Starting phenix.real_space_refine
on Thu Jul  2 03:19:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z4e_39762/07_2026/8z4e_39762.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z4e_39762/07_2026/8z4e_39762.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z4e_39762/07_2026/8z4e_39762.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z4e_39762/07_2026/8z4e_39762.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z4e_39762/07_2026/8z4e_39762.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z4e_39762/07_2026/8z4e_39762.cif"
  }
  resolution = 3.0
  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=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      39      5.16       5
     C    3979      2.51       5
     N    1074      2.21       5
     O    1234      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6327
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2631
          Classifications: {'peptide': 339}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 316}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 811
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 988
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
    Chain: "E"
      Number of atoms: 1024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1024
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 6, 'TRANS': 124}
    Chain: "F"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      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: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 0
          Ad-hoc single atom residues: {' CA': 1}
          Chain breaks: 1
  Time building chain proxies: 1.44, per 1000 atoms: 0.23
  Number of scatterers: 6327
  At special positions: 0
  Unit cell: (68.88, 97.58, 123.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      39     16.00
     O    1234      8.00
     N    1074      7.00
     C    3979      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS A 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 238 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 279 " - pdb=" SG  CYS A 292 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 290 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 319 " - pdb=" SG  CYS A 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 423 " - pdb=" SG  CYS A 449 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.03

  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 D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 201 "
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 444.7 milliseconds
  

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1482

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 16 sheets defined
      2.8% alpha, 39.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 4.007A  pdb=" N   THR C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.621A  pdb=" N   ASP E  31 " --> pdb=" O   LYS E  28 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 28 through 32'
    Processing helix  chain 'E' and resid 61 through 64
      removed outlier: 3.670A  pdb=" N   LYS E  64 " --> pdb=" O   ASP E  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 61 through 64'
    Processing helix  chain 'F' and resid 79 through 83
      removed outlier: 3.896A  pdb=" N   PHE F  83 " --> pdb=" O   PRO F  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 125
      removed outlier: 5.499A  pdb=" N   GLU A 119 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU A 134 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   CYS A 176 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   SER A 160 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   VAL A 174 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 185
      removed outlier: 4.102A  pdb=" N   SER A 180 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ALA A 204 " --> pdb=" O   GLU A 215 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLU A 215 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL A 206 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG A 211 " --> pdb=" O   TYR A 208 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 244
      removed outlier: 3.880A  pdb=" N   LYS A 265 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   LYS A 259 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   ILE A 263 " --> pdb=" O   LYS A 259 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 277 through 284
      removed outlier: 5.932A  pdb=" N   GLU A 278 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ARG A 293 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS A 292 " --> pdb=" O   PRO A 302 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 357
      removed outlier: 5.896A  pdb=" N   SER A 373 " --> pdb=" O   ASN A 400 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   ASN A 400 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   MET A 377 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   LEU A 396 " --> pdb=" O   MET A 377 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 411
    Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23
    Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 50
