Starting phenix.real_space_refine
on Thu Jun  5 22:23:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fhb_50444/06_2025/9fhb_50444.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fhb_50444/06_2025/9fhb_50444.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fhb_50444/06_2025/9fhb_50444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fhb_50444/06_2025/9fhb_50444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fhb_50444/06_2025/9fhb_50444.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fhb_50444/06_2025/9fhb_50444.cif"
  }
  resolution = 3.87
  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=   0.050 sd=   0.131
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Fe      2      7.16       5
     S      42      5.16       5
     C    4268      2.51       5
     N    1171      2.21       5
     O    1266      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6751
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
    Chain: "B"
      Number of atoms: 1123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
    Chain: "C"
      Number of atoms: 1982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1982
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 12, 'TRANS': 241}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2447
          Classifications: {'peptide': 321}
          Link IDs: {'PTRANS': 3, 'TRANS': 317}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 16
          Unusual residues: {' CA': 2, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.65, per 1000 atoms: 0.69
  Number of scatterers: 6751
  At special positions: 0
  Unit cell: (86.92, 98.58, 108.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      2     26.01
     Ca      2     19.99
     S      42     16.00
     O    1266      8.00
     N    1171      7.00
     C    4268      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 149 " - pdb=" SG  CYS C 266 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 309 " - pdb=" SG  CYS C 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 351 " - pdb=" SG  CYS C 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 168 " - pdb=" SG  CYS D 202 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 184 " - pdb=" SG  CYS D 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 197 " - pdb=" SG  CYS D 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 228 " - pdb=" SG  CYS D 238 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 275 " - pdb=" SG  CYS D 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 291 " - pdb=" SG  CYS D 355 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 304 " - pdb=" SG  CYS D 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 335 " - pdb=" SG  CYS D 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 382 " - pdb=" SG  CYS D 416 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 398 " - pdb=" SG  CYS D 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 411 " - pdb=" SG  CYS D 472 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 442 " - pdb=" SG  CYS D 452 " 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=3, symmetry=0
  Links applied
    NAG-ASN
      " NAG C1001 " - " ASN C 184 "
      " NAG C1002 " - " ASN C 241 "
      " NAG D2003 " - " ASN D 320 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.65
  Conformation dependent library (CDL) restraints added in 940.0 milliseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      39.8% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
      removed outlier: 3.573A  pdb=" N   THR A  41 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 95 through 113
      removed outlier: 3.738A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 137
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.134A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 80 through 85
      removed outlier: 3.508A  pdb=" N   THR B  84 " --> pdb=" O   ASN B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 95
      removed outlier: 3.562A  pdb=" N   LYS B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 119
      removed outlier: 3.857A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'C' and resid 200 through 205
    Processing helix  chain 'C' and resid 213 through 218
    Processing helix  chain 'C' and resid 305 through 314
    Processing helix  chain 'C' and resid 318 through 322
    Processing helix  chain 'C' and resid 395 through 405
    Processing helix  chain 'D' and resid 189 through 200
    Processing helix  chain 'D' and resid 234 through 238
    Processing helix  chain 'D' and resid 249 through 253
    Processing helix  chain 'D' and resid 259 through 263
    Processing helix  chain 'D' and resid 296 through 308
    Processing helix  chain 'D' and resid 341 through 345
    Processing helix  chain 'D' and resid 403 through 414
    Processing helix  chain 'D' and resid 448 through 452
