: 157
  sheet: -1.43 (0.36), residues: 228
  loop : -2.94 (0.21), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A 480 
 HIS   0.008   0.001   HIS B 967 
 PHE   0.010   0.001   PHE A 135 
 TYR   0.017   0.001   TYR B 919 
 ARG   0.004   0.000   ARG B 865 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00492 (    5)
  link_NAG-ASN         : angle       2.48376 (   15)
  link_BETA1-4         : bond        0.00094 (    1)
  link_BETA1-4         : angle       1.32825 (    3)
  hydrogen bonds       : bond        0.03019 (  177)
  hydrogen bonds       : angle       5.04876 (  465)
  SS BOND              : bond        0.00589 (   16)
  SS BOND              : angle       1.85774 (   32)
  covalent geometry    : bond        0.00264 ( 7897)
  covalent geometry    : angle       0.63669 (10672)

*********************** 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
  113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.8166 (ppp) cc_final: 0.7722 (ppp)
REVERT: B  691 CYS cc_start: 0.7506 (t) cc_final: 0.7173 (t)
REVERT: B  807 ILE cc_start: 0.8405 (mm) cc_final: 0.8069 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1944
  time to fit residues: 30.6723
Evaluate side-chains
  90 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 86 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
** B 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 808 GLN
B1006 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.201724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.143065 restraints weight = 89913.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.141353 restraints weight = 52673.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.136190 restraints weight = 43875.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7919  Z= 0.177
  Angle     :  0.718   9.113  10722  Z= 0.364
  Chirality :  0.046   0.277   1197
  Planarity :  0.005   0.046   1357
  Dihedral  :  5.546  41.032   1198
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 15.61 %
    Favored  : 84.00 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.34 %
    Favored  : 97.42 %
  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: -3.06 (0.24), residues: 1006
  helix:  0.18 (0.43), residues: 157
  sheet: -1.47 (0.36), residues: 227
  loop : -3.04 (0.21), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 480 
 HIS   0.007   0.001   HIS B 967 
 PHE   0.017   0.002   PHE A 418 
 TYR   0.019   0.002   TYR B 764 
 ARG   0.002   0.000   ARG B 624 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00355 (    5)
  link_NAG-ASN         : angle       2.49875 (   15)
  link_BETA1-4         : bond        0.00282 (    1)
  link_BETA1-4         : angle       1.22964 (    3)
  hydrogen bonds       : bond        0.03691 (  177)
  hydrogen bonds       : angle       5.12959 (  465)
  SS BOND              : bond        0.00567 (   16)
  SS BOND              : angle       2.00343 (   32)
  covalent geometry    : bond        0.00420 ( 7897)
  covalent geometry    : angle       0.70520 (10672)

*********************** 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
  105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: B  691 CYS cc_start: 0.7723 (t) cc_final: 0.7408 (t)
REVERT: B  807 ILE cc_start: 0.8615 (mm) cc_final: 0.8352 (mt)
REVERT: B  869 SER cc_start: 0.9279 (t) cc_final: 0.8942 (t)
REVERT: B  895 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7756 (ttm-80)
  outliers start: 2
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1871
  time to fit residues: 27.8222
Evaluate side-chains
  86 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
** B 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.198405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.140366 restraints weight = 89680.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.138444 restraints weight = 53638.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.134010 restraints weight = 45323.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   7919  Z= 0.220
  Angle     :  0.780   7.618  10722  Z= 0.397
  Chirality :  0.048   0.286   1197
  Planarity :  0.005   0.047   1357
  Dihedral  :  6.004  43.193   1198
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 15.90 %
    Favored  : 83.50 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.75 %
    Favored  : 96.13 %
  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: -3.26 (0.24), residues: 1006
  helix:  0.16 (0.43), residues: 159
  sheet: -1.64 (0.36), residues: 219
  loop : -3.19 (0.20), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 480 
 HIS   0.008   0.001   HIS B 967 
 PHE   0.018   0.002   PHE A 418 
 TYR   0.021   0.003   TYR B 764 
 ARG   0.004   0.000   ARG A  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00558 (    5)
  link_NAG-ASN         : angle       2.94889 (   15)
  link_BETA1-4         : bond        0.00001 (    1)
  link_BETA1-4         : angle       1.25910 (    3)
  hydrogen bonds       : bond        0.04050 (  177)
  hydrogen bonds       : angle       5.26994 (  465)
  SS BOND              : bond        0.00688 (   16)
  SS BOND              : angle       2.14630 (   32)
  covalent geometry    : bond        0.00529 ( 7897)
  covalent geometry    : angle       0.76466 (10672)