      removed outlier: 5.560A  pdb=" N   LEU B  48 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN B  39 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 50
      removed outlier: 5.560A  pdb=" N   LEU B  48 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN B  39 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12
      removed outlier: 8.315A  pdb=" N   TYR C  32 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ILE C  52 " --> pdb=" O   TYR C  32 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE C  34 " --> pdb=" O   GLY C  50 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLY C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 23
    Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 59
      removed outlier: 3.558A  pdb=" N   VAL E  48 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLY E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   MET E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ARG E  94 " --> pdb=" O   ASP E 101 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 57 through 59
      removed outlier: 3.558A  pdb=" N   VAL E  48 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLY E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   MET E  34 " --> pdb=" O   GLY E  50 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 7
      removed outlier: 3.976A  pdb=" N   ILE F  19 " --> pdb=" O   ILE F  75 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 12
      removed outlier: 7.021A  pdb=" N   LEU F  33 " --> pdb=" O   TYR F  49 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   TYR F  49 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    567 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: 0.75 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: 2030
        1.34 -     1.46: 1672
        1.46 -     1.59: 2730
        1.59 -     1.71: 0
        1.71 -     1.83: 52
  Bond restraints: 6484
  Sorted by residual:
  bond pdb=" C   THR A 392 "
       pdb=" N   SER A 393 "
    ideal  model  delta    sigma   weight residual
    1.332  1.297  0.035 1.40e-02 5.10e+03 6.30e+00
  bond pdb=" N   THR A 392 "
       pdb=" CA  THR A 392 "
    ideal  model  delta    sigma   weight residual
    1.458  1.473 -0.015 6.30e-03 2.52e+04 5.42e+00
  bond pdb=" CA  SER A 393 "
       pdb=" CB  SER A 393 "
    ideal  model  delta    sigma   weight residual
    1.530  1.499  0.032 1.69e-02 3.50e+03 3.50e+00
  bond pdb=" N   SER A 393 "
       pdb=" CA  SER A 393 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.021 1.29e-02 6.01e+03 2.60e+00
  bond pdb=" C   PRO A 391 "
       pdb=" O   PRO A 391 "
    ideal  model  delta    sigma   weight residual
    1.234  1.217  0.017 1.14e-02 7.69e+03 2.21e+00
  ... (remaining 6479 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 8547
        1.56 -     3.13: 229
        3.13 -     4.69: 24
        4.69 -     6.25: 6
        6.25 -     7.81: 3
  Bond angle restraints: 8809
  Sorted by residual:
  angle pdb=" C   PRO A 391 "
        pdb=" CA  PRO A 391 "
        pdb=" CB  PRO A 391 "
      ideal   model   delta    sigma   weight residual
     110.98  103.17    7.81 1.31e+00 5.83e-01 3.56e+01
  angle pdb=" C   THR A 392 "
        pdb=" CA  THR A 392 "
        pdb=" CB  THR A 392 "
      ideal   model   delta    sigma   weight residual
     116.54  123.52   -6.98 1.46e+00 4.69e-01 2.29e+01
  angle pdb=" C   SER A 393 "
        pdb=" N   TYR A 394 "
        pdb=" CA  TYR A 394 "
      ideal   model   delta    sigma   weight residual
     122.65  128.41   -5.76 1.49e+00 4.50e-01 1.49e+01
  angle pdb=" N   LEU A 100 "
        pdb=" CA  LEU A 100 "
        pdb=" C   LEU A 100 "
      ideal   model   delta    sigma   weight residual
     114.04  109.26    4.78 1.24e+00 6.50e-01 1.48e+01
  angle pdb=" N   PRO A 391 "
        pdb=" CA  PRO A 391 "
        pdb=" C   PRO A 391 "
      ideal   model   delta    sigma   weight residual
     111.38  117.17   -5.79 1.59e+00 3.96e-01 1.33e+01
  ... (remaining 8804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 3537
       17.43 -    34.86: 262
       34.86 -    52.30: 51
       52.30 -    69.73: 11
       69.73 -    87.16: 3
  Dihedral angle restraints: 3864
    sinusoidal: 1529
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" CB  CYS A 279 "
           pdb=" SG  CYS A 279 "
           pdb=" SG  CYS A 292 "
           pdb=" CB  CYS A 292 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.05   50.95     1      1.00e+01 1.00e-02 3.55e+01
  dihedral pdb=" CB  CYS A 423 "
           pdb=" SG  CYS A 423 "
           pdb=" SG  CYS A 449 "
           pdb=" CB  CYS A 449 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.33   40.67     1      1.00e+01 1.00e-02 2.32e+01
  dihedral pdb=" C   THR A 392 "
           pdb=" N   THR A 392 "
           pdb=" CA  THR A 392 "
           pdb=" CB  THR A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.80   11.80     0      2.50e+00 1.60e-01 2.23e+01
  ... (remaining 3861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 812
       0.062 -    0.125: 132
       0.125 -    0.187: 7
       0.187 -    0.250: 0
       0.250 -    0.312: 2
  Chirality restraints: 953