    Processing sheet with id=AA1, first strand: chain 'C' and resid 229 through 230
    Processing sheet with id=AA2, first strand: chain 'C' and resid 278 through 283
      removed outlier: 4.742A  pdb=" N   CYS C 340 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL C 388 " --> pdb=" O   SER C 376 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   TRP C 369 " --> pdb=" O   ASP C 363 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ASP C 363 " --> pdb=" O   TRP C 369 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   ALA C 371 " --> pdb=" O   VAL C 361 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL C 361 " --> pdb=" O   ALA C 371 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY C 373 " --> pdb=" O   PHE C 359 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   ALA C 358 " --> pdb=" O   SER C 282 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   SER C 282 " --> pdb=" O   ALA C 358 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   HIS C 362 " --> pdb=" O   VAL C 278 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   VAL C 278 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 158 through 166
      removed outlier: 3.633A  pdb=" N   GLU D 158 " --> pdb=" O   LYS D 175 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   SER D 169 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER D 207 " --> pdb=" O   ILE D 257 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 166
      removed outlier: 3.633A  pdb=" N   GLU D 158 " --> pdb=" O   LYS D 175 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   SER D 169 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ILE D 172 " --> pdb=" O   VAL D 183 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL D 183 " --> pdb=" O   ILE D 172 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   TRP D 222 " --> pdb=" O   TRP D 180 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   THR D 182 " --> pdb=" O   TRP D 222 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 264 through 269
    Processing sheet with id=AA6, first strand: chain 'D' and resid 264 through 269
      removed outlier: 7.038A  pdb=" N   LEU D 279 " --> pdb=" O   ILE D 290 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ILE D 290 " --> pdb=" O   LEU D 279 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   TRP D 329 " --> pdb=" O   TRP D 287 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   THR D 289 " --> pdb=" O   TRP D 329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 372 through 380
      removed outlier: 4.934A  pdb=" N   ALA D 383 " --> pdb=" O   GLY D 378 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 372 through 380
      removed outlier: 4.934A  pdb=" N   ALA D 383 " --> pdb=" O   GLY D 378 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL D 386 " --> pdb=" O   VAL D 397 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL D 397 " --> pdb=" O   VAL D 386 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   LEU D 437 " --> pdb=" O   LEU D 394 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   LYS D 396 " --> pdb=" O   LEU D 437 " (cutoff:3.500A)

    324 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.08

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 2796
        1.39 -     1.55: 4066
        1.55 -     1.72: 1
        1.72 -     1.89: 51
        1.89 -     2.05: 8
  Bond restraints: 6922
  Sorted by residual:
  bond pdb=" CB  CYS C 149 "
       pdb=" SG  CYS C 149 "
    ideal  model  delta    sigma   weight residual
    1.808  1.874 -0.066 3.30e-02 9.18e+02 3.96e+00
  bond pdb=" CB  CYS C 266 "
       pdb=" SG  CYS C 266 "
    ideal  model  delta    sigma   weight residual
    1.808  1.748  0.060 3.30e-02 9.18e+02 3.25e+00
  bond pdb=" CA  ASP A  75 "
       pdb=" C   ASP A  75 "
    ideal  model  delta    sigma   weight residual
    1.522  1.547 -0.026 1.52e-02 4.33e+03 2.81e+00
  bond pdb=" CB  VAL B  54 "
       pdb=" CG2 VAL B  54 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  bond pdb=" CG  ASP A  75 "
       pdb=" OD1 ASP A  75 "
    ideal  model  delta    sigma   weight residual
    1.249  1.220  0.029 1.90e-02 2.77e+03 2.31e+00
  ... (remaining 6917 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9034
        2.19 -     4.38: 319
        4.38 -     6.57: 50
        6.57 -     8.76: 14
        8.76 -    10.95: 2
  Bond angle restraints: 9419
  Sorted by residual:
  angle pdb=" N   ASP A  75 "
        pdb=" CA  ASP A  75 "
        pdb=" C   ASP A  75 "
      ideal   model   delta    sigma   weight residual
     110.61  103.76    6.85 1.25e+00 6.40e-01 3.00e+01
  angle pdb=" CA  ASP A  75 "
        pdb=" C   ASP A  75 "
        pdb=" O   ASP A  75 "
      ideal   model   delta    sigma   weight residual
     121.20  126.75   -5.55 1.04e+00 9.25e-01 2.85e+01
  angle pdb=" N   LYS C 379 "
        pdb=" CA  LYS C 379 "
        pdb=" C   LYS C 379 "
      ideal   model   delta    sigma   weight residual
