Starting phenix.real_space_refine
on Sat May 10 12:43:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z4e_39762/05_2025/8z4e_39762.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z4e_39762/05_2025/8z4e_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_39762/05_2025/8z4e_39762.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z4e_39762/05_2025/8z4e_39762.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z4e_39762/05_2025/8z4e_39762.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z4e_39762/05_2025/8z4e_39762.cif"
  }
  resolution = 3.0
  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=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.15, per 1000 atoms: 0.66
  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: 1.61
  Conformation dependent library (CDL) restraints added in 796.2 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: 0.85
  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: 1.88

  Time building geometry restraints manager: 1.89 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:             1.810
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.830
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (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
 TRP   0.010   0.001   TRP B  37 
 HIS   0.005   0.001   HIS A  98 
 PHE   0.008   0.001   PHE A 132 
 TYR   0.008   0.001   TYR F  86 
 ARG   0.004   0.000   ARG A 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00172 (    1)
  link_NAG-ASN         : angle       0.42911 (    3)
  link_BETA1-4         : bond        0.00218 (    1)
  link_BETA1-4         : angle       1.34418 (    3)
  hydrogen bonds       : bond        0.09536 (  201)
  hydrogen bonds       : angle       6.94040 (  567)
  SS BOND              : bond        0.00459 (   12)
  SS BOND              : angle       1.62686 (   24)
  covalent geometry    : bond        0.00283 ( 6484)
  covalent geometry    : angle       0.61108 ( 8809)

*********************** 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  : 0.680 
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: 0.9458
  time to fit residues: 103.6201
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  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    0.1980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  40 GLN
C   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.161409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.147983 restraints weight = 9121.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 2.50
r_work: 0.3880 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6498  Z= 0.195
  Angle     :  0.626   7.155   8839  Z= 0.323
  Chirality :  0.046   0.166    953
  Planarity :  0.006   0.052   1130
  Dihedral  :  4.626  30.271    931
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 8.32
  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 : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.30), residues: 805
  helix: -1.95 (1.98), residues: 6
  sheet:  1.07 (0.30), residues: 324
  loop : -1.63 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  37 
 HIS   0.006   0.002   HIS A 185 
 PHE   0.014   0.002   PHE F  98 
 TYR   0.018   0.002   TYR C 114 
 ARG   0.004   0.001   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00015 (    1)
  link_NAG-ASN         : angle       0.33001 (    3)
  link_BETA1-4         : bond        0.00305 (    1)
  link_BETA1-4         : angle       0.78572 (    3)
  hydrogen bonds       : bond        0.03261 (  201)
  hydrogen bonds       : angle       6.05043 (  567)
  SS BOND              : bond        0.00516 (   12)
  SS BOND              : angle       1.35899 (   24)
  covalent geometry    : bond        0.00454 ( 6484)
  covalent geometry    : angle       0.62327 ( 8809)

*********************** 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
  118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7818 (p) cc_final: 0.7376 (m)
REVERT: A  211 ARG cc_start: 0.7238 (ptt-90) cc_final: 0.6929 (ptt-90)
REVERT: A  327 SER cc_start: 0.8260 (p) cc_final: 0.8015 (t)
REVERT: B  112 GLN cc_start: 0.6947 (pp30) cc_final: 0.6616 (pp30)
REVERT: C    6 GLN cc_start: 0.8188 (mt0) cc_final: 0.7921 (mt0)
REVERT: C   98 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.7173 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8275 (mtmt) cc_final: 0.8023 (mtmt)
  outliers start: 13
  outliers final: 6
  residues processed: 106
  average time/residue: 0.9725
  time to fit residues: 109.7627
Evaluate side-chains
  107 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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 4 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4133 r_free = 0.4133 target = 0.159847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.145742 restraints weight = 9265.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 2.61
r_work: 0.3853 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6498  Z= 0.186
  Angle     :  0.607   6.543   8839  Z= 0.310
  Chirality :  0.045   0.155    953
  Planarity :  0.006   0.059   1130
  Dihedral  :  4.624  17.557    931
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.46 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.50 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  1.10 (0.29), residues: 322
  loop : -1.64 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 207 
 HIS   0.005   0.001   HIS A 185 
 PHE   0.016   0.002   PHE A 353 
 TYR   0.023   0.002   TYR A 375 
 ARG   0.005   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00097 (    1)
  link_NAG-ASN         : angle       0.44141 (    3)
  link_BETA1-4         : bond        0.00048 (    1)
  link_BETA1-4         : angle       0.77590 (    3)
  hydrogen bonds       : bond        0.03191 (  201)
  hydrogen bonds       : angle       5.89363 (  567)
  SS BOND              : bond        0.00393 (   12)
  SS BOND              : angle       1.33383 (   24)
  covalent geometry    : bond        0.00433 ( 6484)
  covalent geometry    : angle       0.60379 ( 8809)