  Sorted by residual:
  chirality pdb=" CA  SER A 393 "
            pdb=" N   SER A 393 "
            pdb=" C   SER A 393 "
            pdb=" CB  SER A 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CA  THR A 392 "
            pdb=" N   THR A 392 "
            pdb=" C   THR A 392 "
            pdb=" CB  THR A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 201 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 950 not shown)

  Planarity restraints: 1131
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F  39 "   -0.042 5.00e-02 4.00e+02   6.35e-02 6.46e+00
        pdb=" N   PRO F  40 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO F  40 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO F  40 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 168 "    0.032 5.00e-02 4.00e+02   4.82e-02 3.71e+00
        pdb=" N   PRO A 169 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 169 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 169 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 392 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   THR A 392 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   THR A 392 "    0.012 2.00e-02 2.50e+03
        pdb=" N   SER A 393 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1128 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 898
        2.76 -     3.30: 5579
        3.30 -     3.83: 10393
        3.83 -     4.37: 11891
        4.37 -     4.90: 21360
  Nonbonded interactions: 50121
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  11 "
            pdb=" O   THR B 108 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OH  TYR B  32 "
            pdb=" OG  SER B  95 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER A 229 "
            pdb=" O   CYS A 279 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OH  TYR B  93 "
            pdb=" O   SER C 111 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG1 THR A 387 "
            pdb=" OE1 GLN A 388 "
     model   vdw
     2.274 3.040
  ... (remaining 50116 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.790
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.850
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:9.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6757
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   0.035   6498  Z= 0.146
  Angle     :  0.616   7.815   8839  Z= 0.346
  Chirality :  0.046   0.312    953
  Planarity :  0.005   0.064   1130
  Dihedral  : 12.618  87.159   2346
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.09 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.30), residues: 805
  helix: -1.48 (2.33), residues: 6
  sheet:  1.09 (0.30), residues: 313
  loop : -1.55 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 454 
 TYR   0.008   0.001   TYR F  86 
 PHE   0.008   0.001   PHE A 132 
 TRP   0.010   0.001   TRP B  37 
 HIS   0.005   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 ( 6484)
  covalent geometry    : angle       0.61108 /  0.34 ( 8809)
  SS BOND              : bond        0.00459 /  0.29 (   12)
  SS BOND              : angle       1.62686 /  1.35 (   24)
  hydrogen bonds       : bond        0.09536 /  5.96 (  201)
  hydrogen bonds       : angle       6.94040 /  4.93 (  567)
  link_BETA1-4         : bond        0.00218 /  0.11 (    1)
  link_BETA1-4         : angle       1.34418 /  0.69 (    3)
  link_NAG-ASN         : bond        0.00172 /  0.09 (    1)
  link_NAG-ASN         : angle       0.42911 /  0.22 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.6327 (p90) cc_final: 0.4792 (p90)
REVERT: A  327 SER cc_start: 0.7944 (p) cc_final: 0.7675 (t)
REVERT: A  357 ASP cc_start: 0.7460 (t0) cc_final: 0.7096 (t0)
REVERT: C   43 GLN cc_start: 0.7104 (mp10) cc_final: 0.6421 (mp10)
REVERT: C   98 ARG cc_start: 0.6896 (ttp-170) cc_final: 0.6657 (ttp-170)
REVERT: E   83 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7753 (mtmt)
REVERT: F    9 SER cc_start: 0.7361 (m) cc_final: 0.7000 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.4462
  time to fit residues: 48.6514
Evaluate side-chains
  95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 330 ASN
B  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.160081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.146171 restraints weight = 9354.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 2.61
r_work: 0.3863 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6498  Z= 0.233
  Angle     :  0.663   7.137   8839  Z= 0.341
  Chirality :  0.046   0.171    953
  Planarity :  0.006   0.053   1130
  Dihedral  :  4.791  28.468    931
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.20 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.29 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.29), residues: 805
  helix: -2.00 (1.97), residues: 6
  sheet:  1.13 (0.30), residues: 312
  loop : -1.67 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  18 
 TYR   0.022   0.002   TYR C 114 
 PHE   0.017   0.002   PHE F  98 
 TRP   0.013   0.001   TRP A 207 
 HIS   0.007   0.002   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.23 ( 6484)