     113.61  106.28    7.33 1.50e+00 4.44e-01 2.39e+01
  angle pdb=" CA  CYS C 266 "
        pdb=" CB  CYS C 266 "
        pdb=" SG  CYS C 266 "
      ideal   model   delta    sigma   weight residual
     114.40  125.35  -10.95 2.30e+00 1.89e-01 2.27e+01
  angle pdb=" C   CYS C 266 "
        pdb=" CA  CYS C 266 "
        pdb=" CB  CYS C 266 "
      ideal   model   delta    sigma   weight residual
     109.46  117.17   -7.71 1.84e+00 2.95e-01 1.75e+01
  ... (remaining 9414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.84: 3773
       22.84 -    45.67: 241
       45.67 -    68.51: 46
       68.51 -    91.35: 17
       91.35 -   114.18: 1
  Dihedral angle restraints: 4078
    sinusoidal: 1633
      harmonic: 2445
  Sorted by residual:
  dihedral pdb=" CB  CYS D 411 "
           pdb=" SG  CYS D 411 "
           pdb=" SG  CYS D 472 "
           pdb=" CB  CYS D 472 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.09  -70.09     1      1.00e+01 1.00e-02 6.33e+01
  dihedral pdb=" CB  CYS C 149 "
           pdb=" SG  CYS C 149 "
           pdb=" SG  CYS C 266 "
           pdb=" CB  CYS C 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -15.96  -70.04     1      1.00e+01 1.00e-02 6.32e+01
  dihedral pdb=" CB  CYS D 291 "
           pdb=" SG  CYS D 291 "
           pdb=" SG  CYS D 355 "
           pdb=" CB  CYS D 355 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.74   64.26     1      1.00e+01 1.00e-02 5.43e+01
  ... (remaining 4075 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 664
       0.043 -    0.085: 240
       0.085 -    0.128: 89
       0.128 -    0.170: 19
       0.170 -    0.213: 11
  Chirality restraints: 1023
  Sorted by residual:
  chirality pdb=" CA  CYS D 382 "
            pdb=" N   CYS D 382 "
            pdb=" C   CYS D 382 "
            pdb=" CB  CYS D 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  PRO B   5 "
            pdb=" N   PRO B   5 "
            pdb=" C   PRO B   5 "
            pdb=" CB  PRO B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CG  LEU D 264 "
            pdb=" CB  LEU D 264 "
            pdb=" CD1 LEU D 264 "
            pdb=" CD2 LEU D 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1020 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  35 "    0.030 2.00e-02 2.50e+03   3.72e-02 2.77e+01
        pdb=" CG  TYR B  35 "   -0.092 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  35 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  35 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  35 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  35 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR B  35 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  47 "   -0.016 2.00e-02 2.50e+03   3.17e-02 1.01e+01
        pdb=" C   ASP B  47 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ASP B  47 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B  48 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 198 "    0.186 9.50e-02 1.11e+02   8.41e-02 5.71e+00
        pdb=" NE  ARG D 198 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 198 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 198 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 198 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 213
        2.69 -     3.24: 6717
        3.24 -     3.80: 10782
        3.80 -     4.35: 13593
        4.35 -     4.90: 22418
  Nonbonded interactions: 53723
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 249 "
            pdb=" N   HIS D 250 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" O   GLY D 164 "
            pdb=" OG  SER D 169 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" ND2 ASN D 247 "
            pdb="CA    CA D2001 "
     model   vdw
     2.154 2.590
  nonbonded pdb=" OD1 ASP C 349 "
            pdb=" N   THR C 350 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" N   ASP B  99 "
            pdb=" OD1 ASP B  99 "
     model   vdw
     2.225 3.120
  ... (remaining 53718 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.700
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
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      :  0.005   0.117   6943  Z= 0.208
  Angle     :  0.987  12.948   9458  Z= 0.537
  Chirality :  0.054   0.213   1023
  Planarity :  0.006   0.084   1200
  Dihedral  : 15.857 114.181   2467
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  4.11 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 17.51 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.26), residues: 852
  helix:  0.50 (0.27), residues: 289
  sheet: -1.05 (0.48), residues: 92
  loop : -0.54 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP D 455 
 HIS   0.009   0.001   HIS A 122 
 PHE   0.016   0.002   PHE D 438 
 TYR   0.092   0.003   TYR B  35 
 ARG   0.021   0.002   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05610 (    3)