*********************** 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
  117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   94 VAL cc_start: 0.7907 (p) cc_final: 0.7453 (m)
REVERT: A  293 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.6532 (ptp-170)
REVERT: A  310 MET cc_start: 0.6387 (mmp) cc_final: 0.6130 (mmp)
REVERT: A  315 SER cc_start: 0.8702 (m) cc_final: 0.8249 (t)
REVERT: A  327 SER cc_start: 0.8268 (p) cc_final: 0.8029 (t)
REVERT: A  353 PHE cc_start: 0.8168 (p90) cc_final: 0.7770 (p90)
REVERT: A  357 ASP cc_start: 0.7917 (t0) cc_final: 0.7451 (t0)
REVERT: B  112 GLN cc_start: 0.7336 (pp30) cc_final: 0.7084 (pp30)
REVERT: C    6 GLN cc_start: 0.8243 (mt0) cc_final: 0.8021 (mt0)
REVERT: C   43 GLN cc_start: 0.7347 (mp10) cc_final: 0.6534 (mp10)
REVERT: C   98 ARG cc_start: 0.7497 (ttp-170) cc_final: 0.7165 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8266 (mtmt) cc_final: 0.8026 (mtmt)
REVERT: E   86 ASP cc_start: 0.6857 (t0) cc_final: 0.6602 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 104
  average time/residue: 0.9168
  time to fit residues: 101.6259
Evaluate side-chains
  109 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  228 GLU
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   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 57 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 74 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0670
   chunk 66 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
F   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.160381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.146279 restraints weight = 9281.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 2.64
r_work: 0.3845 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.2317

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= 0.139
  Angle     :  0.575   6.321   8839  Z= 0.294
  Chirality :  0.044   0.150    953
  Planarity :  0.005   0.050   1130
  Dihedral  :  4.466  18.993    931
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.09 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.80 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  1.10 (0.29), residues: 323
  loop : -1.58 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  37 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.010   0.001   PHE F  98 
 TYR   0.018   0.001   TYR C 114 
 ARG   0.004   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       0.42404 (    3)
  link_BETA1-4         : bond        0.00040 (    1)
  link_BETA1-4         : angle       0.77901 (    3)
  hydrogen bonds       : bond        0.02878 (  201)
  hydrogen bonds       : angle       5.74452 (  567)
  SS BOND              : bond        0.00329 (   12)
  SS BOND              : angle       1.24316 (   24)
  covalent geometry    : bond        0.00326 ( 6484)
  covalent geometry    : angle       0.57243 ( 8809)