  covalent geometry    : angle       0.65991 /  0.34 ( 8809)
  SS BOND              : bond        0.00537 /  0.32 (   12)
  SS BOND              : angle       1.45166 /  1.14 (   24)
  hydrogen bonds       : bond        0.03492 /  2.38 (  201)
  hydrogen bonds       : angle       6.10815 /  4.28 (  567)
  link_BETA1-4         : bond        0.00395 /  0.21 (    1)
  link_BETA1-4         : angle       0.64969 /  0.34 (    3)
  link_NAG-ASN         : bond        0.00019 /  0.01 (    1)
  link_NAG-ASN         : angle       0.49528 /  0.25 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7869 (p) cc_final: 0.7435 (m)
REVERT: A  209 ARG cc_start: 0.7621 (mtp-110) cc_final: 0.7411 (mtp180)
REVERT: A  211 ARG cc_start: 0.7232 (ptt-90) cc_final: 0.6939 (ptt-90)
REVERT: A  353 PHE cc_start: 0.8151 (p90) cc_final: 0.7786 (p90)
REVERT: A  426 VAL cc_start: 0.6774 (t) cc_final: 0.6513 (p)
REVERT: B  112 GLN cc_start: 0.7246 (pp30) cc_final: 0.6956 (pp30)
REVERT: C   98 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.7150 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8075 (mtmt)
  outliers start: 13
  outliers final: 6
  residues processed: 107
  average time/residue: 0.3898
  time to fit residues: 44.3740
Evaluate side-chains
  105 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  445 MET
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue  108 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.1980
   chunk 62 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0770
   chunk 8 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.2736

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C   6 GLN
F   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.162846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.148980 restraints weight = 9197.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 2.61
r_work: 0.3900 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
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      :  0.002   0.027   6498  Z= 0.104
  Angle     :  0.555   6.732   8839  Z= 0.284
  Chirality :  0.043   0.148    953
  Planarity :  0.005   0.060   1130
  Dihedral  :  4.305  21.475    931
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  4.72 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.35 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.30), residues: 805
  helix: -1.87 (2.05), residues: 6
  sheet:  1.16 (0.29), residues: 322
  loop : -1.54 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  18 
 TYR   0.021   0.001   TYR A 375 
 PHE   0.006   0.001   PHE A 132 
 TRP   0.009   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 313 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.10 ( 6484)
  covalent geometry    : angle       0.55294 /  0.28 ( 8809)
  SS BOND              : bond        0.00272 /  0.17 (   12)
  SS BOND              : angle       0.97390 /  0.74 (   24)
  hydrogen bonds       : bond        0.02815 /  1.99 (  201)
  hydrogen bonds       : angle       5.73973 /  3.99 (  567)
  link_BETA1-4         : bond        0.00356 /  0.19 (    1)
  link_BETA1-4         : angle       0.99340 /  0.53 (    3)
  link_NAG-ASN         : bond        0.00048 /  0.03 (    1)
  link_NAG-ASN         : angle       0.41488 /  0.22 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   94 VAL cc_start: 0.7766 (p) cc_final: 0.7295 (m)
REVERT: A  327 SER cc_start: 0.8313 (p) cc_final: 0.8018 (t)
REVERT: A  353 PHE cc_start: 0.8110 (p90) cc_final: 0.7747 (p90)
REVERT: A  357 ASP cc_start: 0.7904 (t0) cc_final: 0.7436 (t0)
REVERT: B  112 GLN cc_start: 0.6959 (pp30) cc_final: 0.6583 (pp30)
REVERT: C   43 GLN cc_start: 0.7318 (mp10) cc_final: 0.6550 (mp10)
REVERT: C   98 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.7182 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7975 (mtmt)
REVERT: F   17 ASP cc_start: 0.7153 (m-30) cc_final: 0.6931 (m-30)
  outliers start: 15
  outliers final: 8
  residues processed: 99
  average time/residue: 0.3748
  time to fit residues: 39.6873
Evaluate side-chains
  99 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue  108 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0670
   chunk 75 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7522

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 HIS
F   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.159409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.145112 restraints weight = 9311.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.68
r_work: 0.3829 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6498  Z= 0.186
  Angle     :  0.611   8.329   8839  Z= 0.310
  Chirality :  0.045   0.160    953
  Planarity :  0.006   0.062   1130
  Dihedral  :  4.586  17.867    931
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.33 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.08 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.30), residues: 805
  helix: -2.11 (1.90), residues: 6
  sheet:  1.12 (0.29), residues: 323
  loop : -1.59 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  18 
 TYR   0.022   0.002   TYR C 114 
 PHE   0.013   0.002   PHE F  98 
 TRP   0.011   0.001   TRP A 207 