  link_NAG-ASN         : angle       6.50852 (    9)
  hydrogen bonds       : bond        0.13156 (  305)
  hydrogen bonds       : angle       8.17348 (  879)
  SS BOND              : bond        0.00719 (   15)
  SS BOND              : angle       2.80485 (   30)
  covalent geometry    : bond        0.00467 ( 6922)
  covalent geometry    : angle       0.95551 ( 9419)
  Misc. bond           : bond        0.08377 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 GLU cc_start: 0.8062 (tp30) cc_final: 0.7457 (tp30)
REVERT: B   94 ASP cc_start: 0.6962 (t70) cc_final: 0.6367 (m-30)
REVERT: B  122 PHE cc_start: 0.8255 (t80) cc_final: 0.8001 (t80)
REVERT: C  242 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6411 (m-80)
REVERT: C  314 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7606 (mp0)
REVERT: C  354 ASP cc_start: 0.7376 (m-30) cc_final: 0.6805 (m-30)
REVERT: D  161 LEU cc_start: 0.8743 (mt) cc_final: 0.8332 (mt)
REVERT: D  436 TRP cc_start: 0.8404 (m-90) cc_final: 0.8135 (m-10)
  outliers start: 23
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1644
  time to fit residues: 33.4279
Evaluate side-chains
  129 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  242 TYR
Chi-restraints excluded: chain C residue  314 GLU
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  390 VAL
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  331 ASP
Chi-restraints excluded: chain D residue  369 SER
Chi-restraints excluded: chain D residue  414 LEU
Chi-restraints excluded: chain D residue  434 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0770
   chunk 34 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
B  97 HIS
C 195 GLN
C 208 HIS
C 289 ASN
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.140512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.120203 restraints weight = 14167.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.123542 restraints weight = 8031.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.125724 restraints weight = 5398.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109   6943  Z= 0.141
  Angle     :  0.670   8.244   9458  Z= 0.335
  Chirality :  0.045   0.160   1023
  Planarity :  0.004   0.039   1200
  Dihedral  : 10.323 111.506   1013
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.17 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 16.10 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.28), residues: 852
  helix:  2.25 (0.31), residues: 281
  sheet: -0.24 (0.51), residues: 86
  loop : -0.18 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 455 
 HIS   0.005   0.001   HIS A 122 
 PHE   0.011   0.001   PHE C 359 
 TYR   0.025   0.002   TYR B  35 
 ARG   0.007   0.001   ARG B  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00710 (    3)
  link_NAG-ASN         : angle       4.64442 (    9)
  hydrogen bonds       : bond        0.03645 (  305)
  hydrogen bonds       : angle       5.37531 (  879)
  SS BOND              : bond        0.00271 (   15)
  SS BOND              : angle       1.11512 (   30)
  covalent geometry    : bond        0.00338 ( 6922)
  covalent geometry    : angle       0.65322 ( 9419)
  Misc. bond           : bond        0.08723 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 SER cc_start: 0.8920 (m) cc_final: 0.8368 (p)
REVERT: B   35 TYR cc_start: 0.8103 (m-10) cc_final: 0.7420 (m-10)
REVERT: C  242 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6791 (m-80)
REVERT: C  354 ASP cc_start: 0.7626 (m-30) cc_final: 0.7385 (m-30)
REVERT: D  360 ASP cc_start: 0.8458 (m-30) cc_final: 0.7948 (m-30)
REVERT: D  396 LYS cc_start: 0.8322 (pttt) cc_final: 0.7887 (pttt)
REVERT: D  436 TRP cc_start: 0.8558 (m-90) cc_final: 0.8280 (m-10)
  outliers start: 33
  outliers final: 18
  residues processed: 139
  average time/residue: 0.1708
  time to fit residues: 33.0576
Evaluate side-chains
  122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  182 HIS
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  242 TYR
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  361 VAL
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  390 VAL
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain D residue  289 THR
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  373 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0770
   chunk 67 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C 203 ASN
C 208 HIS
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.139842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.119665 restraints weight = 14340.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122991 restraints weight = 8087.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.125204 restraints weight = 5446.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6943  Z= 0.119
  Angle     :  0.606   7.845   9458  Z= 0.302
  Chirality :  0.043   0.150   1023