*********************** 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
  111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7881 (p) cc_final: 0.7436 (m)
REVERT: A  191 MET cc_start: 0.7801 (ttp) cc_final: 0.7185 (tmm)
REVERT: A  310 MET cc_start: 0.6384 (mmp) cc_final: 0.6170 (mmp)
REVERT: A  324 THR cc_start: 0.8131 (p) cc_final: 0.7750 (p)
REVERT: A  327 SER cc_start: 0.8260 (p) cc_final: 0.8017 (t)
REVERT: A  353 PHE cc_start: 0.8200 (p90) cc_final: 0.7700 (p90)
REVERT: B  112 GLN cc_start: 0.7131 (pp30) cc_final: 0.6821 (pp30)
REVERT: C   43 GLN cc_start: 0.7340 (mp10) cc_final: 0.6534 (mp10)
REVERT: C   48 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6606 (mtp)
REVERT: C   98 ARG cc_start: 0.7489 (ttp-170) cc_final: 0.7156 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8275 (mtmt) cc_final: 0.8036 (mtmt)
  outliers start: 17
  outliers final: 9
  residues processed: 100
  average time/residue: 0.8527
  time to fit residues: 91.2756
Evaluate side-chains
  102 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
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  215 GLU
Chi-restraints excluded: chain A residue  292 CYS
Chi-restraints excluded: chain A residue  377 MET
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   19 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 48 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS
A 136 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.158665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.144749 restraints weight = 9204.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.55
r_work: 0.3820 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6498  Z= 0.218
  Angle     :  0.630   6.754   8839  Z= 0.322
  Chirality :  0.046   0.165    953
  Planarity :  0.006   0.064   1130
  Dihedral  :  4.782  18.077    931
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.20 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.80 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.30), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.95 (0.29), residues: 335
  loop : -1.57 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 207 
 HIS   0.006   0.001   HIS A 185 
 PHE   0.017   0.002   PHE F  98 
 TYR   0.026   0.002   TYR C 114 
 ARG   0.006   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    1)
  link_NAG-ASN         : angle       0.58379 (    3)
  link_BETA1-4         : bond        0.00191 (    1)
  link_BETA1-4         : angle       0.86098 (    3)
  hydrogen bonds       : bond        0.03273 (  201)
  hydrogen bonds       : angle       5.88811 (  567)
  SS BOND              : bond        0.00646 (   12)
  SS BOND              : angle       1.95021 (   24)
  covalent geometry    : bond        0.00509 ( 6484)
  covalent geometry    : angle       0.62266 ( 8809)

*********************** 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
  129 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.8002 (p) cc_final: 0.7581 (m)
REVERT: A  262 LYS cc_start: 0.6974 (tmtt) cc_final: 0.6716 (tmtt)
REVERT: A  293 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.6554 (ptp-170)
REVERT: A  310 MET cc_start: 0.6311 (mmp) cc_final: 0.6095 (mmp)
REVERT: A  324 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7771 (p)
REVERT: A  327 SER cc_start: 0.8259 (p) cc_final: 0.8022 (t)
REVERT: A  353 PHE cc_start: 0.8202 (p90) cc_final: 0.7633 (p90)
REVERT: C   43 GLN cc_start: 0.7423 (mp10) cc_final: 0.6573 (mp10)
REVERT: C   48 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6627 (ttp)
REVERT: C   98 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.7139 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8272 (mtmt) cc_final: 0.8014 (mtmt)
  outliers start: 22
  outliers final: 11
  residues processed: 113
  average time/residue: 0.9163
  time to fit residues: 110.1339
Evaluate side-chains
  117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
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  215 GLU
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   20 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 45 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0060
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS
C   6 GLN
F   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.159847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.146105 restraints weight = 9074.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.51
r_work: 0.3836 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6498  Z= 0.147
  Angle     :  0.599   7.166   8839  Z= 0.301
  Chirality :  0.045   0.153    953
  Planarity :  0.005   0.056   1130
  Dihedral  :  4.571  17.294    931
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.71 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.55 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.89 (0.28), residues: 339
  loop : -1.56 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  37 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.010   0.001   PHE F  98 
 TYR   0.018   0.001   TYR C 114 
 ARG   0.004   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00088 (    1)
  link_NAG-ASN         : angle       0.43735 (    3)
  link_BETA1-4         : bond        0.00251 (    1)
  link_BETA1-4         : angle       0.91171 (    3)
  hydrogen bonds       : bond        0.02944 (  201)
  hydrogen bonds       : angle       5.76562 (  567)
  SS BOND              : bond        0.00354 (   12)
  SS BOND              : angle       1.43114 (   24)
  covalent geometry    : bond        0.00347 ( 6484)
  covalent geometry    : angle       0.59461 ( 8809)