 HIS   0.005   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.19 ( 6484)
  covalent geometry    : angle       0.60716 /  0.31 ( 8809)
  SS BOND              : bond        0.00430 /  0.25 (   12)
  SS BOND              : angle       1.42948 /  1.05 (   24)
  hydrogen bonds       : bond        0.03153 /  2.18 (  201)
  hydrogen bonds       : angle       5.81566 /  4.05 (  567)
  link_BETA1-4         : bond        0.00267 /  0.14 (    1)
  link_BETA1-4         : angle       0.78652 /  0.41 (    3)
  link_NAG-ASN         : bond        0.00142 /  0.07 (    1)
  link_NAG-ASN         : angle       0.52785 /  0.28 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   94 VAL cc_start: 0.7888 (p) cc_final: 0.7443 (m)
REVERT: A  293 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.6553 (ptp-170)
REVERT: A  310 MET cc_start: 0.6398 (mmp) cc_final: 0.6169 (mmp)
REVERT: A  324 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7755 (p)
REVERT: A  327 SER cc_start: 0.8294 (p) cc_final: 0.7994 (t)
REVERT: A  353 PHE cc_start: 0.8273 (p90) cc_final: 0.7677 (p90)
REVERT: A  357 ASP cc_start: 0.7896 (t0) cc_final: 0.7435 (t0)
REVERT: B  112 GLN cc_start: 0.7401 (pp30) cc_final: 0.7140 (pp30)
REVERT: C   43 GLN cc_start: 0.7367 (mp10) cc_final: 0.6548 (mp10)
REVERT: C   48 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6586 (ttp)
REVERT: C   98 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.7196 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8248 (mtmt) cc_final: 0.8013 (mtmt)
REVERT: F   75 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.6360 (mt)
  outliers start: 19
  outliers final: 7
  residues processed: 108
  average time/residue: 0.4658
  time to fit residues: 53.3112
Evaluate side-chains
  111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue  108 LEU
Chi-restraints excluded: chain F residue   75 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 HIS
F   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.159207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.144857 restraints weight = 9334.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.70
r_work: 0.3832 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6498  Z= 0.181
  Angle     :  0.610   6.453   8839  Z= 0.310
  Chirality :  0.045   0.166    953
  Planarity :  0.005   0.054   1130
  Dihedral  :  4.646  18.524    931
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.09 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 15.67 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  1.04 (0.29), residues: 329
  loop : -1.53 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  18 
 TYR   0.023   0.002   TYR C 114 
 PHE   0.013   0.001   PHE F  98 
 TRP   0.011   0.001   TRP A 207 
 HIS   0.005   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.18 ( 6484)
  covalent geometry    : angle       0.60417 /  0.31 ( 8809)
  SS BOND              : bond        0.00409 /  0.22 (   12)
  SS BOND              : angle       1.77744 /  1.08 (   24)
  hydrogen bonds       : bond        0.03092 /  2.17 (  201)
  hydrogen bonds       : angle       5.79791 /  4.03 (  567)
  link_BETA1-4         : bond        0.00143 /  0.08 (    1)
  link_BETA1-4         : angle       0.82761 /  0.44 (    3)
  link_NAG-ASN         : bond        0.00111 /  0.06 (    1)
  link_NAG-ASN         : angle       0.49660 /  0.26 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   94 VAL cc_start: 0.7933 (p) cc_final: 0.7494 (m)
REVERT: A  293 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.6546 (ptp-170)
REVERT: A  310 MET cc_start: 0.6364 (mmp) cc_final: 0.6132 (mmp)
REVERT: A  324 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7759 (p)
REVERT: A  327 SER cc_start: 0.8300 (p) cc_final: 0.7994 (t)
REVERT: A  353 PHE cc_start: 0.8244 (p90) cc_final: 0.7716 (p90)
REVERT: A  357 ASP cc_start: 0.7880 (t0) cc_final: 0.7398 (t0)
REVERT: B  112 GLN cc_start: 0.7271 (pp30) cc_final: 0.7063 (pp30)
REVERT: C    6 GLN cc_start: 0.8298 (mt0) cc_final: 0.8056 (mt0)
REVERT: C   43 GLN cc_start: 0.7450 (mp10) cc_final: 0.6593 (mp10)
REVERT: C   48 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6605 (mtp)
REVERT: C   98 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.7167 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7983 (mtmt)
  outliers start: 23
  outliers final: 11
  residues processed: 114
  average time/residue: 0.4054
  time to fit residues: 49.1781
Evaluate side-chains
  116 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue  108 LEU
Chi-restraints excluded: chain F residue   19 ILE
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0570
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 HIS
F   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.159147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.145183 restraints weight = 9237.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.56
r_work: 0.3842 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6498  Z= 0.152
  Angle     :  0.594   6.562   8839  Z= 0.301
  Chirality :  0.045   0.154    953
  Planarity :  0.005   0.050   1130
  Dihedral  :  4.544  16.833    931