  Planarity :  0.004   0.046   1200
  Dihedral  :  9.560 108.608    997
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.17 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 18.08 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.29), residues: 852
  helix:  2.27 (0.32), residues: 283
  sheet: -0.42 (0.54), residues: 77
  loop :  0.01 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  37 
 HIS   0.002   0.001   HIS A 122 
 PHE   0.020   0.002   PHE A  36 
 TYR   0.015   0.001   TYR B  35 
 ARG   0.009   0.001   ARG B  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00536 (    3)
  link_NAG-ASN         : angle       3.51206 (    9)
  hydrogen bonds       : bond        0.03326 (  305)
  hydrogen bonds       : angle       4.96106 (  879)
  SS BOND              : bond        0.00154 (   15)
  SS BOND              : angle       0.89872 (   30)
  covalent geometry    : bond        0.00290 ( 6922)
  covalent geometry    : angle       0.59529 ( 9419)
  Misc. bond           : bond        0.05910 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 TYR cc_start: 0.8297 (m-80) cc_final: 0.7720 (m-10)
REVERT: C  354 ASP cc_start: 0.7892 (m-30) cc_final: 0.7460 (m-30)
REVERT: D  396 LYS cc_start: 0.8322 (pttt) cc_final: 0.7982 (pttt)
REVERT: D  436 TRP cc_start: 0.8519 (m-90) cc_final: 0.8309 (m-10)
  outliers start: 29
  outliers final: 17
  residues processed: 131
  average time/residue: 0.1454
  time to fit residues: 27.4687
Evaluate side-chains
  117 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain D residue  199 GLN
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  373 LEU
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
C 208 HIS
C 331 GLN
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.134979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114565 restraints weight = 14596.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.117891 restraints weight = 8379.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.120005 restraints weight = 5700.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   6943  Z= 0.156
  Angle     :  0.620   9.011   9458  Z= 0.312
  Chirality :  0.043   0.148   1023
  Planarity :  0.004   0.045   1200
  Dihedral  :  9.461 106.759    989
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.17 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 19.35 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.29), residues: 852
  helix:  1.87 (0.32), residues: 292
  sheet: -0.08 (0.54), residues: 73
  loop :  0.17 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  37 
 HIS   0.004   0.001   HIS D 246 
 PHE   0.018   0.002   PHE A  36 
 TYR   0.013   0.002   TYR B  35 
 ARG   0.005   0.001   ARG B  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00455 (    3)
  link_NAG-ASN         : angle       3.08005 (    9)
  hydrogen bonds       : bond        0.03394 (  305)
  hydrogen bonds       : angle       4.90455 (  879)
  SS BOND              : bond        0.00263 (   15)
  SS BOND              : angle       0.86818 (   30)
  covalent geometry    : bond        0.00395 ( 6922)
  covalent geometry    : angle       0.61227 ( 9419)
  Misc. bond           : bond        0.07451 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8793 (p) cc_final: 0.8550 (p)
REVERT: B   35 TYR cc_start: 0.8492 (m-80) cc_final: 0.7933 (m-10)
REVERT: B   80 ASN cc_start: 0.6918 (t0) cc_final: 0.6569 (t0)
REVERT: C  242 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6891 (m-80)
REVERT: D  328 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8170 (mm)
REVERT: D  396 LYS cc_start: 0.8486 (pttt) cc_final: 0.8231 (pttt)
REVERT: D  436 TRP cc_start: 0.8630 (m-90) cc_final: 0.8429 (m-10)
  outliers start: 31
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1714
  time to fit residues: 30.4124
Evaluate side-chains
  127 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  242 TYR
Chi-restraints excluded: chain C residue  261 ARG
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  334 LEU
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  199 GLN
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  373 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.135130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.115005 restraints weight = 14374.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.118277 restraints weight = 8339.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.120381 restraints weight = 5711.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   6943  Z= 0.137
  Angle     :  0.605   7.622   9458  Z= 0.304
  Chirality :  0.043   0.149   1023
  Planarity :  0.004   0.049   1200
  Dihedral  :  9.328 105.353    989
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.40 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.79 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.29), residues: 852
  helix:  1.85 (0.32), residues: 292