*********************** 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
  109 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 MET cc_start: 0.8177 (ppp) cc_final: 0.7735 (ppp)
REVERT: B  691 CYS cc_start: 0.7758 (t) cc_final: 0.7476 (t)
REVERT: B  807 ILE cc_start: 0.8553 (mm) cc_final: 0.8243 (mt)
REVERT: B  895 ARG cc_start: 0.8003 (ttm170) cc_final: 0.7479 (ttm-80)
REVERT: B  898 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7226 (ptp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1731
  time to fit residues: 26.7062
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  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0970
   chunk 58 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 59 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
B 747 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.204888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.150421 restraints weight = 89234.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.148456 restraints weight = 52000.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.142962 restraints weight = 42690.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7919  Z= 0.120
  Angle     :  0.667   7.297  10722  Z= 0.335
  Chirality :  0.044   0.255   1197
  Planarity :  0.005   0.063   1357
  Dihedral  :  5.495  40.283   1198
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 12.92 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.52 %
    Favored  : 98.36 %
  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: -3.10 (0.24), residues: 1006
  helix:  0.43 (0.44), residues: 156
  sheet: -1.70 (0.35), residues: 224
  loop : -3.05 (0.20), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 480 
 HIS   0.007   0.001   HIS B 967 
 PHE   0.013   0.001   PHE A 197 
 TYR   0.013   0.001   TYR A 318 
 ARG   0.002   0.000   ARG B 865 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00531 (    5)
  link_NAG-ASN         : angle       2.67572 (   15)
  link_BETA1-4         : bond        0.00558 (    1)
  link_BETA1-4         : angle       1.23667 (    3)
  hydrogen bonds       : bond        0.03030 (  177)
  hydrogen bonds       : angle       4.92979 (  465)
  SS BOND              : bond        0.00532 (   16)
  SS BOND              : angle       1.87178 (   32)
  covalent geometry    : bond        0.00282 ( 7897)
  covalent geometry    : angle       0.65272 (10672)

*********************** 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
  107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A  499 MET cc_start: 0.5606 (tpt) cc_final: 0.5362 (tpp)
REVERT: B  807 ILE cc_start: 0.8454 (mm) cc_final: 0.8164 (mt)
REVERT: B  895 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7147 (ttm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1869
  time to fit residues: 28.2902
Evaluate side-chains
  89 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.0670
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0270
   chunk 65 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4083 r_free = 0.4083 target = 0.205939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.147456 restraints weight = 86705.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.150737 restraints weight = 51220.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.139992 restraints weight = 39897.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7919  Z= 0.120
  Angle     :  0.677  10.635  10722  Z= 0.338
  Chirality :  0.044   0.242   1197
  Planarity :  0.005   0.056   1357
  Dihedral  :  5.295  39.990   1198
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 13.02 %
    Favored  : 86.38 %
  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 (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: -3.04 (0.24), residues: 1006
  helix:  0.38 (0.43), residues: 160
  sheet: -1.50 (0.35), residues: 225
  loop : -3.07 (0.20), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP A 480 
 HIS   0.006   0.001   HIS B 967 
 PHE   0.014   0.001   PHE A 197 
 TYR   0.014   0.002   TYR B 919 
 ARG   0.002   0.000   ARG B 865 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00460 (    5)
  link_NAG-ASN         : angle       2.62029 (   15)
  link_BETA1-4         : bond        0.00462 (    1)
  link_BETA1-4         : angle       1.17727 (    3)
  hydrogen bonds       : bond        0.02991 (  177)
  hydrogen bonds       : angle       4.87552 (  465)
  SS BOND              : bond        0.00508 (   16)
  SS BOND              : angle       1.77208 (   32)
  covalent geometry    : bond        0.00283 ( 7897)
  covalent geometry    : angle       0.66382 (10672)

*********************** 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
  107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7467 (mtm110)
REVERT: A  499 MET cc_start: 0.5973 (tpt) cc_final: 0.5721 (tpp)
REVERT: B  691 CYS cc_start: 0.7471 (t) cc_final: 0.7131 (t)
REVERT: B  749 MET cc_start: 0.8971 (tpp) cc_final: 0.8769 (tpp)
REVERT: B  807 ILE cc_start: 0.8536 (mm) cc_final: 0.8214 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1767
  time to fit residues: 26.9242
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  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 81 optimal weight:    0.0870
   chunk 84 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.8762

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.205626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.144495 restraints weight = 87174.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.147362 restraints weight = 52456.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.139028 restraints weight = 44044.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7919  Z= 0.124
  Angle     :  0.672   9.844  10722  Z= 0.334
  Chirality :  0.044   0.247   1197
  Planarity :  0.005   0.054   1357
  Dihedral  :  5.246  39.224   1198
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 13.02 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.70 %
    Favored  : 99.18 %
  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: -2.99 (0.24), residues: 1006
  helix:  0.45 (0.44), residues: 160
  sheet: -1.50 (0.36), residues: 220
  loop : -3.03 (0.20), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A 480 
 HIS   0.006   0.001   HIS B 967 
 PHE   0.012   0.001   PHE A 225 
 TYR   0.015   0.001   TYR A 318 
 ARG   0.002   0.000   ARG B 865 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00459 (    5)
  link_NAG-ASN         : angle       2.59984 (   15)
  link_BETA1-4         : bond        0.00574 (    1)
  link_BETA1-4         : angle       1.18374 (    3)
  hydrogen bonds       : bond        0.03041 (  177)
  hydrogen bonds       : angle       4.78285 (  465)
  SS BOND              : bond        0.00526 (   16)
  SS BOND              : angle       1.74155 (   32)
  covalent geometry    : bond        0.00291 ( 7897)
  covalent geometry    : angle       0.65965 (10672)