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.08 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.11 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  1.03 (0.28), residues: 329
  loop : -1.54 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  18 
 TYR   0.019   0.002   TYR C 114 
 PHE   0.010   0.001   PHE F  98 
 TRP   0.010   0.001   TRP B  37 
 HIS   0.004   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 ( 6484)
  covalent geometry    : angle       0.59044 /  0.30 ( 8809)
  SS BOND              : bond        0.00354 /  0.20 (   12)
  SS BOND              : angle       1.41722 /  0.94 (   24)
  hydrogen bonds       : bond        0.02987 /  2.12 (  201)
  hydrogen bonds       : angle       5.74165 /  3.99 (  567)
  link_BETA1-4         : bond        0.00239 /  0.13 (    1)
  link_BETA1-4         : angle       0.90859 /  0.48 (    3)
  link_NAG-ASN         : bond        0.00075 /  0.04 (    1)
  link_NAG-ASN         : angle       0.44769 /  0.24 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7955 (p) cc_final: 0.7521 (m)
REVERT: A  310 MET cc_start: 0.6260 (mmp) cc_final: 0.6032 (mmp)
REVERT: A  324 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7712 (p)
REVERT: A  327 SER cc_start: 0.8231 (p) cc_final: 0.7947 (t)
REVERT: A  353 PHE cc_start: 0.8187 (p90) cc_final: 0.7608 (p90)
REVERT: C    6 GLN cc_start: 0.8281 (mt0) cc_final: 0.8042 (mt0)
REVERT: C   43 GLN cc_start: 0.7365 (mp10) cc_final: 0.6617 (mp10)
REVERT: C   48 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6552 (mtp)
REVERT: C   98 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.7155 (ttp-170)
REVERT: E   66 ARG cc_start: 0.6695 (ptt90) cc_final: 0.6410 (ptt180)
REVERT: E   83 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7956 (mtmt)
  outliers start: 22
  outliers final: 14
  residues processed: 110
  average time/residue: 0.3905
  time to fit residues: 45.8711
Evaluate side-chains
  116 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  231 CYS
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue  108 LEU
Chi-restraints excluded: chain F residue   19 ILE
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0040
   chunk 45 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.4592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.160344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.146370 restraints weight = 9200.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 2.57
r_work: 0.3844 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6498  Z= 0.130
  Angle     :  0.626  14.422   8839  Z= 0.305
  Chirality :  0.046   0.414    953
  Planarity :  0.005   0.049   1130
  Dihedral  :  4.406  16.319    931
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.09 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.85 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.98 (0.28), residues: 333
  loop : -1.50 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  18 
 TYR   0.019   0.001   TYR C 103 
 PHE   0.009   0.001   PHE F  98 
 TRP   0.009   0.001   TRP B  37 
 HIS   0.003   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 6484)
  covalent geometry    : angle       0.62381 /  0.30 ( 8809)
  SS BOND              : bond        0.00299 /  0.18 (   12)
  SS BOND              : angle       1.22278 /  0.87 (   24)
  hydrogen bonds       : bond        0.02914 /  2.09 (  201)
  hydrogen bonds       : angle       5.60574 /  3.91 (  567)
  link_BETA1-4         : bond        0.00299 /  0.16 (    1)
  link_BETA1-4         : angle       0.97582 /  0.51 (    3)
  link_NAG-ASN         : bond        0.00062 /  0.03 (    1)
  link_NAG-ASN         : angle       0.41927 /  0.23 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7907 (p) cc_final: 0.7491 (m)
REVERT: A  131 MET cc_start: 0.6725 (tpt) cc_final: 0.6471 (tpt)
REVERT: A  293 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8196 (ptm160)
REVERT: A  310 MET cc_start: 0.6313 (mmp) cc_final: 0.6071 (mmp)
REVERT: A  324 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7646 (p)
REVERT: A  327 SER cc_start: 0.8270 (p) cc_final: 0.7978 (t)
REVERT: A  353 PHE cc_start: 0.8201 (p90) cc_final: 0.7629 (p90)
REVERT: C    6 GLN cc_start: 0.8290 (mt0) cc_final: 0.8045 (mt0)
REVERT: C   43 GLN cc_start: 0.7417 (mp10) cc_final: 0.6637 (mp10)
REVERT: C   48 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6534 (mtp)
REVERT: C   98 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7154 (ttp-170)
REVERT: E   66 ARG cc_start: 0.6675 (ptt90) cc_final: 0.6374 (ptt90)
REVERT: E   83 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7926 (mtmt)
  outliers start: 19
  outliers final: 13
  residues processed: 110
  average time/residue: 0.4025
  time to fit residues: 47.2430
Evaluate side-chains
  116 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  231 CYS
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  112 GLN
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain E residue   69 VAL
Chi-restraints excluded: chain E residue  108 LEU
Chi-restraints excluded: chain F residue   19 ILE
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0870