  sheet: -0.31 (0.57), residues: 63
  loop :  0.15 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 398 
 HIS   0.005   0.001   HIS A 103 
 PHE   0.018   0.002   PHE A  36 
 TYR   0.010   0.001   TYR C 224 
 ARG   0.005   0.001   ARG D 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00389 (    3)
  link_NAG-ASN         : angle       2.68270 (    9)
  hydrogen bonds       : bond        0.03167 (  305)
  hydrogen bonds       : angle       4.80213 (  879)
  SS BOND              : bond        0.00233 (   15)
  SS BOND              : angle       1.34084 (   30)
  covalent geometry    : bond        0.00348 ( 6922)
  covalent geometry    : angle       0.59604 ( 9419)
  Misc. bond           : bond        0.06200 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8789 (p) cc_final: 0.8510 (p)
REVERT: B   35 TYR cc_start: 0.8479 (m-80) cc_final: 0.7989 (m-10)
REVERT: B   80 ASN cc_start: 0.6857 (t0) cc_final: 0.6484 (t0)
REVERT: B   94 ASP cc_start: 0.7384 (t70) cc_final: 0.7060 (t0)
REVERT: C  242 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6951 (m-80)
REVERT: D  328 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8206 (mm)
REVERT: D  396 LYS cc_start: 0.8391 (pttt) cc_final: 0.8141 (pttt)
  outliers start: 33
  outliers final: 22
  residues processed: 129
  average time/residue: 0.1411
  time to fit residues: 26.0923
Evaluate side-chains
  126 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  242 TYR
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  334 LEU
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  373 LEU
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0060
   chunk 33 optimal weight:    0.0470
   chunk 53 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.4694

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

Flipped N/Q/H residues before XYZ refinement:
C 331 GLN
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.137271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117227 restraints weight = 14542.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.120599 restraints weight = 8386.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.122789 restraints weight = 5705.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   6943  Z= 0.111
  Angle     :  0.581   7.641   9458  Z= 0.290
  Chirality :  0.042   0.148   1023
  Planarity :  0.004   0.051   1200
  Dihedral  :  9.088 102.996    989
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.52 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.06 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.30), residues: 852
  helix:  1.97 (0.32), residues: 292
  sheet: -0.68 (0.52), residues: 83
  loop :  0.20 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 398 
 HIS   0.005   0.001   HIS D 246 
 PHE   0.016   0.001   PHE A  36 
 TYR   0.010   0.001   TYR B  35 
 ARG   0.004   0.001   ARG D 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00356 (    3)
  link_NAG-ASN         : angle       2.42582 (    9)
  hydrogen bonds       : bond        0.02905 (  305)
  hydrogen bonds       : angle       4.62262 (  879)
  SS BOND              : bond        0.00259 (   15)
  SS BOND              : angle       1.25066 (   30)
  covalent geometry    : bond        0.00271 ( 6922)
  covalent geometry    : angle       0.57297 ( 9419)
  Misc. bond           : bond        0.05186 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8789 (p) cc_final: 0.8588 (p)
REVERT: D  396 LYS cc_start: 0.8247 (pttt) cc_final: 0.8038 (pttt)
REVERT: D  436 TRP cc_start: 0.8512 (m-10) cc_final: 0.8204 (m-10)
  outliers start: 28
  outliers final: 25
  residues processed: 130
  average time/residue: 0.1438
  time to fit residues: 26.8255
Evaluate side-chains
  129 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  334 LEU
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  279 LEU
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  373 LEU
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0770
   chunk 25 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116269 restraints weight = 14353.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.119607 restraints weight = 8259.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.121796 restraints weight = 5599.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6943  Z= 0.118
  Angle     :  0.580   7.865   9458  Z= 0.290
  Chirality :  0.042   0.158   1023
  Planarity :  0.004   0.052   1200
  Dihedral  :  8.998 101.013    989
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.76 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.05 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.30), residues: 852
  helix:  2.00 (0.32), residues: 292
  sheet: -0.65 (0.52), residues: 83
  loop :  0.17 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 398 
 HIS   0.004   0.001   HIS D 246 
 PHE   0.012   0.001   PHE C 377 
 TYR   0.009   0.001   TYR C 280 