*********************** 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
  127 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7958 (p) cc_final: 0.7536 (m)
REVERT: A  262 LYS cc_start: 0.6928 (tmtt) cc_final: 0.6693 (tmtt)
REVERT: A  310 MET cc_start: 0.6272 (mmp) cc_final: 0.6022 (mmp)
REVERT: A  324 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7726 (p)
REVERT: A  327 SER cc_start: 0.8247 (p) cc_final: 0.8000 (t)
REVERT: A  353 PHE cc_start: 0.8180 (p90) cc_final: 0.7583 (p90)
REVERT: C   43 GLN cc_start: 0.7394 (mp10) cc_final: 0.6600 (mp10)
REVERT: C   48 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6612 (mtp)
REVERT: C   98 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.7143 (ttp-170)
REVERT: E   66 ARG cc_start: 0.6636 (ptt90) cc_final: 0.6341 (ptt180)
REVERT: E   83 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7967 (mtmt)
  outliers start: 23
  outliers final: 14
  residues processed: 112
  average time/residue: 0.8915
  time to fit residues: 106.7329
Evaluate side-chains
  118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
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  112 GLN
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 72 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 11 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 63 optimal weight:    0.4980
   chunk 52 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS
C   6 GLN
F   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.160272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.146235 restraints weight = 9051.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 2.57
r_work: 0.3838 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.2845

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= 0.137
  Angle     :  0.621  13.796   8839  Z= 0.304
  Chirality :  0.046   0.383    953
  Planarity :  0.005   0.052   1130
  Dihedral  :  4.480  16.637    931
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.58 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.42 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.88 (0.28), residues: 339
  loop : -1.53 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  37 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.010   0.001   PHE F  98 
 TYR   0.018   0.001   TYR C 103 
 ARG   0.004   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00060 (    1)
  link_NAG-ASN         : angle       0.43948 (    3)
  link_BETA1-4         : bond        0.00215 (    1)
  link_BETA1-4         : angle       0.91475 (    3)
  hydrogen bonds       : bond        0.02943 (  201)
  hydrogen bonds       : angle       5.65039 (  567)
  SS BOND              : bond        0.00316 (   12)
  SS BOND              : angle       1.28665 (   24)
  covalent geometry    : bond        0.00326 ( 6484)
  covalent geometry    : angle       0.61836 ( 8809)

*********************** 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
  120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7932 (p) cc_final: 0.7512 (m)
REVERT: A  310 MET cc_start: 0.6326 (mmp) cc_final: 0.6087 (mmp)
REVERT: A  324 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7711 (p)
REVERT: A  327 SER cc_start: 0.8256 (p) cc_final: 0.8012 (t)
REVERT: A  353 PHE cc_start: 0.8191 (p90) cc_final: 0.7595 (p90)
REVERT: A  357 ASP cc_start: 0.7869 (t0) cc_final: 0.7444 (t0)
REVERT: C   43 GLN cc_start: 0.7407 (mp10) cc_final: 0.6632 (mp10)
REVERT: C   48 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6581 (mtp)
REVERT: C   98 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.7147 (ttp-170)
REVERT: E   66 ARG cc_start: 0.6648 (ptt90) cc_final: 0.6334 (ptt180)
REVERT: E   83 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7937 (mtmt)
  outliers start: 19
  outliers final: 13
  residues processed: 107
  average time/residue: 0.8992
  time to fit residues: 102.6212
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  : 0.690 
-------------------------------------------------------------------------------
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  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 B residue  112 GLN
Chi-restraints excluded: chain C residue   48 MET
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 23 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 65 optimal weight:    0.4980
   chunk 6 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.159178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.145298 restraints weight = 9093.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.52
r_work: 0.3829 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.3018