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 58 optimal weight:    0.1980
   chunk 73 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.4358

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.160470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.146525 restraints weight = 9173.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.55
r_work: 0.3860 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6498  Z= 0.126
  Angle     :  0.612  12.389   8839  Z= 0.301
  Chirality :  0.045   0.293    953
  Planarity :  0.005   0.072   1130
  Dihedral  :  4.382  15.904    931
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.09 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.58 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.99 (0.28), residues: 333
  loop : -1.48 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  18 
 TYR   0.015   0.001   TYR C 114 
 PHE   0.008   0.001   PHE F  98 
 TRP   0.009   0.001   TRP B  37 
 HIS   0.003   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 6484)
  covalent geometry    : angle       0.60783 /  0.30 ( 8809)
  SS BOND              : bond        0.00369 /  0.21 (   12)
  SS BOND              : angle       1.46585 /  1.10 (   24)
  hydrogen bonds       : bond        0.02850 /  2.06 (  201)
  hydrogen bonds       : angle       5.53287 /  3.85 (  567)
  link_BETA1-4         : bond        0.00239 /  0.13 (    1)
  link_BETA1-4         : angle       0.95223 /  0.50 (    3)
  link_NAG-ASN         : bond        0.00031 /  0.02 (    1)
  link_NAG-ASN         : angle       0.41828 /  0.23 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7904 (p) cc_final: 0.7496 (m)
REVERT: A  131 MET cc_start: 0.6667 (tpt) cc_final: 0.6432 (tpt)
REVERT: A  158 LEU cc_start: 0.8031 (tp) cc_final: 0.7735 (tp)
REVERT: A  191 MET cc_start: 0.7712 (ttp) cc_final: 0.7235 (ttp)
REVERT: A  324 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7632 (p)
REVERT: A  327 SER cc_start: 0.8226 (p) cc_final: 0.7951 (t)
REVERT: A  353 PHE cc_start: 0.8180 (p90) cc_final: 0.7636 (p90)
REVERT: C    6 GLN cc_start: 0.8276 (mt0) cc_final: 0.8043 (mt0)
REVERT: C   43 GLN cc_start: 0.7427 (mp10) cc_final: 0.6703 (mp10)
REVERT: C   48 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6522 (mtp)
REVERT: C   98 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7189 (ttp-170)
REVERT: E   66 ARG cc_start: 0.6717 (ptt90) cc_final: 0.6387 (ptt90)
REVERT: E   83 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7904 (mtmt)
REVERT: F    6 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.5887 (pt0)
  outliers start: 18
  outliers final: 12
  residues processed: 108
  average time/residue: 0.3903
  time to fit residues: 45.2381
Evaluate side-chains
  115 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  231 CYS
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue  108 LEU
Chi-restraints excluded: chain F residue    6 GLN
Chi-restraints excluded: chain F residue   19 ILE
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0670
   chunk 71 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.159647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.145592 restraints weight = 9309.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.58
r_work: 0.3834 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6498  Z= 0.160
  Angle     :  0.641  11.069   8839  Z= 0.314
  Chirality :  0.047   0.303    953
  Planarity :  0.005   0.072   1130
  Dihedral  :  4.501  16.597    931
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.45 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.87 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.97 (0.28), residues: 333
  loop : -1.52 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  18 
 TYR   0.019   0.002   TYR C 114 
 PHE   0.009   0.001   PHE A 410 
 TRP   0.011   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.16 ( 6484)
  covalent geometry    : angle       0.63655 /  0.31 ( 8809)
  SS BOND              : bond        0.00402 /  0.23 (   12)
  SS BOND              : angle       1.62052 /  1.21 (   24)
  hydrogen bonds       : bond        0.03015 /  2.15 (  201)
  hydrogen bonds       : angle       5.57289 /  3.89 (  567)
  link_BETA1-4         : bond        0.00256 /  0.13 (    1)
  link_BETA1-4         : angle       0.94175 /  0.49 (    3)
  link_NAG-ASN         : bond        0.00066 /  0.03 (    1)
  link_NAG-ASN         : angle       0.48760 /  0.26 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7967 (p) cc_final: 0.7550 (m)
REVERT: A  131 MET cc_start: 0.6715 (tpt) cc_final: 0.6486 (tpt)
REVERT: A  293 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.6296 (ptp-170)
REVERT: A  324 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7645 (p)
REVERT: A  327 SER cc_start: 0.8243 (p) cc_final: 0.7955 (t)
REVERT: A  353 PHE cc_start: 0.8238 (p90) cc_final: 0.7667 (p90)
REVERT: C    6 GLN cc_start: 0.8292 (mt0) cc_final: 0.8046 (mt0)
REVERT: C   43 GLN cc_start: 0.7420 (mp10) cc_final: 0.6650 (mp10)
REVERT: C   48 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6548 (mtp)
REVERT: C   98 ARG cc_start: 0.7499 (ttp-170) cc_final: 0.7166 (ttp-170)