 ARG   0.003   0.000   ARG D 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00339 (    3)
  link_NAG-ASN         : angle       2.31951 (    9)
  hydrogen bonds       : bond        0.02959 (  305)
  hydrogen bonds       : angle       4.65588 (  879)
  SS BOND              : bond        0.00184 (   15)
  SS BOND              : angle       1.14831 (   30)
  covalent geometry    : bond        0.00298 ( 6922)
  covalent geometry    : angle       0.57329 ( 9419)
  Misc. bond           : bond        0.04901 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8763 (p) cc_final: 0.8518 (p)
REVERT: B   40 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8082 (ttm110)
REVERT: B   90 GLU cc_start: 0.8196 (tp30) cc_final: 0.7304 (tp30)
REVERT: B   94 ASP cc_start: 0.7549 (t0) cc_final: 0.7211 (m-30)
REVERT: D  396 LYS cc_start: 0.8349 (pttt) cc_final: 0.8131 (pttt)
  outliers start: 29
  outliers final: 26
  residues processed: 123
  average time/residue: 0.1536
  time to fit residues: 27.0791
Evaluate side-chains
  122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  334 LEU
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  373 LEU
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    0.1980
   chunk 81 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
C 331 GLN
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 250 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.132217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.112220 restraints weight = 14482.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.115460 restraints weight = 8462.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.117601 restraints weight = 5804.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089   6943  Z= 0.166
  Angle     :  0.626   9.522   9458  Z= 0.310
  Chirality :  0.043   0.152   1023
  Planarity :  0.004   0.053   1200
  Dihedral  :  9.299 101.820    989
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.23 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.75 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.30), residues: 852
  helix:  1.89 (0.32), residues: 292
  sheet: -0.57 (0.54), residues: 81
  loop :  0.09 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 398 
 HIS   0.005   0.001   HIS D 246 
 PHE   0.014   0.002   PHE C 173 
 TYR   0.013   0.002   TYR C 224 
 ARG   0.003   0.001   ARG D 171 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00319 (    3)
  link_NAG-ASN         : angle       2.37054 (    9)
  hydrogen bonds       : bond        0.03334 (  305)
  hydrogen bonds       : angle       4.89972 (  879)
  SS BOND              : bond        0.00404 (   15)
  SS BOND              : angle       1.09692 (   30)
  covalent geometry    : bond        0.00425 ( 6922)
  covalent geometry    : angle       0.62001 ( 9419)
  Misc. bond           : bond        0.06565 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 TYR cc_start: 0.8482 (m-80) cc_final: 0.8144 (m-10)
REVERT: B   40 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8063 (ttm110)
REVERT: B   80 ASN cc_start: 0.6964 (t0) cc_final: 0.6414 (t0)
REVERT: C  151 LYS cc_start: 0.7944 (mttt) cc_final: 0.7421 (ptpt)
REVERT: D  396 LYS cc_start: 0.8449 (pttt) cc_final: 0.8240 (pttt)
  outliers start: 29
  outliers final: 26
  residues processed: 115
  average time/residue: 0.1544
  time to fit residues: 25.3874
Evaluate side-chains
  121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain C residue  182 HIS
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  331 GLN
Chi-restraints excluded: chain C residue  334 LEU
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 THR
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  365 CYS
Chi-restraints excluded: chain D residue  373 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 72 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 331 GLN
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.134884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115165 restraints weight = 14364.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.118462 restraints weight = 8269.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.120649 restraints weight = 5622.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6943  Z= 0.123
  Angle     :  0.601   8.296   9458  Z= 0.299
  Chirality :  0.042   0.148   1023
  Planarity :  0.004   0.053   1200
  Dihedral  :  9.072 101.760    987
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.99 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 22.74 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.30), residues: 852
  helix:  1.93 (0.33), residues: 291
  sheet: -0.84 (0.53), residues: 83
  loop :  0.08 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 398 
 HIS   0.004   0.001   HIS D 246 
 PHE   0.014   0.001   PHE C 377 
 TYR   0.010   0.001   TYR C 280 