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= 0.170
  Angle     :  0.629  11.946   8839  Z= 0.312
  Chirality :  0.047   0.392    953
  Planarity :  0.005   0.050   1130
  Dihedral  :  4.610  17.568    931
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.20 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.56 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.89 (0.28), residues: 327
  loop : -1.54 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.013   0.001   PHE F  98 
 TYR   0.020   0.002   TYR C 114 
 ARG   0.005   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00109 (    1)
  link_NAG-ASN         : angle       0.52982 (    3)
  link_BETA1-4         : bond        0.00188 (    1)
  link_BETA1-4         : angle       0.90052 (    3)
  hydrogen bonds       : bond        0.03107 (  201)
  hydrogen bonds       : angle       5.68542 (  567)
  SS BOND              : bond        0.00349 (   12)
  SS BOND              : angle       1.36876 (   24)
  covalent geometry    : bond        0.00401 ( 6484)
  covalent geometry    : angle       0.62558 ( 8809)

*********************** 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
  128 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7998 (p) cc_final: 0.7568 (m)
REVERT: A  158 LEU cc_start: 0.8044 (tp) cc_final: 0.7738 (tp)
REVERT: A  262 LYS cc_start: 0.6955 (tmtt) cc_final: 0.6706 (tmtt)
REVERT: A  293 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6404 (ptp-170)
REVERT: A  324 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7726 (p)
REVERT: A  327 SER cc_start: 0.8245 (p) cc_final: 0.8015 (t)
REVERT: A  353 PHE cc_start: 0.8210 (p90) cc_final: 0.7697 (p90)
REVERT: A  357 ASP cc_start: 0.7861 (t0) cc_final: 0.7429 (t0)
REVERT: C   43 GLN cc_start: 0.7391 (mp10) cc_final: 0.6610 (mp10)
REVERT: C   48 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6611 (mtp)
REVERT: C   98 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.7124 (ttp-170)
REVERT: E   66 ARG cc_start: 0.6730 (ptt90) cc_final: 0.6399 (ptt180)
REVERT: E   83 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7929 (mtmt)
REVERT: F    6 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.5945 (pt0)
  outliers start: 20
  outliers final: 13
  residues processed: 116
  average time/residue: 0.9353
  time to fit residues: 115.5880
Evaluate side-chains
  124 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
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  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    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 14 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0030
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.158972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.145290 restraints weight = 9084.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.53
r_work: 0.3823 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
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      :  0.004   0.039   6498  Z= 0.175
  Angle     :  0.644  11.955   8839  Z= 0.319
  Chirality :  0.046   0.300    953
  Planarity :  0.005   0.050   1130
  Dihedral  :  4.658  17.791    931
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.33 %
    Favored  : 92.17 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.84 (0.28), residues: 327
  loop : -1.54 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 207 
 HIS   0.006   0.001   HIS A 185 
 PHE   0.014   0.001   PHE F  98 
 TYR   0.021   0.002   TYR C 114 
 ARG   0.005   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00126 (    1)
  link_NAG-ASN         : angle       0.54131 (    3)
  link_BETA1-4         : bond        0.00166 (    1)
  link_BETA1-4         : angle       0.91483 (    3)
  hydrogen bonds       : bond        0.03125 (  201)
  hydrogen bonds       : angle       5.67183 (  567)
  SS BOND              : bond        0.00356 (   12)
  SS BOND              : angle       1.38907 (   24)
  covalent geometry    : bond        0.00412 ( 6484)
  covalent geometry    : angle       0.64079 ( 8809)

*********************** 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
  122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.8010 (p) cc_final: 0.7606 (m)
REVERT: A  262 LYS cc_start: 0.6963 (tmtt) cc_final: 0.6706 (tmtt)
REVERT: A  293 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6328 (ptp-170)
REVERT: A  324 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7671 (p)
REVERT: A  327 SER cc_start: 0.8262 (p) cc_final: 0.8019 (t)
REVERT: A  353 PHE cc_start: 0.8231 (p90) cc_final: 0.7691 (p90)
REVERT: A  357 ASP cc_start: 0.7840 (t0) cc_final: 0.7416 (t0)
REVERT: A  426 VAL cc_start: 0.6724 (t) cc_final: 0.6304 (p)
REVERT: C   43 GLN cc_start: 0.7390 (mp10) cc_final: 0.6581 (mp10)
REVERT: C   48 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6621 (mtp)
REVERT: C   98 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7127 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7954 (mtmt)
REVERT: F    6 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.6001 (pt0)
  outliers start: 18
  outliers final: 13
  residues processed: 111
  average time/residue: 0.9747
  time to fit residues: 115.2266
Evaluate side-chains
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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  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    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 15 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0870
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS
C   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.160133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.146109 restraints weight = 9278.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 2.65
r_work: 0.3847 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.3150