REVERT: E   66 ARG cc_start: 0.6740 (ptt90) cc_final: 0.6395 (ptt180)
REVERT: E   83 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7944 (mtmt)
REVERT: F    6 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5987 (pt0)
  outliers start: 18
  outliers final: 13
  residues processed: 109
  average time/residue: 0.4229
  time to fit residues: 49.0731
Evaluate side-chains
  119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  231 CYS
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue  108 LEU
Chi-restraints excluded: chain F residue    6 GLN
Chi-restraints excluded: chain F residue   19 ILE
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 HIS
A 234 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.159375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.145326 restraints weight = 9233.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.64
r_work: 0.3835 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6498  Z= 0.184
  Angle     :  0.672  10.188   8839  Z= 0.332
  Chirality :  0.047   0.295    953
  Planarity :  0.005   0.073   1130
  Dihedral  :  4.631  17.343    931
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.45 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 19.30 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.94 (0.28), residues: 333
  loop : -1.53 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  82 
 TYR   0.020   0.002   TYR C 114 
 PHE   0.010   0.001   PHE A 410 
 TRP   0.012   0.001   TRP A 207 
 HIS   0.005   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.18 ( 6484)
  covalent geometry    : angle       0.66661 /  0.33 ( 8809)
  SS BOND              : bond        0.00399 /  0.23 (   12)
  SS BOND              : angle       1.72113 /  1.28 (   24)
  hydrogen bonds       : bond        0.03133 /  2.23 (  201)
  hydrogen bonds       : angle       5.63529 /  3.93 (  567)
  link_BETA1-4         : bond        0.00216 /  0.11 (    1)
  link_BETA1-4         : angle       0.92827 /  0.49 (    3)
  link_NAG-ASN         : bond        0.00125 /  0.07 (    1)
  link_NAG-ASN         : angle       0.61425 /  0.33 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7969 (p) cc_final: 0.7568 (m)
REVERT: A  131 MET cc_start: 0.6703 (tpt) cc_final: 0.6457 (tpt)
REVERT: A  191 MET cc_start: 0.7726 (ttp) cc_final: 0.7155 (ttp)
REVERT: A  262 LYS cc_start: 0.7006 (tmtt) cc_final: 0.6779 (tmtt)
REVERT: A  293 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.6334 (ptp-170)
REVERT: A  324 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7680 (p)
REVERT: A  327 SER cc_start: 0.8251 (p) cc_final: 0.7971 (t)
REVERT: A  353 PHE cc_start: 0.8264 (p90) cc_final: 0.7697 (p90)
REVERT: C    6 GLN cc_start: 0.8294 (mt0) cc_final: 0.8038 (mt0)
REVERT: C   43 GLN cc_start: 0.7430 (mp10) cc_final: 0.6615 (mp10)
REVERT: C   48 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6637 (mtp)
REVERT: C   98 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.7147 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7926 (mtmt)
REVERT: F    6 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.6032 (pt0)
  outliers start: 19
  outliers final: 14
  residues processed: 110
  average time/residue: 0.4024
  time to fit residues: 47.1271
Evaluate side-chains
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  231 CYS
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain E residue   69 VAL
Chi-restraints excluded: chain E residue  108 LEU
Chi-restraints excluded: chain F residue    6 GLN
Chi-restraints excluded: chain F residue   19 ILE
Chi-restraints excluded: chain F residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0270
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.160565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.146196 restraints weight = 9380.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.70
r_work: 0.3842 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6498  Z= 0.129
  Angle     :  0.637   9.536   8839  Z= 0.314
  Chirality :  0.045   0.243    953
  Planarity :  0.005   0.070   1130
  Dihedral  :  4.433  16.185    931
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.96 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.45 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  1.05 (0.28), residues: 320
  loop : -1.49 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  18 
 TYR   0.015   0.001   TYR C 114 
 PHE   0.007   0.001   PHE A 410 
 TRP   0.010   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 6484)
  covalent geometry    : angle       0.63370 /  0.31 ( 8809)
  SS BOND              : bond        0.00301 /  0.19 (   12)
  SS BOND              : angle       1.42801 /  1.09 (   24)
  hydrogen bonds       : bond        0.02880 /  2.10 (  201)
  hydrogen bonds       : angle       5.50180 /  3.84 (  567)
  link_BETA1-4         : bond        0.00320 /  0.17 (    1)
  link_BETA1-4         : angle       1.03455 /  0.54 (    3)
  link_NAG-ASN         : bond        0.00077 /  0.04 (    1)
  link_NAG-ASN         : angle       0.46926 /  0.26 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1886.08 seconds
wall clock time: 33 minutes 6.26 seconds (1986.26 seconds total)