 ARG   0.003   0.000   ARG D 163 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00323 (    3)
  link_NAG-ASN         : angle       2.29583 (    9)
  hydrogen bonds       : bond        0.03057 (  305)
  hydrogen bonds       : angle       4.77496 (  879)
  SS BOND              : bond        0.00195 (   15)
  SS BOND              : angle       0.83538 (   30)
  covalent geometry    : bond        0.00315 ( 6922)
  covalent geometry    : angle       0.59581 ( 9419)
  Misc. bond           : bond        0.03650 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
REVERT: B   80 ASN cc_start: 0.6679 (t0) cc_final: 0.6388 (t0)
REVERT: B   92 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.8222 (m90)
REVERT: C  151 LYS cc_start: 0.7820 (mttt) cc_final: 0.7486 (ptpt)
  outliers start: 26
  outliers final: 22
  residues processed: 111
  average time/residue: 0.1467
  time to fit residues: 23.2508
Evaluate side-chains
  114 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 HIS
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  373 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 49 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0970
   chunk 7 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.134910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115109 restraints weight = 14493.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.118378 restraints weight = 8375.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.120581 restraints weight = 5701.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6943  Z= 0.126
  Angle     :  0.605   7.860   9458  Z= 0.300
  Chirality :  0.042   0.150   1023
  Planarity :  0.004   0.053   1200
  Dihedral  :  9.004 101.013    987
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.23 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.45 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.30), residues: 852
  helix:  2.00 (0.33), residues: 290
  sheet: -0.87 (0.54), residues: 83
  loop :  0.09 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 398 
 HIS   0.004   0.001   HIS D 246 
 PHE   0.014   0.001   PHE A  36 
 TYR   0.009   0.001   TYR C 280 
 ARG   0.008   0.001   ARG B  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00320 (    3)
  link_NAG-ASN         : angle       2.25356 (    9)
  hydrogen bonds       : bond        0.03028 (  305)
  hydrogen bonds       : angle       4.73191 (  879)
  SS BOND              : bond        0.00216 (   15)
  SS BOND              : angle       0.81198 (   30)
  covalent geometry    : bond        0.00324 ( 6922)
  covalent geometry    : angle       0.60060 ( 9419)
  Misc. bond           : bond        0.04018 (    3)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: B   80 ASN cc_start: 0.6617 (t0) cc_final: 0.6350 (t0)
REVERT: B   92 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8239 (m90)
  outliers start: 24
  outliers final: 22
  residues processed: 111
  average time/residue: 0.1676
  time to fit residues: 25.8251
Evaluate side-chains
  113 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 HIS
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain C residue  182 HIS
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  373 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0870
   chunk 48 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0470
   chunk 77 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.116566 restraints weight = 14528.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.119849 restraints weight = 8367.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122066 restraints weight = 5663.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6943  Z= 0.115
  Angle     :  0.603   8.963   9458  Z= 0.298
  Chirality :  0.042   0.149   1023
  Planarity :  0.004   0.052   1200
  Dihedral  :  8.893 100.240    987
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.87 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 24.58 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.30), residues: 852
  helix:  2.08 (0.33), residues: 289
  sheet: -0.84 (0.54), residues: 83
  loop :  0.15 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 398 
 HIS   0.004   0.001   HIS D 246 
 PHE   0.016   0.001   PHE A  36 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.007   0.001   ARG B  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00333 (    3)
  link_NAG-ASN         : angle       2.22921 (    9)
  hydrogen bonds       : bond        0.02893 (  305)
  hydrogen bonds       : angle       4.64935 (  879)
  SS BOND              : bond        0.00233 (   15)
  SS BOND              : angle       0.98420 (   30)
  covalent geometry    : bond        0.00291 ( 6922)
  covalent geometry    : angle       0.59738 ( 9419)
  Misc. bond           : bond        0.03287 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2365.07 seconds
wall clock time: 41 minutes 47.53 seconds (2507.53 seconds total)