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= 0.132
  Angle     :  0.641  11.670   8839  Z= 0.317
  Chirality :  0.046   0.276    953
  Planarity :  0.005   0.050   1130
  Dihedral  :  4.527  16.722    931
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  6.21 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.30 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.92 (0.28), residues: 324
  loop : -1.54 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  47 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.008   0.001   PHE F  98 
 TYR   0.016   0.001   TYR A 375 
 ARG   0.010   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00088 (    1)
  link_NAG-ASN         : angle       0.48123 (    3)
  link_BETA1-4         : bond        0.00206 (    1)
  link_BETA1-4         : angle       0.98384 (    3)
  hydrogen bonds       : bond        0.02949 (  201)
  hydrogen bonds       : angle       5.60525 (  567)
  SS BOND              : bond        0.00501 (   12)
  SS BOND              : angle       1.71079 (   24)
  covalent geometry    : bond        0.00314 ( 6484)
  covalent geometry    : angle       0.63571 ( 8809)

********************** 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
  118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 VAL cc_start: 0.7901 (p) cc_final: 0.7505 (m)
REVERT: A  158 LEU cc_start: 0.8027 (tp) cc_final: 0.7784 (tp)
REVERT: A  191 MET cc_start: 0.7736 (ttp) cc_final: 0.7202 (ttp)
REVERT: A  262 LYS cc_start: 0.6954 (tmtt) cc_final: 0.6710 (tmtt)
REVERT: A  324 THR cc_start: 0.8063 (p) cc_final: 0.7668 (p)
REVERT: A  327 SER cc_start: 0.8287 (p) cc_final: 0.8029 (t)
REVERT: A  353 PHE cc_start: 0.8238 (p90) cc_final: 0.7675 (p90)
REVERT: C   43 GLN cc_start: 0.7405 (mp10) cc_final: 0.6588 (mp10)
REVERT: C   48 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6609 (mtp)
REVERT: C   98 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7118 (ttp-170)
REVERT: E   83 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7854 (mtmt)
REVERT: F    6 GLN cc_start: 0.6230 (OUTLIER) cc_final: 0.5949 (pt0)
  outliers start: 16
  outliers final: 12
  residues processed: 107
  average time/residue: 0.9724
  time to fit residues: 111.2377
Evaluate side-chains
  114 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  377 MET
Chi-restraints excluded: chain A residue  457 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    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 63 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  98 HIS
A 234 HIS
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.159242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.145100 restraints weight = 9366.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.67
r_work: 0.3829 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6498  Z= 0.168
  Angle     :  0.661  11.474   8839  Z= 0.327
  Chirality :  0.047   0.275    953
  Planarity :  0.005   0.077   1130
  Dihedral  :  4.630  17.502    931
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.83 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.45 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    Cis-general     : 0.13 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.29), residues: 805
  helix:  None (None), residues: 0
  sheet:  0.95 (0.28), residues: 323
  loop : -1.59 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 185 
 PHE   0.013   0.001   PHE F  98 
 TYR   0.019   0.002   TYR C 103 
 ARG   0.008   0.000   ARG F  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00099 (    1)
  link_NAG-ASN         : angle       0.55650 (    3)
  link_BETA1-4         : bond        0.00248 (    1)
  link_BETA1-4         : angle       0.97120 (    3)
  hydrogen bonds       : bond        0.03093 (  201)
  hydrogen bonds       : angle       5.64365 (  567)
  SS BOND              : bond        0.00432 (   12)
  SS BOND              : angle       1.72380 (   24)
  covalent geometry    : bond        0.00398 ( 6484)
  covalent geometry    : angle       0.65530 ( 8809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3935.94 seconds
wall clock time: 68 minutes 52.59 seconds (4132.59 seconds total)