*********************** 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
  102 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7398 (mtm110)
REVERT: A  499 MET cc_start: 0.5900 (tpt) cc_final: 0.5660 (tpp)
REVERT: B  691 CYS cc_start: 0.7420 (t) cc_final: 0.7114 (t)
REVERT: B  807 ILE cc_start: 0.8501 (mm) cc_final: 0.8219 (mt)
REVERT: B  894 TYR cc_start: 0.8696 (p90) cc_final: 0.8487 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1666
  time to fit residues: 24.5310
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  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.0020
   chunk 66 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 79 optimal weight:    0.1980
   chunk 8 optimal weight:    0.4980
   chunk 61 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 63 optimal weight:   20.0000
   chunk 84 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.4388

-------------------------------------------------------------------------------
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 = 0.4106 r_free = 0.4106 target = 0.208546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.151465 restraints weight = 87019.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.149582 restraints weight = 50495.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.145639 restraints weight = 43541.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7919  Z= 0.109
  Angle     :  0.659   9.781  10722  Z= 0.326
  Chirality :  0.044   0.246   1197
  Planarity :  0.005   0.056   1357
  Dihedral  :  5.042  37.298   1198
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 12.03 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.47 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.86 (0.24), residues: 1006
  helix:  0.51 (0.44), residues: 160
  sheet: -1.34 (0.36), residues: 216
  loop : -2.95 (0.20), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP A 480 
 HIS   0.005   0.001   HIS B 967 
 PHE   0.013   0.001   PHE A 197 
 TYR   0.017   0.001   TYR A 318 
 ARG   0.009   0.000   ARG A 241 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00503 (    5)
  link_NAG-ASN         : angle       2.54476 (   15)
  link_BETA1-4         : bond        0.00514 (    1)
  link_BETA1-4         : angle       1.20591 (    3)
  hydrogen bonds       : bond        0.02685 (  177)
  hydrogen bonds       : angle       4.82757 (  465)
  SS BOND              : bond        0.00467 (   16)
  SS BOND              : angle       1.85712 (   32)
  covalent geometry    : bond        0.00256 ( 7897)
  covalent geometry    : angle       0.64518 (10672)

********************** 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
  108 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7386 (mtm110)
REVERT: A  333 MET cc_start: 0.6851 (mtt) cc_final: 0.6010 (mtt)
REVERT: A  499 MET cc_start: 0.5811 (tpt) cc_final: 0.5568 (tpp)
REVERT: B  691 CYS cc_start: 0.7526 (t) cc_final: 0.7201 (t)
REVERT: B  807 ILE cc_start: 0.8496 (mm) cc_final: 0.8238 (mt)
REVERT: B  894 TYR cc_start: 0.8874 (p90) cc_final: 0.8354 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1685
  time to fit residues: 26.8620
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  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 10 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   overall best weight:    1.4584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.203792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.143745 restraints weight = 89613.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.142501 restraints weight = 52293.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.138480 restraints weight = 45713.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7919  Z= 0.162
  Angle     :  0.721   9.296  10722  Z= 0.362
  Chirality :  0.046   0.269   1197
  Planarity :  0.005   0.052   1357
  Dihedral  :  5.376  39.837   1198
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  : 14.51 %
    Favored  : 84.89 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.47 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.98 (0.24), residues: 1006
  helix:  0.39 (0.43), residues: 160
  sheet: -1.35 (0.37), residues: 215
  loop : -3.05 (0.20), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 480 
 HIS   0.006   0.001   HIS B 967 
 PHE   0.016   0.002   PHE A 225 
 TYR   0.019   0.002   TYR A 464 
 ARG   0.002   0.000   ARG B 865 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00395 (    5)
  link_NAG-ASN         : angle       2.57919 (   15)
  link_BETA1-4         : bond        0.00411 (    1)
  link_BETA1-4         : angle       1.16328 (    3)
  hydrogen bonds       : bond        0.03341 (  177)
  hydrogen bonds       : angle       4.93022 (  465)
  SS BOND              : bond        0.00589 (   16)
  SS BOND              : angle       2.24081 (   32)
  covalent geometry    : bond        0.00385 ( 7897)
  covalent geometry    : angle       0.70499 (10672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2852.11 seconds
wall clock time: 50 minutes 18.98 seconds (3018.98 seconds total)